bioRxiv Subject Collection: Genomics
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This feed contains articles for bioRxiv Subject Collection "Genomics"
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Cohesin residence time gates 3D genome response to histone hyperacetylation
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https://www.biorxiv.org/content/10.64898/2026.07.01.735920v1?rss=1
2026-07-04doi:10.64898/2026.07.01.735920Cold Spring Harbor Laboratory2026-07-04
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Accurate, comprehensive gene annotation and ortholog identification across thousands of vertebrate genomes with TOGA2
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https://www.biorxiv.org/content/10.64898/2026.06.30.735536v1?rss=1
2026-07-04doi:10.64898/2026.06.30.735536Cold Spring Harbor Laboratory2026-07-04
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Saturation-seq integrates single-cell saturation genome editing and RNA-seq to quantify NFE2L2 (NRF2) variant effects
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https://www.biorxiv.org/content/10.64898/2026.06.30.735631v1?rss=1
90% accuracy and enabled interpretation of TCGA and TRACERx patient tumor data, as well as a rare NFE2L2 germline variant linked to a developmental syndrome. Thus, we establish a broadly applicable high-resolution single-cell variant-to-function platform with a rich phenotypic readout.
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Long-read sequencing maps transposable element variation and its regulatory and epigenetic effects in the human brain
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https://www.biorxiv.org/content/10.64898/2026.07.02.735893v1?rss=1
2026-07-03doi:10.64898/2026.07.02.735893Cold Spring Harbor Laboratory2026-07-03
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Spatial and functional mapping of the human pancreas reveals endocrine and exocrine cell states in health and metabolic disease
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https://www.biorxiv.org/content/10.64898/2026.06.30.735261v1?rss=1
2026-07-03doi:10.64898/2026.06.30.735261Cold Spring Harbor Laboratory2026-07-03
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Long-range regulatory target prediction reveals shared genetic background across ulcerative colitis, Crohn's disease, primary sclerosing cholangitis and ankylosing spondylitis
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https://www.biorxiv.org/content/10.64898/2026.06.29.735270v1?rss=1
2026-07-03doi:10.64898/2026.06.29.735270Cold Spring Harbor Laboratory2026-07-03
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From junk to deleterious: Natural subtelomeric repeat amplifications impact fitness and cellular phenotypes in yeast
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https://www.biorxiv.org/content/10.64898/2026.06.29.735415v1?rss=1
2026-07-03doi:10.64898/2026.06.29.735415Cold Spring Harbor Laboratory2026-07-03
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Variable latency between the founder genetic event and rhabdoid tumor expansion
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https://www.biorxiv.org/content/10.64898/2026.06.30.735306v1?rss=1
2026-07-03doi:10.64898/2026.06.30.735306Cold Spring Harbor Laboratory2026-07-03
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Systematic benchmarking of low-input whole exome sequencing workflows for longitudinal ctDNA profiling in pancreatic ductal adenocarcinoma
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https://www.biorxiv.org/content/10.64898/2026.06.29.734743v1?rss=1
2026-07-03doi:10.64898/2026.06.29.734743Cold Spring Harbor Laboratory2026-07-03
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Recombinogenic G-quadruplexes in the Newtonian DNA Sequence Space
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https://www.biorxiv.org/content/10.64898/2026.06.30.735570v1?rss=1
2026-07-03doi:10.64898/2026.06.30.735570Cold Spring Harbor Laboratory2026-07-03
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glmmDMR reveals replicate-level methylation variance as a major determinant of false-positive DMR detection
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https://www.biorxiv.org/content/10.64898/2026.06.29.734667v1?rss=1
2026-07-03doi:10.64898/2026.06.29.734667Cold Spring Harbor Laboratory2026-07-03
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Higher-order Architecture Shapes Concerted Evolution in a Y-linked repeat array
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https://www.biorxiv.org/content/10.64898/2026.06.30.735624v1?rss=1
2026-07-03doi:10.64898/2026.06.30.735624Cold Spring Harbor Laboratory2026-07-03
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Genome-Wide Markers Predict Metribuzin Tolerance in Southern Soft Red Winter Wheat
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https://www.biorxiv.org/content/10.64898/2026.06.28.733875v1?rss=1
2026-07-03doi:10.64898/2026.06.28.733875Cold Spring Harbor Laboratory2026-07-03
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Evo 2's Perception of Single Nucleotide Substitutions in the Genes of Two Plant Model Organisms
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https://www.biorxiv.org/content/10.64898/2026.07.01.729829v1?rss=1
2026-07-03doi:10.64898/2026.07.01.729829Cold Spring Harbor Laboratory2026-07-03
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Comparative genomics reveals shared accessory regions between members of two Fusarium species complexes virulent on garden pea
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https://www.biorxiv.org/content/10.64898/2026.06.29.735274v1?rss=1
2026-07-03doi:10.64898/2026.06.29.735274Cold Spring Harbor Laboratory2026-07-03
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Ultra-accurate sequencing reveals an extreme transmission bottleneck in a deep-sea clam symbiosis
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https://www.biorxiv.org/content/10.64898/2026.06.29.735038v1?rss=1
2026-07-03doi:10.64898/2026.06.29.735038Cold Spring Harbor Laboratory2026-07-03
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From mountaintops to metacollections: using genomics to evaluate ex situ conservation collections. A case study from tropical montane cloud forest plants
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https://www.biorxiv.org/content/10.64898/2026.06.27.734930v1?rss=1
2026-07-03doi:10.64898/2026.06.27.734930Cold Spring Harbor Laboratory2026-07-03
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A chromosome-level genome assembly of the Eurasian great grey owl, Strix nebulosa lapponica (Thunberg 1798)
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https://www.biorxiv.org/content/10.64898/2026.06.29.735218v1?rss=1
2026-07-02doi:10.64898/2026.06.29.735218Cold Spring Harbor Laboratory2026-07-02
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HiFi-ST: High-Fidelity Reconstruction of Continuous Spatial Transcriptomic Expression Fields via Conditional Neural Fields
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https://www.biorxiv.org/content/10.64898/2026.06.29.735170v1?rss=1
2026-07-02doi:10.64898/2026.06.29.735170Cold Spring Harbor Laboratory2026-07-02
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Scalable multi-group nonnegative spatial factorization for spatial genomics data with cell-type heterogeneity
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https://www.biorxiv.org/content/10.64898/2026.06.29.735224v1?rss=1
2026-07-03doi:10.64898/2026.06.29.735224Cold Spring Harbor Laboratory2026-07-03
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Initiation codon context governs translation-coupled mRNA decay and coordinated expression in the human parasite Leishmania
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https://www.biorxiv.org/content/10.64898/2026.07.01.735800v1?rss=1
2026-07-02doi:10.64898/2026.07.01.735800Cold Spring Harbor Laboratory2026-07-02
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Genomic impact of the second plague pandemic on three human populations
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https://www.biorxiv.org/content/10.64898/2026.06.29.730585v1?rss=1
2026-07-02doi:10.64898/2026.06.29.730585Cold Spring Harbor Laboratory2026-07-02
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simSOMA: a cell-lineage based simulator of the somatic VAF spectrum in plants
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https://www.biorxiv.org/content/10.64898/2026.06.28.735079v1?rss=1
2026-07-01doi:10.64898/2026.06.28.735079Cold Spring Harbor Laboratory2026-07-01
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The E2F1 regulon orchestrates a proliferative emergency and vascular programming in fetal endothelial progenitors exposed to GDM: a sex-stratified systems medicine approach
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https://www.biorxiv.org/content/10.64898/2026.06.26.734910v1?rss=1
2026-07-01doi:10.64898/2026.06.26.734910Cold Spring Harbor Laboratory2026-07-01
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Unveiling the Hidden Rules: Enhancing NMD Prediction for Protein-Truncating Variants
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https://www.biorxiv.org/content/10.64898/2026.06.26.734884v1?rss=1
2026-07-01doi:10.64898/2026.06.26.734884Cold Spring Harbor Laboratory2026-07-01
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Nitrogen use efficiency in pigs is associated with transcriptomic signatures related to amino acid metabolism, immune activity, and nutrient partitioning
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https://www.biorxiv.org/content/10.64898/2026.06.26.733976v1?rss=1
2026-07-01doi:10.64898/2026.06.26.733976Cold Spring Harbor Laboratory2026-07-01
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Pericystic brain transcriptomics reveals molecular signatures of immune activation and neurovascular remodelling in viable and post-treatment porcine neurocysticercosis
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https://www.biorxiv.org/content/10.64898/2026.06.26.734379v1?rss=1
2026-07-01doi:10.64898/2026.06.26.734379Cold Spring Harbor Laboratory2026-07-01
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Fly Viral Atlas: A single-nucleus transcriptomic atlas of RNA viruses and transposable elements (TEs) in Drosophila melanogaster
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https://www.biorxiv.org/content/10.64898/2026.06.28.735102v1?rss=1
2026-07-01doi:10.64898/2026.06.28.735102Cold Spring Harbor Laboratory2026-07-01
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Evolutionary Stratification of Codon Usage Bias In Plants Arises from GC3 Composition and Translational Optimization
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https://www.biorxiv.org/content/10.64898/2026.06.26.734692v1?rss=1
11 million coding sequences. Relative synonymous codon usage, codon adaptation index, codon-anticodon mapping, effective number of codon (ENC)-GC3, GC1,2-GC3, parity rule 2 (PR2-bias), molecular economy, and machine learning approaches were used for the study. It was found that codon usage bias was strongly non-random and exhibited a clear phylogenetic structuring. The higher plants favoured A/T-ending, whereas early-diverging lineages were enriched in G/C-ending codons. Analysis of RSCU, codon adaptation index, and codon-anticodon pairing indicated that translational selection is mediated by tRNA availability, contributing sustainability to these molecular patterns. Machine-learning approaches identified a small subset of codons having outsized influence on genome-wide codon usage landscapes. Further studies revealed the presence of robust inverse relationships between the effective number of codons and GC content at synonymous third positions. Neutrality analysis revealed approximately 61% of variation was driven by mutational pressure, tempered by selective constraints. Phylogenetic reconstruction showed a progressive relaxation of codon bias from algae to angiosperms while maintaining a conserved molecular economy cost of [~] 30 ATP per codon across the lineages. The study revealed codon usage bias is lineage-specific evolutionary conserved trait governed by mutation, selection, and translational optimization.
Research HighlightsO_LILargest genome-wide study of codon usage in the plant kingdom, covering approximately 4.6 billion codons from 262 plant species that covers algae to angiosperms.
C_LIO_LIShowed non-random AT-based codon usage with lineage-specific pattern where higher GC-ending codons are found in the lower plants and AT-ending codons in the higher plants.
C_LIO_LIGC3-associated mutational pressure was the primary driver of codon usage bias, with approximately 61% of the variation explained by mutation.
C_LIO_LIGC3 showed an inverse relationship with effective number of codons (ENC), establishing the role of GC3 as major axis of evolutionary divergence.
C_LIO_LITranslational selection and codon adaptation shaped the genome-wide codon and amino acid usage.
C_LIO_LICodon anticodon co-evolution is shaped by lineage-specific optimization driven by tRNA anticodon availability
C_LIO_LIApproximately 30 ATPs/codon are required as translational energy cost, revealing strong evolutionary constraints on molecular economy.
C_LI
Author SummaryAlthough the genetic code is degenerate, synonymous codons are not used universally across the entire genome. Although codon bias is determined as one of the major determinants of translation and molecular evolution, its genome-wide evolutionary architecture across the plant kingdom still remains unresolved. Here the author presented a large and comprehensive analysis of genome-wide codon usage bias across the plant kingdom by integrating more than 4.6 billion codons from over 11 million sequences and 262 plant species. We found that codon usage bias is deeply conserved through the evolutionary stratification that tracks the plant phylogeny. The early diverging lineages algae and bryophytes preferred GC-ending codons, while higher plants preferred AT-ending codons. GC3 composition was found to play a major role towards divergence of codon usage, while mutational pressure played approximately 61% of genome-wide variation. Translational selection also added to the lineage-specific constraints. By integrating codon-anticodon mapping, codon-adaptation index, and machine-learning approaches, it was found that translational optimization is tightly regulated by tRNA availability. A small subset of codons showed disproportionate influence on the global codon usage landscape. Although there is extensive diversification in genome composition and codon preference, plants still showed a conserved energetic investment of approximately 30 ATP per codon. This indicates a strong conserved evolutionary constraint of translational economy. Collectively, the study demonstrates that codon usage bias is a property that is both evolutionarily conserved and dependent on lineage. These findings are resulted from the interplay between mutation, selection, and translational optimization. The study provides a comprehensive framework towards understanding the evolution of synonymous codon usage in plants and offers future efforts in evolutionary genomics, synthetic biology, and transgene design.
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A conserved architectural domain shapes centromere evolution in Drosophila
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https://www.biorxiv.org/content/10.64898/2026.06.30.735607v1?rss=1
2026-07-01doi:10.64898/2026.06.30.735607Cold Spring Harbor Laboratory2026-07-01