<?xml version="1.0" encoding="UTF-8" ?>
<rdf:RDF xmlns:admin="http://webns.net/mvcb/" xmlns="http://purl.org/rss/1.0/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:prism="http://purl.org/rss/1.0/modules/prism/" xmlns:taxo="http://purl.org/rss/1.0/modules/taxonomy/" xmlns:content="http://purl.org/rss/1.0/modules/content/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:syn="http://purl.org/rss/1.0/modules/syndication/">
<channel rdf:about="https://biorxiv.org">
<admin:errorReportsTo rdf:resource="mailto:biorxiv@cshlpress.edu"/>
<title>bioRxiv Subject Collection: Genetics</title>
<link>https://biorxiv.org</link>
<description>
This feed contains articles for bioRxiv Subject Collection "Genetics"
</description>

<items>
<rdf:Seq>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.29.735377v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.01.735728v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.30.735680v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.29.734312v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.28.735120v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.29.735307v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.01.735899v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.28.735054v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.27.734984v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.07.01.735767v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.26.734831v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.27.734959v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.26.734650v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.25.734683v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.26.734851v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.25.734236v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.25.734557v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.24.734305v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.24.733714v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.24.734157v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.26.734753v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.25.734482v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.24.733965v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.22.733791v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.24.734286v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.22.733755v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.19.733321v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.18.730290v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.23.733901v1?rss=1"/>
<rdf:li rdf:resource="https://www.biorxiv.org/content/10.64898/2026.06.20.733520v1?rss=1"/>
</rdf:Seq>
</items>
<prism:eIssn/>
<prism:publicationName>bioRxiv</prism:publicationName>
<prism:issn/>

<image rdf:resource=""/>
</channel>
<image rdf:about="">
<title>bioRxiv</title>
<url>https://www.biorxiv.org/sites/default/files/bioRxiv_article.jpg</url>
<link>https://www.biorxiv.org</link>
</image>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.29.735377v1?rss=1">
<title>
<![CDATA[
The Effect of Depriving the Aedes aegypti Mosquito of Natural Levels of Radiation 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.29.735377v1?rss=1
</link>
<description><![CDATA[
Organisms have spent their life histories exposed to background levels of natural ionizing radiation. To document the role that radiation plays, the deprivation of these natural levels has been studied by incubating organisms in the shielded space of underground laboratories. We report here on two studies (Study I and Study II) using Aedes aegypti for the first time as a model organism incubated 655 meters underground at the Waste Isolation Pilot Plant (WIPP) outside of Carlsbad, New Mexico, U.S.A. Male mosquitos were incubated at the surface exposed to natural background radiation, and were compared to two underground treatments in which incubators were supplemented with radiation sources used to mimic background and these groups were compared to the underground, radiation-deprived treatment. In Study I, the mosquitos incubated underground in the absence of natural radiation had higher levels of mortality compared to those incubated at the surface and PCA plots of the two transcriptomes were clearly differentiated. Study II was conducted the following year and the experiment was narrowed to include only the surface control and underground, radiation-deprived treatment which allowed for four biological replicates. Again, there was a higher level of mortality in the mosquitos grown underground compared mosquitos grown at the surface. Transcriptomes were not as clearly differentiated by PCA analysis and fecundity data were similar between the two groups. Functional analysis of transcriptomic DEGs from two independent studies suggested there are stress responses in radiation deprived mosquitoes. The absence of a secondary stressor in Study II is discussed as an explanation for the transcriptome differences in the two experiments.
]]></description>
<dc:creator><![CDATA[ Goodale, L., Thawng, C., Hansen, I., Smith, G. ]]></dc:creator>
<dc:date>2026-07-03</dc:date>
<dc:identifier>doi:10.64898/2026.06.29.735377</dc:identifier>
<dc:title><![CDATA[The Effect of Depriving the Aedes aegypti Mosquito of Natural Levels of Radiation]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-03</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.01.735728v1?rss=1">
<title>
<![CDATA[
Pangenome-based human genome analysis improves trait association and genomic prediction 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.01.735728v1?rss=1
</link>
<description><![CDATA[
The Human Pangenome Reference Consortium has generated 462 open-access reference genomes and a variation graph that represents differences among them, providing a substrate for pangenome-based analysis methods that overcome the longstanding limitation of comparing all genomic data to a single linear reference. A key unresolved question is the extent to which these approaches can improve trait mapping. We investigate this using the genetics of gene expression variation as a model. We developed a graph-based method (EdgeDepth) for associating sequence variation with traits using short-read genome sequencing data, and show that it captures complex forms of genetic variation missed by other methods. We evaluated trait mapping performance using 430 samples with deep RNA-seq data, and found that pangenomic methods enable the detection of expression quantitative trait loci involving multiallelic indels and structural variants, leading to increased power at a subset of genes. These include 812 genes (7.9% of total) with [&ge;]20% improvement in statistical significance relative to the 1000 Genomes Project callset, and 185 (1.8%) with a 50% improvement, 10 of which are candidates to explain prior GWAS results. Notably, these analyses implicate GBAP1 pseudogene copy number as a causal factor in Crohn's disease, likely via miRNA-mediated regulation of GBA1, which explains prior GWAS results based on flanking SNPs. The inclusion of pangenome-specific variation also improved the performance of gene expression prediction models, with median variance explained increasing from 10.1% to 12.5%, and 14.6% of genes showing significant improvement ({Delta}r2>0.05). Taken together, these results suggest that integration of pangenomic methods into human genetic studies will improve trait association and genomic prediction at a meaningful subset of genes.
]]></description>
<dc:creator><![CDATA[ Lu, S., Liao, W.-W., DeGorter, M. K., Goddard, P. C., Ebler, J., Lu, T.-Y., Chaisson, M. J. P., Marschall, T., Montgomery, S. B., Stitziel, N. O., Hall, I. M. ]]></dc:creator>
<dc:date>2026-07-03</dc:date>
<dc:identifier>doi:10.64898/2026.07.01.735728</dc:identifier>
<dc:title><![CDATA[Pangenome-based human genome analysis improves trait association and genomic prediction]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-03</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.30.735680v1?rss=1">
<title>
<![CDATA[
Towards genetic indicators in ectomycorrhizal fungi: estimating the effective population size 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.30.735680v1?rss=1
</link>
<description><![CDATA[
Ectomycorrhizal (EM) fungi are vital to forest ecosystems, supporting tree growth and survival. However, their inclusion in conservation policy and action remains limited and little is known about the status of their genetic diversity, which is essential for their long-term survival and adaptation. The Global Biodiversity Framework adopted a genetic indicator based on the effective population size, Ne, to monitor genetic diversity in all species. To date, it is still uncertain how Ne, a key parameter, can be reliably assessed in species with complex life history traits. Ectomycorrhizal fungi are a highly diverse group of taxa displaying haplodiplontic life cycles with partially clonal reproduction. Here, we review the literature to understand how these life history traits might affect Ne and its estimation in six species of EM fungi. We estimated Ne in 19 populations using eight genetic and genomic datasets from selected studies. We compared Ne estimates using Linkage Disequilibrium (LD) and Sibship Frequency (SF) methods. We tested how Ne estimates change due to partial clonality and genetic structure gradients and whether the number of genetic markers influence the precision of the estimates. We show a systematic bias in Ne estimations when large clones are present and when populations are not correctly delimited. We found both methods are not robust to these factors, which makes them unreliable for conservation assessment purposes in EM fungi. This study provides new perspectives for further research into the links between life history traits and the effective population size of ectomycorrhizal fungi.
]]></description>
<dc:creator><![CDATA[ Champion, A., Bazzicalupo, A., Heuertz, M., Gargiulo, R. ]]></dc:creator>
<dc:date>2026-07-03</dc:date>
<dc:identifier>doi:10.64898/2026.06.30.735680</dc:identifier>
<dc:title><![CDATA[Towards genetic indicators in ectomycorrhizal fungi: estimating the effective population size]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-03</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.29.734312v1?rss=1">
<title>
<![CDATA[
Preclinical translation of Neurofibromatosis type 1 (NF1) exon 17 skipping using targeted U7-SnRNA packaged into engineered AAV serotypes. 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.29.734312v1?rss=1
</link>
<description><![CDATA[
To facilitate the translation of NF1 exon 17 skipping as a mutation-specific therapy for Neurofibromatosis type 1 into in vivo testing, we have continued to develop more efficient antisense oligonucleotides (ASOs), humanized mouse models, and explored multiple delivery platforms including an adeno-associated virus (AAV)-U7-SnRNA vector approach. We evaluated both biodistribution and exon skipping efficacy of a U7-SnRNA targeting NF1 exon 17 with an SFFV-driven cassette containing T2A-linked Luciferase (Luc) and eGFP packaged in AAV-9, AAV-F and AAV-B1 capsids. We show that AAV-F is superior to AAV-9 and AAV-B1 for mouse brain delivery based on DNA transduction, GFP expression, and luciferase activity, but AAV-B1 delivers 2-4 fold more to sciatic nerve (SCN). In terms of exon skipping, AAV-F appears to induce the most skipping in liver and optic nerve (ON), while AAV-B1 mediates highest skipping in the liver, SCN, and ON. The identification of AAV serotypes that allow efficient transduction and delivery of transgenes to the mouse CNS and PNS is impactful for preclinical research in murine models of other diseases. Furthermore, this is both the first report of NF1 exon skipping efficacy in vivo and the first successful application of an U7-SnRNA for the restoration of functional neurofibromin for NF1.
]]></description>
<dc:creator><![CDATA[ Moore, M., Rayat-Sanati, K., Zhang, X., Liu, H., Rostamitehrani, Z., Vijayasarathy, T., Westin, E., Esteves, M., Maguire, C. A., Kesterson, R. A., Popplewell, L., Wallis, D. ]]></dc:creator>
<dc:date>2026-07-02</dc:date>
<dc:identifier>doi:10.64898/2026.06.29.734312</dc:identifier>
<dc:title><![CDATA[Preclinical translation of Neurofibromatosis type 1 (NF1) exon 17 skipping using targeted U7-SnRNA packaged into engineered AAV serotypes.]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-02</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.28.735120v1?rss=1">
<title>
<![CDATA[
CATaN maps gene regulatory programs that shape genetic risk across complex diseases 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.28.735120v1?rss=1
</link>
<description><![CDATA[
Causal variants of complex traits are enriched at transcription factor (TF) binding sites and are thought to contribute to pathology by disrupting TF activity and thereby causing transcriptome dysregulation. However, existing approaches typically address TF-mediated gene regulatory networks (TF-GRNs) and transcriptomes separately, and methods that jointly leverage both to systematically assess disease heritability remain limited. We aimed to develop a framework that jointly leverages TF-GRNs and transcriptomes to assess disease heritability. Here, we constructed a matrix encoding TF-GRNs and developed an unsupervised analytical pipeline, Canonical correlation Analysis of Transcriptome and TF-gene regulatory Networks (CATaN). CATaN applies canonical correlation analysis (CCA) to extract canonical correlation (CC) components, i.e., shared variation components between transcriptomes and TF-GRNs, and converts them into genome-wide functional annotation scores connected to stratified LD score regression (S-LDSC) for heritability analysis. We applied CATaN to eight datasets, including 19,198 bulk samples and 611,772 single cells from human and mouse sources, identifying 588 CC components that are significantly enriched for SNP heritability across 69 complex traits. Notably, functional annotation tracks based on these TF-GRNs are distinct from transcriptome signatures prioritized by LDSC-SEG, with greater heritability enrichment for a subset of traits. Finally, we suggest that CATaN may help prioritize candidate causal variants for experimental fine-mapping using genome editing. Together, integrating TF-GRNs with transcriptomes reveals disease-relevant regulatory programs that are not fully captured by transcriptome-based analyses alone.
]]></description>
<dc:creator><![CDATA[ Takahashi, H., Hatano, H., Kono, M., Haruta, K., Nakano, M., Bagherzadeh, R., Drees, M. M., Oguma, Y., Harita, D., Kawashima, T., Arakawa, T., Inokuchi, H., Nishino, T., Asahara, K., Itamiya, T., Inamo, J., Natsumoto, B., Tsuchida, Y., Sumitomo, S., Suzuki, A., Kochi, Y., Fujio, K., Yamamoto, K., Ohta, T., Kawakami, E., Ishigaki, K. ]]></dc:creator>
<dc:date>2026-07-02</dc:date>
<dc:identifier>doi:10.64898/2026.06.28.735120</dc:identifier>
<dc:title><![CDATA[CATaN maps gene regulatory programs that shape genetic risk across complex diseases]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-02</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.29.735307v1?rss=1">
<title>
<![CDATA[
Paralogs of the <em>Candida albicans TLO</em> gene family form interconnected functional networks with incomplete redundancy 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.29.735307v1?rss=1
</link>
<description><![CDATA[
Gene duplication typically fails to confer a selective advantage to an organism, prompting their removal from a population. In the rare instance that duplication either does not incur a fitness cost or it enhances fitness, gene families can form through repeating the duplication process. While the function of gene duplicates has been studied in detail, little work has explored how repeated duplication impacts paralog redundancy and may restrict the emergence of new paralogs or novel function. Here, we constructed a panel of single deletion mutants for each of the 14 members of the <em>Candida albicans</em> telomere-associated (<em>TLO</em>) gene family to test the redundancy in molecular and biological function among paralogs from a lineage-specific expansion. Tlo proteins function as interchangeable subunits of the Mediator transcriptional regulatory complex and have the potential to alter gene expression and an array of cellular responses. Redundancy was the most common outcome, being observed for approximately 80% of the phenotypic assays in strains lacking single <em>TLO </em>genes. However, mutants for all 14 paralogs displayed non-redundant functions in phenotypes ranging from carbon utilization to <em>in vivo</em> virulence. Analysis of gene expression in single <em>TLO </em>mutants found similar trends in redundancy, and loss of single <em>TLO</em>s disproportionately affected genes involved in filamentation, adhesion, redox reactions, and transporter activity at the cell surface. Importantly, sequence divergence between paralogs positively correlated with the frequency of altered phenotypes in single <em>TLO </em>mutants, indicating the acquisition of non-redundant function with increased evolutionary distance. Double mutants lacking two <em>TLO</em> genes produced both positive and negative synergistic phenotypes, suggesting that crosstalk or coordinated regulation is common among paralogs. Together, this study demonstrates that recently emergent paralogs acquire non-redundant functions despite often retaining redundancy with other gene family members to form a highly interconnected functional network.
]]></description>
<dc:creator><![CDATA[ Simonton, E., Cangelosi, N., Zhou, M., Hendricks, P. S., Woodruff, A. L., Anderson, M. Z. ]]></dc:creator>
<dc:date>2026-07-02</dc:date>
<dc:identifier>doi:10.64898/2026.06.29.735307</dc:identifier>
<dc:title><![CDATA[Paralogs of the <em>Candida albicans TLO</em> gene family form interconnected functional networks with incomplete redundancy]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-02</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.01.735899v1?rss=1">
<title>
<![CDATA[
Effects of Deficient Glycosylation and Deglycosylation on Sperm Condition in Zebrafish (Danio rerio) 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.01.735899v1?rss=1
</link>
<description><![CDATA[
Congenital disorders of glycosylation and deglycosylation are rare, serious, and lethal disorders afflicting humans. CDGs and CDDGs result in loss of function enzymes which fail to build or break down oligosaccharides on proteins. This can produce protein aggregates and, in turn, reactive oxygen species that harm the cell eventually leading to autophagy and apoptosis. Because sperm contain high concentrations of polyunsaturated fatty acids, they are especially sensitive to these effects, which is understood as one of the leading factors in human male infertility. Sperm are developed in zebrafish similarly to humans and are useful models to examine human reproductive health, as well as genetic disorders. The combination of these advantages makes the analysis of sperm from zebrafish with heterozygous ALG1 or DPAGT1 CDGs or the NGLY1 CDDG suitable. Analysis of sperm concentration, motility, status, viability, and hypoosmotic swelling demonstrated the effects of these disorders on sperm quality. Results showed a significant decrease in sperm concentration, motility, and hypoosmotic swelling for all mutant zebrafish compared to the wild type. This suggests that CDGs and CDDGs influence the amount of sperm produced, the percentage of sperm cells that are mobile, and the integrity of the plasma membrane.
]]></description>
<dc:creator><![CDATA[ McGraw, K., Mooney, M. ]]></dc:creator>
<dc:date>2026-07-02</dc:date>
<dc:identifier>doi:10.64898/2026.07.01.735899</dc:identifier>
<dc:title><![CDATA[Effects of Deficient Glycosylation and Deglycosylation on Sperm Condition in Zebrafish (Danio rerio)]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-02</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.28.735054v1?rss=1">
<title>
<![CDATA[
The impact of P-Element-induced hybrid dysgenesis on the male germline in Drosophila simulans 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.28.735054v1?rss=1
</link>
<description><![CDATA[
The P-element, a DNA transposon, has independently invaded two Drosophila species, accompanied by rapid evolution of suppression. In the germline, suppression is mediated primarily by maternally expressed piRNAs, a class of regulatory small RNAs associated with PIWI proteins. The offspring of females that lack P-element-specific piRNAs and males that contain P-elements suffer a syndrome of deleterious phenotypes, including sterility, genome rearrangements, gonadal atrophy, and mutations, while the offspring of the reciprocal cross are normal. These effects, collectively termed hybrid dysgenesis, have been investigated primarily in female D. melanogaster. Here, we study hybrid dysgenesis in male D. simulans. Using an attached-X chromosome stock, we generated genetically identical F1 males that differed only in maternal suppression of the P-element. Using targeted sequencing of P-element breakpoints, we show that P-element transposition is elevated in dysgenic males and confirm a preference for insertion near origins of replication. Using transcriptomics, we show that dysgenic males have elevated P-element expression and reduced splicing suppression, with patterns of gene expression suggesting the loss of mature sperm cells. Fertility assays show higher rates of male sterility but otherwise modest effects on fertility. In conjunction with the transcriptomic data, small RNA sequencing confirms that the piRNA pathway functions in testes. Our results suggest that the P-element may spread more readily through males than females, as transposition rates are similar while fertility defects are less severe in males.

SummaryTransposable elements (TEs) are selfish genes that replicate independently of host genomes. Hosts produce piRNA molecules to suppress established TEs, but for new TEs, piRNAs are not available. This has strong negative consequences for females, but effects in males are unclear. The fly Drosophila simulans has recently acquired a TE, the P-element, and males from lines lacking P-element piRNAs suffer more P-element expression and replication than controls, leading to reduced expression of genes associated with mature sperm cells, and sometime sterility. Yet unsterilised males did not suffer fertility loss, suggesting that TEs may spread more easily in males than females.
]]></description>
<dc:creator><![CDATA[ Griffin, J. S., Harney, E., Capes, C., Connell, R., Betancourt, A. J., Romero-Soriano, V. ]]></dc:creator>
<dc:date>2026-07-01</dc:date>
<dc:identifier>doi:10.64898/2026.06.28.735054</dc:identifier>
<dc:title><![CDATA[The impact of P-Element-induced hybrid dysgenesis on the male germline in Drosophila simulans]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.27.734984v1?rss=1">
<title>
<![CDATA[
Female genetic variation controlling timing of mating plug ejection in Drosophila melanogaster 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.27.734984v1?rss=1
</link>
<description><![CDATA[
In multiply-mating species, male-female postcopulatory, prezygotic interactions can influence reproductive outcomes. In Drosophila melanogaster, females can bias sperm storage and usage and thereby influence paternity outcomes. One mechanism by which females may regulate paternity contributions from specific males is through modulation of mating plug ejection timing. The D. melanogaster mating plug is composed of seminal fluid proteins, and some female-derived proteins, that coagulate in the female reproductive tract during mating. The mating plug facilitates sperm storage; thus, timing of female mating plug ejection is associated with sperm storage and relative paternity contributions in cases of multiple mating. However, whether there is natural genetic variation among females that shapes mating plug ejection timing, and genes or phenomena that might mediate it are unknown. We examined mating plug ejection in females from 69 lines of the Drosophila Genetic Reference Panel and observed dramatic differences in median plug ejection timing ranging from less than 1 to over 6 hours. We used this variation to perform a genome-wide association study to identify gene candidates associated with this phenotype. Many gene candidates are expressed in the brain and/or function in neurodevelopment. The candidate pool was also enriched for genes expressed in the ovary and functioning in oogenesis, indicating a link between female reproductive physiology and mating plug ejection. Consistent with this interpretation, females without a germline delay mating plug ejection. Our results demonstrate that female mating plug ejection is a physiologically integrated reproductive trait with a genetic basis that can be shaped by selection.

Article SummaryThe D. melanogaster mating plug is composed of seminal fluid proteins and some female-derived proteins that coagulate in the female reproductive tract during mating. The mating plug facilitates sperm storage; thus, timing of female mating plug ejection is associated with sperm storage and relative paternity contributions in cases of multiple mating. Using the DGRP, we observed heritable genetic variation in female timing of mating plug ejection and through a GWAS find associated gene candidates. Gene candidates are enriched for neurodevelopment function and oogenesis function. We experimentally validate the connection between female mating plug ejection and the ovary.
]]></description>
<dc:creator><![CDATA[ Carlisle, J. A., Craig, R. M. J., Matera-Vatnick, M., Villanuenva, B. M., Andrus, A. R., Cosgrove, E. J., Chen, D. S., Clark, A. G., Wolfner, M. F. ]]></dc:creator>
<dc:date>2026-07-01</dc:date>
<dc:identifier>doi:10.64898/2026.06.27.734984</dc:identifier>
<dc:title><![CDATA[Female genetic variation controlling timing of mating plug ejection in Drosophila melanogaster]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.07.01.735767v1?rss=1">
<title>
<![CDATA[
Formation, persistence, and breakdown of carrier-set topology in linkage disequilibrium: empirical structure in 1000 Genomes and a two locus Wright Fisher model 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.07.01.735767v1?rss=1
</link>
<description><![CDATA[
Linkage disequilibrium between two biallelic loci is usually summarized by scalar association measures such as r2 and D'. These measures quantify how visible an allelic association is to a symmetric LD scan, but they do not directly represent the topology of carrier sets: whether the carriers of one variant are contained within, partially overlap with, or are disjoint from the carriers of the other. This distinction is structural. On the haplotype-frequency simplex, carrier-set inclusion corresponds to a boundary face where one haplotype class is absent. In the rare-common regime, a nested rare variant is further constrained by the ceiling r2 [&le;] pA/pB, so that complete carrier-set inclusion can remain nearly invisible to r2.

Here, as a companion to the Fisher-geometry preprint 1, we examine the empirical and dynamic behavior of this carrier-set topology. In 1000 Genomes Phase 3, across 156,604,320 SNP pairs from the MHC and NEGR1 regions, pairs on the | D' |= 1 boundary span a wide range of r2 and | C |. Within fixed r2 strata, r2 poorly distinguishes nested from non-nested carrier-set configurations, with AUROC values of approximately 0.54-0.62, whereas the boundary-sensitive normalization | D' | separates them much more effectively, with AUROC values of approximately 0.90-0.92. The empirical data also obey the predicted r2 [&le;] pA/pB ceiling.

We then introduce a temporal axis using a two-locus Wright-Fisher model on the same simplex. Carrier-set topology evolves through three motions relative to the | D' |= 1 boundary: formation or persistence, in which recombination suppression establishes and maintains inclusion without requiring selection; visibility change, in which selection or drift moves r2 along the boundary while preserving the inclusion relation; and breaking, in which a recombination pulse introduces the previously absent haplotype and dissolves inclusion. A fourth mode, specificity erosion, expands the partner carrier set while preserving inclusion, thereby lowering P(A | B) while keeping P(B | A) and | D' | equal to one. This mode shows that asymmetric conditional probabilities are best understood as diagnostic coordinates for carrier-set topology, not as the primary object itself.

Together, these results show that topology and visibility are separable axes of LD structure. Conventional r2-based scans and carrier-set topology scans therefore answer complementary, not interchangeable, questions.
]]></description>
<dc:creator><![CDATA[ Ichikawa, Y. ]]></dc:creator>
<dc:date>2026-07-01</dc:date>
<dc:identifier>doi:10.64898/2026.07.01.735767</dc:identifier>
<dc:title><![CDATA[Formation, persistence, and breakdown of carrier-set topology in linkage disequilibrium: empirical structure in 1000 Genomes and a two locus Wright Fisher model]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.26.734831v1?rss=1">
<title>
<![CDATA[
A geometric representation of gene-by-gene and gene-by-environment interactions on the extended complex plane 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.26.734831v1?rss=1
</link>
<description><![CDATA[
The relationship between genotypic and phenotypic variation is determined by the complex interaction of genetic and environmental factors. While statistical methods capable of detecting such interactions exist, an axiomatic mathematical framework that seamlessly describes the combined effects of genetic modifications and environmental exposures on a common scale is lacking. In this report, buffering concepts are used to construct a measurement system that enables the geometric representation of both gene-by-gene and gene-by-environment interactions on the extended complex plane (i.e., as projections on the Riemann sphere). In this manner, any such interaction, or combination thereof, can be precisely defined and quantified as the deviation from the neutral value calculated through the applicable complex transformation. When thus conceptualized, the frameworks parameterization defines the "state space" of a given measurable phenotype along both the real and imaginary dimensions, thus establishing an unambiguous and broadly applicable method for determining the phenotypic value expected upon combinatorial changes in genetic and/or environmental variables. Remarkably, by applying these methods, it is possible to quantify the effects of any gene-by-environment interaction using the equation, [Formula], where zobs and zexp are complex numbers representing the observed and expected phenotypes of a given genotype expressed in terms of the buffering parameters,  and b.
]]></description>
<dc:creator><![CDATA[ Karagiannis, J. ]]></dc:creator>
<dc:date>2026-07-01</dc:date>
<dc:identifier>doi:10.64898/2026.06.26.734831</dc:identifier>
<dc:title><![CDATA[A geometric representation of gene-by-gene and gene-by-environment interactions on the extended complex plane]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.27.734959v1?rss=1">
<title>
<![CDATA[
An axiomatic approach to cultivar ranking in multi-environment trials 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.27.734959v1?rss=1
</link>
<description><![CDATA[
AO_SCPLOWBSTRACTC_SCPLOWMulti-environment trials are central to cultivar evaluation because they reveal how candidate cultivars perform across locations, years, management conditions, and stress environments. The resulting yield matrix is a rich source of data on genotype-by-environment interaction, and a wide literature on estimation, decomposition, visualisation, and prediction of yield potential and stability has flourished. However the ultimate question of which cultivar to recommend on the basis of such a matrix is often left implicit. The question is far from trivial, and in this paper we formulate cultivar recommendation as an axiomatic ranking problem. This framework is rich enough to encompass the existing literature on stability indices, as well as any other deterministic ranking procedure. We show that many commonly used stability-based procedures can violate minimal criteria of efficiency or consistency. The result of such violations is that a cultivar with uniformly high yield could be ranked below a cultivar with uniformly low yield, or the relative ranks of two cultivars could depend on whether or not a third cultivar is present in the matrix. Our results prove that under a small number of such criteria the space of admissible rules collapses to the family of power means and their limiting cases. If we further wish to allow multiplication normalisation of yield, we are left with the geometric mean as the unique solution.
]]></description>
<dc:creator><![CDATA[ Kondratev, A. Y., Ianovski, E., Voronina, E., Crossa, J. ]]></dc:creator>
<dc:date>2026-07-01</dc:date>
<dc:identifier>doi:10.64898/2026.06.27.734959</dc:identifier>
<dc:title><![CDATA[An axiomatic approach to cultivar ranking in multi-environment trials]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.26.734650v1?rss=1">
<title>
<![CDATA[
Revising the genetic and epigenetic architecture of in vitro regeneration capacity in natural Arabidopsis thaliana populations 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.26.734650v1?rss=1
</link>
<description><![CDATA[
Plant regeneration is a dynamic developmental process that spans from cell dedifferentiation to organ reconstruction in response to inductive cues, such as wounding stress and hormonal signals. Although this capacity varies widely both between and within species, a comprehensive understanding of the genetic and epigenetic bases of this variation remains incomplete. To address this issue, we revisited published datasets on natural variation in in vitro regeneration capacity in Arabidopsis thaliana. Using quantitative genetic approaches, including meta-analyses of genome-wide association studies (GWAS) and multi-locus models, we dissected the genetic architecture underlying regeneration traits. Our results showed that shoot regeneration capacity is primarily explained by allelic variation in the cis-regulatory region of WUSCHEL (WUS), a key regulator of shoot meristem formation. Notably, these polymorphisms are also associated with epigenetic variants of the DNA transposon ATDNA2T9C, which is located within the regulatory region. Furthermore, allelic variation in ARABIDOPSIS RESPONSE REGULATOR 2 (ARR2), a positive regulator of cytokinin signaling, is associated with callus formation and greening traits and may promote shoot formation through genetic interactions with WUS alleles. Although in vitro regeneration is controlled by complex, multilayered gene regulatory networks, our results suggest that, in A. thaliana, natural variation in regeneration capacity is largely shaped by a small number of major-effect modifiers together with epigenetic variation and genetic interactions, despite the substantial heterogeneity observed among natural populations.
]]></description>
<dc:creator><![CDATA[ Arima, K., Chen, Y., Sugimoto, K., Sasaki, E. ]]></dc:creator>
<dc:date>2026-07-01</dc:date>
<dc:identifier>doi:10.64898/2026.06.26.734650</dc:identifier>
<dc:title><![CDATA[Revising the genetic and epigenetic architecture of in vitro regeneration capacity in natural Arabidopsis thaliana populations]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.25.734683v1?rss=1">
<title>
<![CDATA[
Pathogenic impact of ABCA4 missense variants in the structurally uncharacterized ECD1 region: implications for Stargardt disease. 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.25.734683v1?rss=1
</link>
<description><![CDATA[
Pathogenic mutations in the ABCA4 gene cause several inherited retinal diseases, particularly Stargardt disease (STGD1). However, many missense variants remain classified as variants of uncertain significance (VUS) due to inconclusive evidence regarding their pathogenic impact. The missense VUS span across all the domains of ABCA4, with the majority found in the larger extracellular domains (ECDs). The largest uncharacterized region of ABCA4 is located in ECD1, where limited structural information and inconsistent computational predictions hinder clinical interpretation of missense VUS in this region. Here, we integrated in silico analysis with in vitro functional assays to evaluate the pathogenicity of VUS in this region and improve their diagnostic classification. Missense VUS in the ECD1 uncharacterized region were curated from ClinVar. Six multiallelic sites were identified in the uncharacterized region and 13 missense VUS on these multiallelic sites were characterized using the integrated analysis. In the in silico platform, the pathogenicity of the VUS were predicted using multiple algorithms, and the structural effects of the variants were analyzed compared to the wild type. Recombinant variants were expressed in virus-like particles (VLPs), and protein expression, membrane localization, and ATPase activity were quantified relative to wild type to identify potential disease-causing variants.

From the integrated analysis, variants with pronounced structural destabilization, impaired membrane trafficking, and reduced or absent N-retinylidene-phosphatidylethanolamine (NRPE) substrate stimulated ATPase activities were identified as potentially deleterious. Notably, VUS at p.H193P and p.I214N showed loss of function, with p.I214N reflecting selectively impaired membrane targeting and p.H193P reflecting combined expression and trafficking defects. Additionally, NRPE-stimulated ATPase activities were impaired in VUS, p.V195L, p.V195I, p.D197H, p.I214F and p.N269S. Overall structural destabilization interfered with the NRPE-stimulated ATPase activities of p.N269S, while the lack of NRPE-stimulated ATPase activities of p.D197H, p.V195L, p.V195I and p.I214F are thought to be due to impaired NRPE interactions with ABCA4. All the VUS at p.R140, p.H193Y, p.D197N and p.N269H showed both the basal and NRPE-stimulated ATPase activities but less than that of the wild type displaying a mild functional deficit. Together, these findings demonstrated that certain VUS within the unresolved ECD1 region disrupts ABCA4 stability and function, supporting their contribution to disease pathogenesis. This integrative approach highlights key residues likely to be pathogenic and advances the interpretation of VUS in inherited retinal disorders.
]]></description>
<dc:creator><![CDATA[ Matarage Don, N. N. J., Biswas, S. B., Biswas-Fiss, E. E. ]]></dc:creator>
<dc:date>2026-07-01</dc:date>
<dc:identifier>doi:10.64898/2026.06.25.734683</dc:identifier>
<dc:title><![CDATA[Pathogenic impact of ABCA4 missense variants in the structurally uncharacterized ECD1 region: implications for Stargardt disease.]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.26.734851v1?rss=1">
<title>
<![CDATA[
Genome architecture shapes the evolutionary origins of redundant enhancers in fly and mouse 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.26.734851v1?rss=1
</link>
<description><![CDATA[
Shadow enhancers are groups of DNA regulatory elements that control the same target gene and drive overlapping expression patterns. Large-scale surveys have found shadow enhancers control most developmental genes in animal genomes. The way in which shadow enhancers arise and how they subsequently evolve may further illuminate their regulatory logic and mechanisms of action. To investigate the evolutionary origins of shadow enhancers, we searched for sequence signatures of three birth mechanisms: duplication of existing enhancers, transposable element (TE) co-option, and TE-mediated splitting of ancestral regulatory elements in the Drosophila melanogaster and mouse genomes. Using 420 fly shadow enhancer sets and 9,051 mouse shadow enhancer sets, we found detectable duplication evidence in 18.3% of fly shadow enhancer sets and 33.9% of mouse sets. Duplication signatures were more frequent in larger shadow sets, suggesting that repeated duplication can expand regulatory landscapes. TE-derived enhancers were present in both species but were not enriched in shadow enhancers relative to single enhancers, suggesting that TE co-option contributes to enhancer evolution generally rather than preferentially generating redundant enhancer architectures. Finally, TE-mediated enhancer splitting was rare in both genomes. These results indicate that shadow enhancer birth is mechanistically heterogeneous, reflecting a mixture of duplication, TE co-option, and other mechanisms, whose contributions are shaped by genome architecture and evolutionary time. Therefore, we find that overlapping regulatory functions can arise through multiple evolutionary routes and that birth mechanisms can influence, but do not strictly determine, the regulatory logic of the resulting enhancer set.
]]></description>
<dc:creator><![CDATA[ Ness, J., Kosztyo, B., Wunderlich, Z. ]]></dc:creator>
<dc:date>2026-07-01</dc:date>
<dc:identifier>doi:10.64898/2026.06.26.734851</dc:identifier>
<dc:title><![CDATA[Genome architecture shapes the evolutionary origins of redundant enhancers in fly and mouse]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-07-01</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.25.734236v1?rss=1">
<title>
<![CDATA[
Epigenetic signatures of infection within and across generations in the endangered Loggerhead sea turtle 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.25.734236v1?rss=1
</link>
<description><![CDATA[
Infection can substantially reduce host fitness and influence population dynamics, yet it is often difficult to detect and quantify in wild animal populations. Molecular tools offer a valuable means of identifying cryptic infection in natural systems. Using whole-genome bisulfite sequencing, we examined whether infection with the parasitic leech Ozobranchus margoi is associated with DNA methylation variation in loggerhead sea turtles (Caretta caretta), while also assessing the potential value of this variation as a biomarker of parasite infection. In nesting females, we identified infection-associated differentially methylated CpG sites associated with genes implicated in immune signalling and cellular regulation. Offspring of infected females also showed infection-associated methylation patterns, despite not being directly exposed to the parasite themselves. Differential methylation analyses identified genes involved in immunity, neurodevelopment and metabolic activity, with limited overlap in associated genes and no overlap in differentially methylated sites between generations. Maternal and offspring genome-wide methylation levels showed a non-linear association that differed subtly with maternal infection status, indicating that infection modifies intergenerational methylation associations. Finally, methylation profiles showed strong discriminatory power for maternal infection status in both maternal and hatchling samples using machine learning models, supporting their potential as candidate biomarkers of cryptic infection. Together, these results show that parasite infection is associated with distinct, generation-specific DNA methylation signatures, and highlight the potential value of epigenetic data for monitoring cryptic infection states in conservation-relevant systems.
]]></description>
<dc:creator><![CDATA[ Bazely, J. O., Yen, E. C., Balard, A., Gilbert, J. D., Fairweather, K., Lopes, A., Taxonera, A., Rossiter, S. J., Eizaguirre, C. ]]></dc:creator>
<dc:date>2026-06-30</dc:date>
<dc:identifier>doi:10.64898/2026.06.25.734236</dc:identifier>
<dc:title><![CDATA[Epigenetic signatures of infection within and across generations in the endangered Loggerhead sea turtle]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-06-30</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.25.734557v1?rss=1">
<title>
<![CDATA[
Gut-derived serine protease reduces sleep but extends lifespan 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.25.734557v1?rss=1
</link>
<description><![CDATA[
Sleep has historically been viewed through a brain-centric lens with little known about the contribution of the periphery. Through a targeted screen of secreted peptides from the fat body, gut, and body wall muscle in Drosophila, we identified CG11037, a trypsin-like serine endopeptidase secreted from midgut enterocytes, as a previously unrecognized regulator of sleep. Loss of CG11037 reduces daily sleep, as well as sleep following injury/infection, although recovery is enhanced suggesting reduced need for sleep during sickness. Proteomic analysis of flies with reduced CG11037 revealed altered oxidative stress response pathways including cytochrome P450-related proteins. Indeed, gut-specific knockdown of Cyp6a2 or Cyp28d1 phenocopies CG11037 sleep defects, and loss of CG11037 or P450 elevates reactive oxygen species (ROS) selectively in the gut without affecting brain ROS. Rescue of sleep by antioxidant treatment demonstrates that peripheral ROS accumulation drives the behavioral phenotype. Strikingly, despite physiological dysfunction and reduced sleep, CG11037 or Cytochrome P450 knockdown extends lifespan in a ROS-dependent manner, suggesting that stress adaptation of these knockdowns allows them to live longer. Together, these findings uncover a mechanism for the unexpected association of reduced sleep and extended lifespan.
]]></description>
<dc:creator><![CDATA[ Moore, R. S., Xiong, R., Astacio, E., Williams, J. A., Brooks, T., Grant, G., Stucynski, J., Fazelinia, H., Nash, E., Spruce, L., Sehgal, A. ]]></dc:creator>
<dc:date>2026-06-29</dc:date>
<dc:identifier>doi:10.64898/2026.06.25.734557</dc:identifier>
<dc:title><![CDATA[Gut-derived serine protease reduces sleep but extends lifespan]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-06-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.24.734305v1?rss=1">
<title>
<![CDATA[
Intestinal lipid metabolism controls immune response through NHR-68 and gut-brain signaling in C. elegans 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.24.734305v1?rss=1
</link>
<description><![CDATA[
Animals must allocate limited energetic resources across competing defense programs in response to infection. Here, we show that the conserved nuclear hormone receptor NHR-68 integrates fatty acid metabolism with the neural control of molecular and behavioral immunity in Caenorhabditis elegans. Acting in parallel with NHR-10, NHR-68 controls genes involved in polyunsaturated fatty acid (PUFA) metabolism. Loss of NHR-68 disrupts linoleic acid (LA) homeostasis, impairing pathogen avoidance behavior. Supplementation with LA restores avoidance, and fat-3 inhibition, which elevates LA, enhances pathogen avoidance, whereas loss of LA synthesis by fat-2 inhibition diminishes this behavior, indicating that LA promotes behavioral immunity. We further show that NHR-68 acts in the intestine to regulate linoleic acid homeostasis, and that changes in intestinal lipid metabolism influence an AWC-dependent pathogen-avoidance circuit through intestine-to-neuron communication. NHR-68 suppresses activation of the PMK-1/p38 MAPK and DAF-16/FOXO pathways, which mediate molecular immune responses. These findings identify a gut-brain transcriptional circuit that connects intestinal lipid metabolism to neural and immune outputs, revealing a mechanism by which the metabolic state coordinates behavioral and molecular defenses to optimize host protection.
]]></description>
<dc:creator><![CDATA[ Ren, J., Sang, Y., Nakayasu, E. S., Kim, Y.-M., Aballay, A. ]]></dc:creator>
<dc:date>2026-06-29</dc:date>
<dc:identifier>doi:10.64898/2026.06.24.734305</dc:identifier>
<dc:title><![CDATA[Intestinal lipid metabolism controls immune response through NHR-68 and gut-brain signaling in C. elegans]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-06-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.24.733714v1?rss=1">
<title>
<![CDATA[
Haplotype-specific chromosome painting unveils recombination patterns in the holocentric species Rhynchospora breviuscula H.Pfeiff. 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.24.733714v1?rss=1
</link>
<description><![CDATA[
The genus Rhynchospora Vahl (beak-sedges) comprises approximately 381 accepted species with a worldwide distribution, all of which possess holocentric chromosomes, where centromeric activity is distributed almost along the entire chromosome. Despite the recent advances, the mechanisms governing the dynamics of meiotic recombination in holocentric plants remain poorly understood. Here, we developed haplotype-specific oligo-FISH probes for chromosomes 1, 2, and 3 based on a haplotype-phased genome assembly of Rhynchospora breviuscula (n = 5), enabling homolog-specific chromosome painting. Each probe set was labelled with a distinct fluorophore and hybridised in situ to metaphase chromosomes of the reference plant and seven F1 individuals derived from self-crossed reference plants. This approach allowed the unambiguous discrimination of homologous haplotypes and the indirect visualisation of crossover (CO) events in recombined chromosomes. We observed that recombination events were predominantly located in terminal chromosomal regions, consistent across individuals. These results corroborate previous findings from single-cell recombination mapping and provide independent cytological validation of the recombination landscape in this species. Our study establishes haplotype-specific chromosome painting as a robust tool for high-resolution mapping of meiotic recombination in holocentric plants across generations. Furthermore, these probes provided a foundation for future investigations into inverted meiosis, a mechanism characterized by an alternative pattern of chromosome segregation in holocentric species.
]]></description>
<dc:creator><![CDATA[ Nascimento, T., Marques, A. ]]></dc:creator>
<dc:date>2026-06-29</dc:date>
<dc:identifier>doi:10.64898/2026.06.24.733714</dc:identifier>
<dc:title><![CDATA[Haplotype-specific chromosome painting unveils recombination patterns in the holocentric species Rhynchospora breviuscula H.Pfeiff.]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-06-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.24.734157v1?rss=1">
<title>
<![CDATA[
Paralogous lncRNAs CYTOR and MORRBID share a conserved trans acting function in MEK ERK signaling 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.24.734157v1?rss=1
</link>
<description><![CDATA[
BackgroundLong non-coding RNAs (lncRNAs) exhibit rapid evolutionary turnover, often driven by genomic duplication. How paralogous lncRNAs maintain, partition, or diverge in function across distinct genomic contexts remains poorly understood. The evolutionarily conserved lncRNA MORRBID and its primate-specific paralog CYTOR provide a natural framework to interrogate the functional consequences of lncRNA duplication.

ResultsAlthough CYTOR and MORRBID have acquired distinct transcript variants influenced by their divergent genomic environments, we demonstrate that they maintain a robust, shared core function encoded by near-identical dominant two-exon transcripts. Using SNP-based paralog-specific quantification, we found that CYTOR contributes more strongly to the shared transcript pool, while both transcripts localize predominantly to the cytoplasm, consistent with a shared trans-acting function. Simultaneous repression of CYTOR and MORRBID consistently impairs cell adhesion and migration across multiple cancer models. Mechanistically, the shared CYTOR/MORRBID transcript pool associates with MEK2 and sustains MEK-ERK signaling. This signaling axis promotes FOSL1 expression and AP-1-linked transcriptional output, including expression of the downstream effector EPHA4, whose role was supported by rescue experiments. Patient tumor transcriptomes and healthy single-cell datasets further supported the associated mesenchymal, adhesion, and epithelial-mesenchymal transition program.

ConclusionsOur findings establish that paralogous lncRNAs can retain a conserved mechanistic core despite context-dependent transcriptional divergence. The CYTOR/MORRBID transcript pool defines a shared lncRNA signaling module that supports MAPK-ERK signaling and adhesion-migration programs across cancer and mesenchymal-like cellular contexts. This defines a unified mechanistic framework for the shared core function of these widely studied paralogous lncRNAs.
]]></description>
<dc:creator><![CDATA[ Ali-Nasser, T., Khoury, C., Altalef Mishaan, S., Bhonkar, O., Lin, Z., Qian, Y., Lahoud-Jeries, N. L.-J., Aran, D., Bester, A. C. ]]></dc:creator>
<dc:date>2026-06-29</dc:date>
<dc:identifier>doi:10.64898/2026.06.24.734157</dc:identifier>
<dc:title><![CDATA[Paralogous lncRNAs CYTOR and MORRBID share a conserved trans acting function in MEK ERK signaling]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-06-29</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.26.734753v1?rss=1">
<title>
<![CDATA[
A cryptic local genetic cluster in Northern France amid the European mosaic of flat oyster lineages revealed by integrating SNP array and whole-genome sequencing 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.26.734753v1?rss=1
</link>
<description><![CDATA[
The European flat oyster (Ostrea edulis), like numerous other oyster species, has been exploited for millennia and cultivated and translocated for centuries. Following a severe population decline, and in the context of ongoing conservation and restoration programs, genetic considerations must now be addressed to avoid mistakes. The objective of our study was to complement population genetic studies conducted at various scales along European coasts. Our sampling primarily targeted the French Atlantic, English Channel, and Mediterranean coasts, aiming to provide a fine-scale genetic characterization of populations in these regions. By integrating SNP array and low-coverage sequencing datasets, we obtained a comprehensive overview of the population genetic structure of Ostrea edulis across western Europe. Most previously identified clusters in Western Europe were confirmed. In France, populations assigned to these clusters exhibited notable within-patch homogeneity. However, two key findings emerged: (1) an extensive overlap zone between the Atlantic and western Mediterranean clusters, spanning at least from southern Portugal to southern France, and (2) the detection of a novel, clearly distinct cryptic cluster east of the English Channel, whose geographic range remains to be better delineated. These insights are critical for informing management decisions, particularly as restoration and conservation plans are currently being implemented across the species range.
]]></description>
<dc:creator><![CDATA[ Lapegue, S., Cornette, F., Heurtebise, S., Pouvreau, S., Carpentier, C., Colston-Nepali, L., Bierne, N., Reisser, C. ]]></dc:creator>
<dc:date>2026-06-28</dc:date>
<dc:identifier>doi:10.64898/2026.06.26.734753</dc:identifier>
<dc:title><![CDATA[A cryptic local genetic cluster in Northern France amid the European mosaic of flat oyster lineages revealed by integrating SNP array and whole-genome sequencing]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-06-28</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.25.734482v1?rss=1">
<title>
<![CDATA[
Genomic insights into bacterial kidney disease resistance in Arctic charr (Salvelinus alpinus) via a 72k SNP array 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.25.734482v1?rss=1
</link>
<description><![CDATA[
Selection for disease resistance forms one of the most highlighted areas of aquaculture breeding. A breeding program for Arctic charr has been operating in Sweden for over 40 years, making it the oldest of its kind worldwide for this species. However, the lack of available genomic resources prevented selection for any disease-resistance traits. A 72k Axiom SNP array was produced in this study and used to assess the potential to select for charr resistant to bacterial kidney disease (BKD), which is currently a major threat to the industry. Following a challenge experiment with Renibacterium salmoninarum, the causative agent of BKD, relevant phenotypic proxies were collected from approximately 2,000 charr. Thereafter, those animals were genotyped with the new 72k SNP array. The magnitude of the estimated variance components suggested potential for breeding for BKD resistance in charr, with relevant heritabilities ranging from 0.05 to 0.56 depending on the resistance proxy used. In addition, GWAS suggested that BKD resistance is a polygenic trait. Furthermore, genomic prediction approaches indicated that BKD-resistant animals can be identified using their SNP genotypes. Accuracies, expressed as Pearson correlation coefficients, when BKD resistance was analysed as a continuous trait, ranged from 0.42 to 0.52. In the scenario where BKD resistance was treated as a binary trait, the efficiency of genomic prediction was assessed using ROC curves, with an area under the curve of 0.72. Finally, no unfavourable correlations were found with growth traits. The developed 72k SNP array has the potential of being a pivotal tool for the Swedish Arctic charr breeding program. Moreover, our data support the use of genomic prediction in breeding BKD-resistant Arctic charr. As a critical next step, further validations in actual industry conditions would be required.
]]></description>
<dc:creator><![CDATA[ Palaiokostas, C., Jeuthe, H., Nilsson, K. N., Hallbom, H., Axen, C., Evensen, O., Eriksson, S., Johnsson, M. ]]></dc:creator>
<dc:date>2026-06-27</dc:date>
<dc:identifier>doi:10.64898/2026.06.25.734482</dc:identifier>
<dc:title><![CDATA[Genomic insights into bacterial kidney disease resistance in Arctic charr (Salvelinus alpinus) via a 72k SNP array]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-06-27</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.24.733965v1?rss=1">
<title>
<![CDATA[
Genetic Association of Somatic Incompatibility and NLR-like Protein Domains in Coprinopsis cinerea 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.24.733965v1?rss=1
</link>
<description><![CDATA[
In fungi, hyphal fusion is beneficial within an individual, but fusion between individuals comes with the risks of infection or exploitation. To manage this risk, fungi have developed mechanisms to restrict sustained fusion to be within a genetic individual, called allorecognition. In Ascomycete fungi, this recognition is based on allelic identity at several polymorphic allorecognition genes, often triggering cell death. However, the genetic basis of allorecognition is unknown in basidiomycetes, the clade that includes mushroom-forming fungi. Here, we map the first locus for this trait, which we call somA, in the mushroom-forming fungus Coprinopsis cinerea. We combined F1 offspring phenotypes with independent backcross lines to identify a region on chromosome 5 linked with the production of a barrage zone, a classic allorecognition phenotype. Fine-mapping of this region resulted in a region with a set of kinases and NACHT domain proteins, flanked by a leucine-rich repeat (LRR) protein. While the NACHT and kinase proteins are diverse between the parents, the LRR-encoding protein shows signs of purifying selection. Additional C. cinerea genomes show that this region contains several highly divergent alleles, consistent with long-term balancing selection. These polymorphic alleles all contain a single monomorphic LRR, which may indicate a novel mechanism for fungal nonself recognition. Based on a phylogenetic survey of related Basidiomycetes, this specific locus architecture appears to be restricted to closely related species. This finding of a multiallelic locus may explain the general trend of few nonself recognition loci in basidiomycetes. These results provide a first understanding of how individuality is maintained in basidiomycetes.

Significance StatementHow mushroom-forming fungi recognize each other as individuals is an open question. Here, we identify the first genes that trigger this recognition in a mushroom-forming fungus. As these fungi have very distinctive lifecycles compared to mold-forming fungi, it was hypothesized that the process would operate from different mechanisms. Our results show the molecular mechanisms are in fact quite similar. These results provide a first step towards understanding how these fungi can both fuse with themselves and still discriminate against other individuals.
]]></description>
<dc:creator><![CDATA[ Auxier, B., Ament Velasquez, L., Baars, J. J. P., Scholtmeijer, K., F. van Peer, A., Debets, A. J., Aanen, D. K. ]]></dc:creator>
<dc:date>2026-06-27</dc:date>
<dc:identifier>doi:10.64898/2026.06.24.733965</dc:identifier>
<dc:title><![CDATA[Genetic Association of Somatic Incompatibility and NLR-like Protein Domains in Coprinopsis cinerea]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-06-27</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.22.733791v1?rss=1">
<title>
<![CDATA[
Transformation and allelic exchange in Orientia tsutsugamushi 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.22.733791v1?rss=1
</link>
<description><![CDATA[
Orientia tsutsugamushi is a mite-transmitted obligate intracellular bacterium that causes the potentially deadly zoonosis, scrub typhus. The absence of genetic tools for Orientia have limited studies of the microbe-host interactions that underlie scrub typhus. To address this gap, we developed a protocol for transforming and achieving allelic exchange in O. tsutsugamushi str. Ikeda. From evaluating multiple cell lines and antibiotics, we found that contact-inhibited EA.hy926 human endothelial-like cells best supported Orientia replication and that chloramphenicol was an effective selection marker. We engineered a homologous recombination cassette encoding a codon-modified version of the O. tsutsugamushi ank13 gene (OTT_RS04140) (CMank13) and its promoter alongside genes for mScarlet-I and chloramphenicol acetyltransferase under control of the O. tsutsugamushi tsa22-up and tsa56-down promoters, respectively. A PCR product encompassing the cassette and chromosomal flanking regions was transformed into O. tsutsugamushi via electroporation or CaCl2, the latter of which better preserved bacterial and host cell viability. EA.hy926 cells inoculated with transformed O. tsutsugamushi were grown in glass-bottom plates in the presence of chloramphenicol and imaged by live-cell microscopy to identify cultures containing mScarlet-I positive bacteria, which could be maintained in perpetuity. Chromosomal integration of the CMank13 cassette and loss of wild-type ank13 were verified by PCR and nanopore sequencing. This report establishes platforms for genetically manipulating O. tsutsugamushi and building additional genetic tools to investigate this globally significant pathogen.

IMPORTANCEOrientia tsutsugamushi causes scrub typhus, a globally emerging rickettsiosis that can have a high mortality rate and has been a known human disease since the fourth century. Of the genera of obligate intracellular bacterial pathogens that cause human disease, Orientia is the only one for which genetic tools have not been developed. This has limited understanding of O. tsutsugamushi-host dynamics that drive the bacteriums pathobiology and hindered development of novel treatment or protection strategies against scrub typhus. Here, we successfully transformed and achieved allelic exchange in O. tsutsugamushi. Transgenic bacteria were selected via antibiotic resistance, validated by PCR and nanopore sequencing, and visualized by immunofluorescence and live-cell fluorescence imaging. Our report includes detailed descriptions of empirically determined host cell cultivation, multiplicity of infection, transformation, and selection conditions to provide a foundation on which other researchers can build. Overall, this work begins to establish a genetic toolbox for O. tsutsugamushi.
]]></description>
<dc:creator><![CDATA[ Carlyon, J. A., Allen, P. E., Hunt, J. R., Chiarelli, T. J. ]]></dc:creator>
<dc:date>2026-06-26</dc:date>
<dc:identifier>doi:10.64898/2026.06.22.733791</dc:identifier>
<dc:title><![CDATA[Transformation and allelic exchange in Orientia tsutsugamushi]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-06-26</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.24.734286v1?rss=1">
<title>
<![CDATA[
Evaluating the potential role and contribution of transposable elements to the evolution of microbial multicellularity across the tree of eukaryotes 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.24.734286v1?rss=1
</link>
<description><![CDATA[
Multicellularity has evolved multiple times across the eukaryotic tree of life, including among protist lineages. Because transposable elements (TEs) strongly influence genome architecture and gene regulation, understanding their potential impact on genome structure and their relationship with gene expression may provide insight into the evolution of multicellularity.

Here, we generated a new genome assembly for the facultatively multicellular amoeba Acrasis kona and performed comparative analyses of TE composition, TE diversity, and TE-density organization across diverse protist lineages. Comparative analyses included unicellular and multicellular representatives from across the tree of eukaryotes, (Heterolobosea, Filasterea, Cristidiscoidea, and Chlorophyceae), including Naegleria spp., Tetramitus jugosus, Capsaspora owczarzaki, Pigoraptor spp., Fonticula alba, Parvularia atlantis, Volvox carteri, and Chlamydomonas reinhardtii.

To examine relationships between TEs and gene regulation, we integrated transcriptomic datasets from A. kona, Capsaspora owczarzaki, and Volvox carteri with genome-wide TE-density analyses of differentially expressed genes. TE abundance and composition varied substantially among lineages, with species that exhibit more complex developmental or cellular organization generally containing higher TE proportions than closely related unicellular taxa. Patterns of TE-density organization near up-regulated, down-regulated, and non-differentially expressed genes also differed among systems, ranging from strong TE depletion in A. kona to weaker or cell-type-specific patterns in Capsaspora and Volvox.

Together, these findings suggest that transposable elements are associated with multicellularity across diverse protist lineages, although the specific roles they play appear to be complex, lineage-specific, and not yet fully understood.
]]></description>
<dc:creator><![CDATA[ Correa Perdomo, A. X., Brown, M. W., Banson, I., Robert, J. E., Thompson, C., Kalulu, P., Tice, A. K., Ray, D. A. ]]></dc:creator>
<dc:date>2026-06-25</dc:date>
<dc:identifier>doi:10.64898/2026.06.24.734286</dc:identifier>
<dc:title><![CDATA[Evaluating the potential role and contribution of transposable elements to the evolution of microbial multicellularity across the tree of eukaryotes]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-06-25</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.22.733755v1?rss=1">
<title>
<![CDATA[
Defining the molecular tolerance-to-damage landscape of SMARCA4 helicase genetic alterations 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.22.733755v1?rss=1
</link>
<description><![CDATA[
Evaluating the impact of genomic variation is essential for identifying underlying mechanistic causes of human diseases. The spectrum of neurodevelopmental disorders is driven by diverse genetic alterations with genes like SMARCA4 being prototypical examples. There have been significant hurdles to implementing the protein-specific and mechanism-informed variation effect predictors that are anticipated to have the highest yield of mechanistic information. Yet, there is a pressing need, for example, within SMARCA4 where 98% of the 2780 reported variants lack a disposition and remain of uncertain significance (VUS). Further, the field has yet to identify each variants specific molecular mechanism, which will inform targeted therapeutic development strategies. In this study we developed a mechanistic structure-informed helicase-specific variant effect predictor by leveraging diverse information with state-specific calculations. Our approach has 100% recall of pathogenic variants while classifying 87.23% of VUS into damaging (55.74%, n=262) versus tolerated effects (31.49%, n=148), including those with conflicting interpretations. This analysis reveals significant enrichment of integrated functional metrics, such as conservation and solvent exposure, that parallel allele frequences in health populations, and emphasizes the robustness of the method. Thus, we have demonstrated a novel approach for the development of mechanism-informed protein-specific interpretation of human genetic information.
]]></description>
<dc:creator><![CDATA[ NESHATUL, H., Wagenknecht, J., Dong, X., Zimmermann, M. T. ]]></dc:creator>
<dc:date>2026-06-24</dc:date>
<dc:identifier>doi:10.64898/2026.06.22.733755</dc:identifier>
<dc:title><![CDATA[Defining the molecular tolerance-to-damage landscape of SMARCA4 helicase genetic alterations]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-06-24</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.19.733321v1?rss=1">
<title>
<![CDATA[
Primary-Level Meta-Analysis of Diversity Outbred Mice Identifies a Fasting Plasma Trimethylamine N-Oxide (TMAO) Locus Modified by Sex and Diet 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.19.733321v1?rss=1
</link>
<description><![CDATA[
Trimethylamine n-oxide (TMAO) is a plasma metabolite linked to adverse cardiometabolic health with complex regulation involving diet, sex, and host genetics. We explored the role of these factors in the genetic regulation of TMAO by performing a primary-level meta-analysis in 1,482 female and male Diversity Outbred (DO) mice from five distinct studies conducted in various regions of the United States. We identified a quantitative trait locus (QTL) associated with TMAO concentration at [~]86 megabase pairs on mouse chromosome 12 with a highly significant LOD score of 67.67. Alleles at the chromosome 12 QTL inherited from the Cast/EiJ (CAST) and PWK/PhJ (PWK) mouse strains primarily drove the association with reduced TMAO concentrations. The chromosome 12 QTL remained significant in sex-stratified analyses and the mode of inheritance appeared additive; furthermore, the QTL was regulated by sex-by-genotype and sex-by-diet interactions. Using a CAST/EiJ X C57BL/6J F2 cross, positional candidates were prioritized by eQTL analysis. Further analysis in a study utilizing the eight DO founding strains identified that Acyp1 was differentially expressed in hepatic tissue from CAST mice, prompting investigation into its genetic regulation. Acyp1 demonstrated relevant cis- and trans-regulation and was significantly correlated with TMAO and hepatic Fmo3. However, no significant relationships between Acyp1 and TMAO were identified in mice inactivated for Acyp1 or with AAV overexpression of Acyp1 in the liver. Genes within the chromosome 12 QTL have synteny with humans and may translate to the genetic regulation of human plasma TMAO concentrations and atherosclerosis.

Author SummaryWe explored the roles of diet, sex, and genetics on the regulation of fasting plasma trimethylamine n-oxide (TMAO) concentration by performing a meta-analysis in 1,482 female and male Diversity Outbred (DO) mice from five unique studies. We identified a QTL associated with TMAO concentration on chromosome 12 at [~]86 mega base pair (Mb) with a highly significant LOD score of 67.67. The locus is modified by both sex and diet.
]]></description>
<dc:creator><![CDATA[ Sutton, K., Gertz, E. R., Evans, L. W., Budke, D., Huda, N., Yam, P., Kim, M., Rutkowsky, J., Shih, D., Hartiala, J., Pomp, D., Lusis, A. J., Allayee, H., Bennett, B. J. ]]></dc:creator>
<dc:date>2026-06-24</dc:date>
<dc:identifier>doi:10.64898/2026.06.19.733321</dc:identifier>
<dc:title><![CDATA[Primary-Level Meta-Analysis of Diversity Outbred Mice Identifies a Fasting Plasma Trimethylamine N-Oxide (TMAO) Locus Modified by Sex and Diet]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-06-24</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.18.730290v1?rss=1">
<title>
<![CDATA[
Large-scale meta-analysis of over one million individuals reveals the genetic architecture of 127 complex traits in East Asian populations 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.18.730290v1?rss=1
</link>
<description><![CDATA[
Genome-wide association studies (GWASs) have disproportionately focused on European (EUR) populations, limiting the characterization of genetic architecture in other ancestries. To address this imbalance, we integrated large-scale biobanks from Japan, Korea, Taiwan, and China to perform the largest phenome-wide meta-analysis to date in East Asian (EAS) populations, encompassing over one million individuals across 127 complex traits.

We identified 8,010 previously unreported associations and observed substantial genetic sharing across EAS subpopulations, while also detecting cohort-specific heterogeneity within the broader EAS context. Transethnic analyses revealed moderate genetic correlations between EAS and EUR populations, indicating both shared and ancestry-specific components of disease risk. Pleiotropy analyses highlighted prominent signals within the HLA region, supported by protein-protein interaction connectivity and immune-related pathway enrichment. Decomposition of genome-wide association matrices further uncovered structured cross-trait architectures, revealing a predominantly shared polygenic backbone driven by metabolic, biochemical, and anthropometric traits, together with two discrete latent components enriched for immune-related processes.

Together, our findings refine the genetic architecture of complex traits in East Asian populations at unprecedented scale and clarify the balance between shared and population-specific determinants of human diseases.
]]></description>
<dc:creator><![CDATA[ Jo, J., Khor, S.-S., Chu, S.-K., Ji, Y., Ueno, K., Ono, A., Chen, C.-W., Do, A., Han, H., Kawai, Y., Kim, N.-E., Chen, C.-h., Tokunaga, K., Won, S., Yang, H.-C. ]]></dc:creator>
<dc:date>2026-06-23</dc:date>
<dc:identifier>doi:10.64898/2026.06.18.730290</dc:identifier>
<dc:title><![CDATA[Large-scale meta-analysis of over one million individuals reveals the genetic architecture of 127 complex traits in East Asian populations]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-06-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.23.733901v1?rss=1">
<title>
<![CDATA[
Repair outcomes after germline homing endonuclease cleavage in Anopheles gambiae inform the design of synthetic gene drives 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.23.733901v1?rss=1
</link>
<description><![CDATA[
Homing endonuclease genes spread by cleaving homologous chromosomes that lack the endonuclease cassette, after which repair from the endonuclease-containing chromosome converts the cut allele into a copy of the drive allele. This mechanism has provided a conceptual foundation for synthetic gene drive systems, including CRISPR-based drives, that represent promising strategies for the genetic control of insect pests. However gene drive performance depends critically on the repair pathways available in the germline of the target organism. Here, we report a set of transgenic assays originally developed as part of an attempt to establish gene targeting in the malaria mosquito Anopheles gambiae using an in vivo-generated linear targeting molecule. Although the intended FLP-mediated excision step was not achieved in the mosquito germline, analysis of the component strains revealed efficient germline activity of the rare-cutting homing endonuclease I-SceI and a striking bias towards homology-based repair of I-SceI-induced double-strand breaks. Across reporter and donor configurations, cleavage outcomes were dominated by single-strand annealing, microhomology-mediated repair, synthesis-dependent strand annealing and gene conversion-like events, with comparatively limited evidence for classical non-homologous end joining. In reciprocal crosses designed to distinguish gene conversion from gamete loss, I-SceI cleavage also produced inheritance distortion consistent with both conversion of the cleaved allele and reduced recovery of gametes carrying extensively damaged donor alleles. These findings indicate that the An. gambiae germline can strongly favour homology-dependent repair following homing endonuclease cleavage and that cleavage can also generate meiotic drive-like distortion through selective loss of damaged gametes. The results have direct relevance for the design and interpretation of homing endonuclease and CRISPR-based gene drives in malaria mosquitoes, where the balance between homology-directed repair, end joining and gamete viability will determine drive efficiency, resistance formation and transmission bias.

Author summaryGene drives depend on a simple but demanding principle: a nuclease cuts one chromosome, and the cell repairs the break using the homologous chromosome as a template, copying the drive element in the process. Before CRISPR, this type of system was explored using naturally occurring homing endonucleases such as I-SceI. We attempted to develop a gene targeting system in Anopheles gambiae based on the Rong and Golic strategy, in which FLP recombinase would excise a donor molecule and I-SceI would linearise it to stimulate recombination. The full knockout technology did not work because FLP-mediated excision was not detected in the mosquito germline. However, the component tests revealed something more broadly important: I-SceI-induced breaks were repaired predominantly through homology-based pathways rather than simple end joining. We also observed inheritance distortion consistent with both gene conversion and loss of damaged gametes. These results help explain why homing-based systems can work in mosquitoes, while also highlighting why repair pathway choice and gamete viability need to be measured directly in any new drive configuration.
]]></description>
<dc:creator><![CDATA[ Naujoks, D., Nolan, T. ]]></dc:creator>
<dc:date>2026-06-23</dc:date>
<dc:identifier>doi:10.64898/2026.06.23.733901</dc:identifier>
<dc:title><![CDATA[Repair outcomes after germline homing endonuclease cleavage in Anopheles gambiae inform the design of synthetic gene drives]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-06-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.06.20.733520v1?rss=1">
<title>
<![CDATA[
Is APOE ε2 always a protective allele? Deviations in Hardy-Weinberg equilibrium in admixed Brazilian elderly individuals 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.06.20.733520v1?rss=1
</link>
<description><![CDATA[
The APOE gene is a critical determinant of human healthspan and longevity, with the rare{varepsilon} 2 allele traditionally viewed as a universal protective factor against Alzheimer s disease (AD) and a driver of exceptional lifespan. However, this protective paradigm is predominantly derived from European-centric cohorts, leaving the evolutionary and clinical impacts of{varepsilon} 2 across diverse, highly admixed populations largely unknown due to a lack of local ancestry (LA) resolution. To investigate how local genomic backgrounds modulate APOE survival dynamics we analyzed two Brazilian sample collection of older adults from Sao Paulo city: the Biobank for Aging Studies (BAS, n = 716), a post-mortem autopsy study of naturally deceased individuals; and the Health, Well-being and Aging Study (SABE, n = 952), a census-based elderly sample collection. We evaluated deviations from Hardy-Weinberg equilibrium (HWE) using robust permutation-based models to capture ongoing selective and mortality pressures at the APOE locus. While global APOE frequencies adhered to HWE, integrating LA unveiled striking, mirrored ancestral deviations. Our findings reveal that APOE {varepsilon}2 homozygotes with African ancestry significantly contribute to deviations from HWE in the BAS, with an excess of {varepsilon}2AFR/{varepsilon}2AFR homozygotes observed (p = 0.0196). These distinct HWE deviations demonstrate that an African LA background acts as a genetic buffer, attenuating the phenotypic extreme effects of APOE alleles. Furthermore, we observed an excess of the{varepsilon} 4 European haplotypes in the BAS, which is consistent with a mortality pressure allelic effect in the European LA context. Conversely, the{varepsilon} 4AFR/{varepsilon}4AFR combination was overrepresented in the SABE. While this buffering mechanism mitigates{varepsilon} 4 toxicity, it simultaneously dampens the exceptional longevity advantage typically conferred by the{varepsilon} 2 allele, leading to its neutral accumulation in the post-mortem cohort. Our study challenges the "one-size-fits-all" assumption of APOE biomarkers, demonstrating that{varepsilon} 2 protective mechanisms are context-dependent and modulated by local genomic backgrounds in admixed populations.
]]></description>
<dc:creator><![CDATA[ Santos, G. d. N., Rodrigues, P. H. S., Passos, C. H., Paco, S. L. G., Ignacio, I. B., de Alexandria, M. A. L. S., Bastos, A. O., Veronezz, L. A., Neto, F. A. d. O., Bardella, M. U., Suemoto, C. K., Leite, R., Meyer, D., Grinberg, L., Naslavsky, M. S. ]]></dc:creator>
<dc:date>2026-06-23</dc:date>
<dc:identifier>doi:10.64898/2026.06.20.733520</dc:identifier>
<dc:title><![CDATA[Is APOE ε2 always a protective allele? Deviations in Hardy-Weinberg equilibrium in admixed Brazilian elderly individuals]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-06-23</prism:publicationDate>
<prism:section></prism:section>
</item>
</rdf:RDF>
