Genome Biology And Evolution[JOURNAL]
Sun
200 papers
Emergence and Tandem Repeat-Mediated Elongation of a Translated De Novo Open Reading Frame in Human Oncogenic RNA Gene VPS9D1-AS1 (MYU).
Chou L, Cho ST, Lee J … +4 more , Laub D, Meyer D, Carter H, Carvunis AR
Genome Biol Evol · 2026 Jan · PMID 41527363 · Full text
New protein-coding genes can arise de novo from ancestrally noncoding regions when open reading frames (ORFs) outside existing genes are exposed to selection via pervasive translation. These ORFs are usually born short,...
New protein-coding genes can arise de novo from ancestrally noncoding regions when open reading frames (ORFs) outside existing genes are exposed to selection via pervasive translation. These ORFs are usually born short, and their elongation is considered a key step in de novo gene birth. However, mechanisms of de novo gene elongation remain understudied. Here, we reconstructed the evolutionary history of c16riboseqorf143 (orf143), one of the longest unannotated human translated ORFs. orf143 is encoded in the oncogenic long noncoding RNA (lncRNA) VPS9D1-AS1 (MYU). Evolutionary reconstruction showed that orf143 originated de novo in the common ancestor of simians through a point mutation that introduced a start codon. A subsequent stop-codon-disrupting mutation extended translation into a downstream region that, in humans, includes multiple binding sites and a tandem repeat (TR) array previously reported to mediate the oncogenicity of VPS9D1-AS1. The TR array frequently expanded in human populations. The overlaps between orf143 and the oncogenic binding sites in VPS9D1-AS1 raise the possibility that orf143 translation may be tumor-suppressive, since ribosomes may compete with oncogenic binding events via steric hindrance. In line with this possibility, we observed an enrichment of somatic mutations in the ORF regions of VPS9D1-AS1 in cancer patients and a positive association between in-ORF mutations and adenomas/adenocarcinomas. Some of these mutations induced truncation of the ORF, potentially impairing ribosome binding to VPS9D1-AS1. This study reveals stop codon disruption and TR array expansion as the mechanisms of orf143 elongation and illustrates how elongation of de novo ORFs may provide a selective advantage.
Correlated Evolutionary Rates Reveal Novel Components and Cross-Compartment Connectivity in Plant Proteostasis Systems.
Gatts TC, Rehmann EA, Lane LE … +2 more , Sloan DB, Forsythe ES
Genome Biol Evol · 2026 Jan · PMID 41518017 · Full text
Plant cells rely on an interconnected network of proteins interacting at many levels (e.g. physical enzyme complexes, gene regulatory modules, and biosynthetic pathways). Pairs of proteins that interact at any of these l...
Plant cells rely on an interconnected network of proteins interacting at many levels (e.g. physical enzyme complexes, gene regulatory modules, and biosynthetic pathways). Pairs of proteins that interact at any of these levels have been shown to exhibit phylogenetic signatures of evolutionary rate covariation (ERC), providing a basis for detecting functional interactions among proteins. Here, we perform genome-scale ERC analyses to predict a plant protein-protein interactome network. We find a clustered set of proteins that exhibit strong signatures of ERC with the plastid caseinolytic protease (Clp) and other plastid proteostasis components, thereby forming a functional module within the network. In addition to including proteins with known or predicted functions in protein import, transcription, translation, and degradation in plastids, the module also includes proteins with previously unknown molecular function, thus raising the possibility that these proteins may contribute to plastid proteostasis in novel ways. Perhaps the most surprising members of this module are a set of proteins that are not thought to localize to the plastid at all. These proteins include a mitochondrial-localized pentatricopeptide repeat (PPR) protein with genetic evidence of interaction with the mitochondrial Clp system and two nuclear-localized actin-related proteins involved in chromatin remodeling and epigenetic regulation of nuclear genes. We speculate that these non-plastid-localized proteins act as mediators of organellar crosstalk and retrograde signaling of cellular proteostasis status in plants. In summary, our results highlight the connected nature of plant proteostasis systems and point to a promising set of novel proteostasis protein candidates.
From Rigid Order to Radical Variation: Mitogenome Evolution in the Main Lineages of a Lesser-Known Animal Phylum (Gastrotricha).
Kosakyan A, Gammuto L, Cesaretti A … +7 more , Saponi F, Serra V, Petroni G, Macher JN, Wallnoefer O, Plazzi F, Todaro MA
Genome Biol Evol · 2026 Jan · PMID 41517991 · Full text
Mitochondrial genomes offer valuable insights into biological and phylogenetic processes, yet the factors shaping their architecture across metazoan lineages remain poorly understood, largely due to limited taxonomic sam...
Mitochondrial genomes offer valuable insights into biological and phylogenetic processes, yet the factors shaping their architecture across metazoan lineages remain poorly understood, largely due to limited taxonomic sampling. To address this gap, we analyzed mitochondrial genomes from 20 species spanning a broad taxonomic spectrum of the phylum Gastrotricha. Our findings, supported by phylogenetic analyses based on mitochondrial datasets, reveal two distinct evolutionary patterns: one lineage displays remarkable conservation in genome structure, while the other exhibits variability in gene content, arrangement, strand polarity, and repeat abundance. These contrasting patterns appear to be related to differences in reproductive strategies (hermaphroditism vs. parthenogenesis) and ecological habitats (marine vs. freshwater). While these associations are intriguing, further data are needed to understand the underlying processes. This study highlights the importance of broad phylum-scale mitogenomic sampling for uncovering genomic diversity and advancing our understanding of mitochondrial evolution across Metazoa.
Characterizing a Novel Symbiopectobacterium purcellii MEX Strain at the Early Stages of Establishing a Symbiotic Relationship.
Gunasekaran D, Sicard A, Almeida RPP … +1 more , Bennett GM
Genome Biol Evol · 2026 Jan · PMID 41512111 · Full text
Insects ally with microbial symbionts for a diversity of services. The range of these interactions is wide, spanning from beneficial to pathogenic and facultative to obligate. In many cases, such insect-microbial interac...
Insects ally with microbial symbionts for a diversity of services. The range of these interactions is wide, spanning from beneficial to pathogenic and facultative to obligate. In many cases, such insect-microbial interactions veer towards mutual dependency with integrated physiologies. This evolutionary outcome is relatively common in insects that depend on microbes to fill gaps in their nutritional ecologies (e.g. plant-sap feeding). However, the initiation and transition towards such dependent symbiotic interactions are difficult to observe in nature. Identifying these events can provide key insights into the origins and evolutionary processes that shape symbiotic interactions. Here, we report on a novel interaction between a leafhopper (Typhlocybinae: Empoasca mexicana) and a bacterium, Symbiopectobacterium purcellii MEX strain (S-MEX). To characterize this symbiont, we assembled and annotated its complete genome. We compared its content and structure to the genomes of other Symbiopectobacterium. The S-MEX genome is unique among members of this genus. It is the largest yet sequenced at 5.3 Mb, encoding 6,838 genes (∼25% more than other strains). S-MEX's genome has significantly expanded due to the proliferation of insertion sequences and 2,723 identifiable pseudogenes-processes generally seen as accelerators of genome reduction and emerging host dependence. S-MEX and other Symbiopectobacterium strains have a core set of 818 genes shared in >90% of strains, of which S-MEX has uniquely lost 36 genes. Taken together, we hypothesize that due to expansion of IS elements, extensive pseudogenization, and loss of genes in important free-living functions, S-MEX is in the early stages of establishing a host-dependent symbiosis.
A Chromosome-Level Genome Assembly and Resequencing Data Reveal Low DNA Methylation and Reduced Diversity in the Solitary Bee Pollinator Osmia cornuta.
Möllmann JS, Hu X, Baumgarten EA … +4 more , Hartleib A, Nowick K, Colgan TJ, Stolle E
Genome Biol Evol · 2026 Jan · PMID 41503865 · Full text
Bees provide essential pollination services that contribute to ecosystem stability, as well as the sustainability of economic crop yields. Due to concerns over global and local declines, improving our understanding of th...
Bees provide essential pollination services that contribute to ecosystem stability, as well as the sustainability of economic crop yields. Due to concerns over global and local declines, improving our understanding of these ecologically and commercially important species is crucial for determining their capacity to respond and adapt to environmental challenges. The European orchard bee (Osmia cornuta) is a solitary bee of increasing agricultural importance due to its role in the pollination of fruit crops, yet lacks genomic resources. Using cost-effective Nanopore-only long-read sequencing, we report the first genome assembly for O. cornuta, spanning 647.56 Mb across 727 contigs (N50 = 3.94 Mb) at a high level of completeness (99.88% BUSCO complete). In line with the expected number of chromosomes in this species, 16 major scaffolds were assembled to chromosome level. Also, we provisionally investigated the epigenomic architecture of O. cornuta, finding low numbers of CG dinucleotides that were either 5'-methylated or 5'-hydroxymethylated, providing additional evidence for the limited role methylation plays in gene regulation in Hymenopterans. To generate improved gene annotations, we combined transcriptomic- and orthology-based approaches, leading to the prediction of 12,144 genes and 25,964 proteins, showing exceptionally high BUSCO completeness (99.64%). Lastly, through whole-genome resequencing of a representative dataset, we provisionally find patterns of reduced nucleotide diversity and lower recombination rates within O. cornuta compared to other bee species. Collectively, our study provides a novel insight into the genome architecture of a key pollinator, providing an important resource to facilitate further genomic studies.
Myriapod Metallothioneins Conserve the Ancestral Architecture of Arthropods While Displaying Lineage-Specific Adaptations in Metal Binding.
Palacios Ò, Capdevila M, Albalat R
Genome Biol Evol · 2026 Jan · PMID 41503633 · Full text
Metallothioneins (MTs) are central to metal metabolism and contribute to organismal adaptation to variable metal bioavailability across ecosystems. Although well studied in chordates and mollusks, MTs remain poorly inves...
Metallothioneins (MTs) are central to metal metabolism and contribute to organismal adaptation to variable metal bioavailability across ecosystems. Although well studied in chordates and mollusks, MTs remain poorly investigated in many arthropod lineages, particularly within the Myriapoda subphylum. Myriapods, comprising thousands of millipede (Diplopoda) and centipede (Chilopoda) species, are especially relevant for evolutionary studies because they are the sister group to Pancrustacea (crustaceans and insects), and they are some of the earliest arthropods to colonize land. Their MTs therefore provide critical insights into the origin and evolution of arthropod MTs and into the molecular adaptations underlying the colonization of new environments. In this work, we have identified 48 putative MTs from 30 myriapod species, all classified as type 1 (MT1) and occurring in two configurations: the bidomain MT1S (S for short) or the multidomain MT1L (L for long) variants. Evolutionary analyses suggest that MT1S represents the ancestral type not only in myriapods but across Arthropoda, whereas MT1L likely arose during chilopod diversification, probably restricted to the order Glomerida. Despite shared structural features, metal-binding characterization of three myriapod MTs-GminMT1Sa, GminMT1La from Glomeridella minima, and LforMT1S from Lithobius forficatus-revealed marked functional differences. The diplopod proteins GminMT1Sa and GminMT1La displayed a Cd-thionein character, while the chilopod LforMT1S was a multipurpose protein, binding cadmium, zinc, and copper without a clear metal preference. These differences likely reflect distinct metal uptake, retention, and excretion strategies in diplopods and chilopods, associated with their ecological adaptations as peaceful decomposers and voracious predators, respectively.
The Evolution of Bees: Insights from 'Omic Studies.
Brenman-Suttner D, Zayed A
Genome Biol Evol · 2026 Jan · PMID 41486496 · Full text
Bees are important global pollinators that play a vital role in maintaining ecosystems and supporting global food production. They also exhibit a diversity of social organization, making them ideal model organisms for st...
Bees are important global pollinators that play a vital role in maintaining ecosystems and supporting global food production. They also exhibit a diversity of social organization, making them ideal model organisms for studying the evolution of sociality in animals. Recent advancements in genome sequencing have enabled researchers to address longstanding questions about the evolution of social behaviour in bees, particularly in the relatively few species that exhibit complex social structures, such as Apis. Whole genome phylogenies have enhanced our understanding of the complex evolutionary history of bees, providing a foundation for studying the evolution of specific traits, including eusociality. Recent transcriptomic and alternative splicing studies have advanced our understanding of how gene regulation and expression patterns contribute to behavioural plasticity, caste differentiation, and the emergence of social complexity. Comparative genomics across a range of bees with varying social behaviours has aided our understanding of the genomic features associated with social evolution and has shed light on its molecular underpinnings. Genomic approaches like GWAS and population genomic comparisons, combined with advanced sequencing technologies, have revolutionized the study of bee evolution, social behaviour, and environmental interactions. Pollen metabarcoding and environmental DNA (eDNA) techniques are now being used to quantify the intricate and complex interactions between bees and the plants they visit, and to identify other environmental factors, including pathogens that impact bee health. Additionally, techniques like museomics (using DNA from museum specimens) and broader genomic approaches have been instrumental in revealing how bees have been affected by anthropogenic changes. These tools offer valuable insights into population genetics, conservation biology, and the impact of environmental changes on bee populations. These advancements both provide critical insights into the molecular basis of eusociality and species adaptation and offer valuable tools for addressing the urgent challenges facing bee conservation due to anthropogenic change. By leveraging these genomic approaches, researchers can inform strategies for the preservation and sustainable management of bee populations worldwide.
Mapping the Genomic Limits of De-Extinction in the Face of Ancient DNA Degradation.
Lin J, Long X, Gao Y … +2 more , Liu W, Gilbert MTP
Genome Biol Evol · 2026 Jan · PMID 41482712 · Full text
The de-extinction of species using genome-editing approaches depends on acquiring high-quality genomic information from the extinct target. However, the degraded nature of the ancient DNA (aDNA) that is typical for most...
The de-extinction of species using genome-editing approaches depends on acquiring high-quality genomic information from the extinct target. However, the degraded nature of the ancient DNA (aDNA) that is typical for most extinct species, poses significant challenges to achieving comprehensive genome reconstruction. A systematic evaluation of the minimum sequencing effort that is required to reliably map the genome under varying DNA quality conditions to different reference genome remains lacking across different extinct species. Here, we systematically assess the impact of sequencing depth on genome coverage, heterozygosity estimation, and variant calling accuracy, when mapping both true aDNA data generated from the extinct Christmas Island rat (Rattus macleari), as well as in silico simulated modern- and ancient-like data generated from a modern relation (the brown rat, Rattus norvegicus), to the black rat (Rattus rattus) reference genomes. Our results demonstrate that even sequencing depths of 100× fail to yield stable heterozygosity estimates, and leave approximately 3.38% to 4.03% of its genome uncovered. These uncovered regions contained functionally relevant SNPs and indels, highlighting the limitations of reconstructing extinct genomes using reference sequences from extant relatives. Furthermore, simulations using computationally generated "degraded haploid and diploid" data based on the high-quality brown rat genome, revealed that false-positive SNPs primarily arise from insufficient coverage and low data quality, rather than aDNA damage (e.g. miscoding lesions, size of fragments, etc.) per se. These findings underscore the need to tailor sequencing depth standards by considering sample type, degradation level, and sequencing error profiles. This study provides a theoretical framework and methodological support for optimizing data strategies in aDNA research, and ultimately informing de-extinction efforts.
Evolutionary Balancing of Genetic Consequence and Innovation in Mammals Through Variable Number Tandem Repeats.
Pajic P, Gokcumen O
Genome Biol Evol · 2026 Jan · PMID 41437782 · Full text
Understanding genomic function has historically relied on sequence conservation across evolutionary time. However, advances in genomics have revealed that functional innovations often arise from rapidly evolving, noncons...
Understanding genomic function has historically relied on sequence conservation across evolutionary time. However, advances in genomics have revealed that functional innovations often arise from rapidly evolving, nonconserved elements that are frequently overlooked by conservation-based approaches. Among these, variable number tandem repeats (VNTRs) act as engines of both functional innovation and phenotypic consequence. VNTRs are repetitive genomic sequences whose copy numbers can vary significantly between individuals and species, influencing gene regulation, protein structure, and eventually, phenotypic diversity. Recent long-read assemblies and pangenomes now resolve VNTR loci accurately, enabling robust evolutionary reconstruction and functional associations. Here, we synthesize emerging insights into the functional and evolutionary impact of VNTRs in mammals. Specifically, we outline pressing questions on the mutational mechanisms driving VNTR evolution in humans, the selective forces maintaining their structural heterogeneity, and propose a theoretical framework for their persistence through evolutionary tradeoffs.
Sex-biased Expression of Genes and Transposable Elements in Hybrids from Drosophila mojavensis and Drosophila arizonae.
Simão MC, Oliveira DS, Nunes WVB … +4 more , Banho CA, Ferrarini MG, Carareto CMA, Vieira C
Genome Biol Evol · 2026 Jan · PMID 41430479 · Full text
Sex-biased gene expression is one of the main forces driving differences between sexes. Transposable elements (TEs) have also been shown to display sex-specific expression, mainly in the gonads. Despite this clear sexual...
Sex-biased gene expression is one of the main forces driving differences between sexes. Transposable elements (TEs) have also been shown to display sex-specific expression, mainly in the gonads. Despite this clear sexual dimorphism in the transcriptome, their contribution to postzygotic isolation remains poorly understood. Here, we tested whether the balance of gene and TE expression between ovaries and testes is disrupted in hybrids, potentially contributing to reproductive barriers. We analyzed Drosophila mojavensis and Drosophila arizonae, sibling species that produce sterile hybrids with differences in sperm motility. We found that genes and TEs exhibit testis-biased expression in both parental species and their hybrids. Hybrid sterility appears to be driven by a few deregulated genes rather than global transcriptome disruption. Our results demonstrated that seven candidate genes, including dyneins (Dhc98D, Dhc16F, Dic61B, Dhc36c, and Dnah3), an ATPase (Vha100-3), and a fatty acyl-CoA reductase (FAR), may underlie sterility, with Dic61B and FAR potentially linked to sperm immobility in H♀ari♂mwri hybrids. In addition, we found a subset of testis-biased genes under positive selection. The majority appear to evolve under relaxed purifying selection, in contrast to ovary-biased genes. We also identified that 22% of TE families in the parental genomes have different evolutionary dynamics, with some families remaining potentially active in one genome while becoming silenced or fragmented in the other. However, these TEs do not support the genome-mismatch hypothesis, as most are not sex-biased or deregulated in hybrids. Overall, our results highlight the role of sex-biased gene and TE expression in reproductive isolation.
Eukaryotic Recombinases Duplicated After Divergence From Known Asgard Archaeal RadA: Implications for the Evolution of Sex During Eukaryogenesis.
Matsuo L, Novák Vanclová AMG, Pomiankowski A … +2 more , Lane N, Dacks JB
Genome Biol Evol · 2025 Nov · PMID 41428662 · Full text
The origin of meiotic sex was a key milestone in the evolution of the eukaryotic cell. The paralogous DNA recombinases Rad51 and meiosis-specific DMC1 are nearly universal among eukaryotes and have been used previously t...
The origin of meiotic sex was a key milestone in the evolution of the eukaryotic cell. The paralogous DNA recombinases Rad51 and meiosis-specific DMC1 are nearly universal among eukaryotes and have been used previously to trace the timing and origins of the meiotic machinery. Here we perform comparative genomics and phylogenetic analyses of Rad51 and DMC1 drawn from diverse eukaryotes with RadA recombinase sequences from a broad sampling of archaeal taxa, focusing on the recently sequenced diversity of Asgard archaeal taxa. We show that even with increased and new sampling, the eukaryotic Rad51 and DMC1 proteins still resolve separately from any archaeal RadA sequences. These findings suggest that the duplication of RadA into general and meiosis-specific paralogues occurred after the divergence of the eukaryotic progenitor and did not evolve at an earlier stage. These findings raise the important question of how the evolution of meiotic sex was linked to genome size expansion and the acquisition of the mitochondrial endosymbiont in early eukaryotes.
Genomic Insights into Historical Adaptation of Three Key Fungal Plant Pathogens.
Alkemade JA, Wong ELY, Buddie AG … +2 more , Ryan MJ, Barraclough TG
Genome Biol Evol · 2025 Nov · PMID 41424404 · Full text
Fungal culture collections hold a wealth of historical isolates that could be used to study fungal evolution over the past decades, an era that coincided with agricultural industrialization. We performed population struc...
Fungal culture collections hold a wealth of historical isolates that could be used to study fungal evolution over the past decades, an era that coincided with agricultural industrialization. We performed population structure and temporal association analysis on three major fungal crop pathogens, Verticillium nonalfalfae, Fusarium culmorum, and Botrytis cinerea, collected between 1956 and 2023. Population structure analysis indicated predominantly sexual reproduction in F. culmorum and B. cinerea, whereas V. nonalfalfae was shown to be largely asexual. Single nucleotide polymorphisms (SNPs) of the recombining species F. culmorum and B. cinerea that showed major temporal changes fell within or close to coding genes, whereas time-variant SNPs in V. nonalfalfae were located within or close to transposable elements (TEs) and a Starship element. This is consistent with the hypothesis that rare-sex fungal species often rely on TE-mediated genomic diversification rather than sexual recombination. Across all three species, rapidly evolving SNPs were associated with genes encoding Major Facilitator Superfamily transporters, which are frequently implicated in fungicide resistance, and Zn2Cys6 fungal-type transcription factors, which play key roles in stress responses and pathogenesis. Our findings demonstrate the value of temporal association analysis as an untargeted approach for exploring fungal evolution since the advent of the green revolution. Applying this method across a broader range of fungal crop pathogens could provide deeper insights into their evolution and adaptation.
Speciation Genomics in the Tiger Whiptail Lizards (Aspidoscelis tigris Complex).
Barley AJ, Ho DV, Baumann P … +13 more , Wang IJ, Shaffer HB, Fisher RN, Gray LN, Krabbenhoft TJ, Espinoza RE, Escalona M, Toffelmier E, Sahasrabudhe R, Nguyen O, Fairbairn CW, Beraut E, Thomson RC
Genome Biol Evol · 2025 Nov · PMID 41424403 · Full text
The transition from small genetic to genome-scale datasets for studying biodiversity has revealed that genetic exchange through introgressive hybridization is a widespread phenomenon in nature. Despite this, a lack of hi...
The transition from small genetic to genome-scale datasets for studying biodiversity has revealed that genetic exchange through introgressive hybridization is a widespread phenomenon in nature. Despite this, a lack of high-quality reference genomes for most non-model species limits our understanding of the impact of this process for many taxonomic groups. This restricts the range of insights that genomic tools can provide for conservation biologists, who often hope to employ genomic datasets to accurately identify historically isolated lineages to protect and to predict their evolutionary fate in the face of environmental change. Tiger whiptail lizards (Aspidoscelis tigris complex) are an abundant and important ecological component of ecosystems across the southwestern United States. In this study, we assembled and annotated a chromosome-level reference genome for A. t. stejnegeri from coastal California. We then used this reference genome to reconstruct patterns of speciation and admixture within the larger species complex, finding evidence that gene flow is widespread both geographically and across the genome.
Origin and Evolution of Key Enzymes in the Anammox Pathway Revisited.
Hägglund E, Jiménez-González A, Hagström E … +3 more , Björkholm P, Guy L, Andersson SGE
Genome Biol Evol · 2026 Jan · PMID 41410107 · Full text
Anaerobic ammonium oxidizing bacteria in the class "Candidatus Brocadiia" in the Planctomycetota are the only known group of bacteria capable of producing energy by coupling the oxidation of ammonium to the reduction of...
Anaerobic ammonium oxidizing bacteria in the class "Candidatus Brocadiia" in the Planctomycetota are the only known group of bacteria capable of producing energy by coupling the oxidation of ammonium to the reduction of nitrite within a unique bacterial organelle called the anammoxosome. Due to the lack of homologs in other species, it is hypothesized that the key enzyme in this process, the hydrazine synthase complex, originated by de novo birth. We performed extensive searches for proteins that exhibited similarity in sequence and structure to the hydrazine synthase subunits and identified distantly related homologs in anaerobic bacteria from the phyla Planctomycetota and Desulfobacterota. However, key residues of importance for the enzymatic function were not conserved, rejecting the hypothesis that the identified genes represent previously unrecognized anammox bacteria. Phylogenetic analyses indicate that the anammox pathway has been assembled from genes acquired by horizontal gene transfer from a variety of anaerobic bacteria. The ancestral states of enzymes in the hydroxylamine oxidoreductase family were inferred, and transitions between reductive and oxidative forms of the enzymes were mapped onto the phylogenetic tree. Finally, it is shown that the signal sequences of key enzymes in the anammox pathway are able to transport a reporter gene into the periplasm of Escherichia coli cells. In conclusion, our findings suggest that the hydrazine synthase complex has evolved from already existing heme-binding periplasmic proteins and that the anammoxosome has an endogenous origin.
The Golden Lancehead Genome Reveals Distinct Selective Processes Acting on Venom Genes of an Island Endemic Snake.
Nachtigall PG, Mason AJ, Rokyta DR … +3 more , Gibbs HL, Grazziotin FG, Junqueira-de-Azevedo ILM
Genome Biol Evol · 2026 Jan · PMID 41388530 · Full text
High-quality genomic resources are important for accurate assessments of adaptive evolution in rapidly evolving island endemic species. The golden lancehead (Bothrops insularis) is a critically endangered venomous specie...
High-quality genomic resources are important for accurate assessments of adaptive evolution in rapidly evolving island endemic species. The golden lancehead (Bothrops insularis) is a critically endangered venomous species endemic to the Queimada Grande island located on the southeast coast of Brazil, with no reference genome available. Here, we present a high-quality near chromosome-level and well-annotated genome for the golden lancehead. A macrosyntenic analysis using genomes from other viper species revealed that microchromosomes present higher rearrangements consisting of fission and fusion events. Using our genome and genomic data from eight individuals, we conducted a survey of the genetic variation of toxin genes, which included the nucleotide diversity and copy-number variation (CNV). We also inferred a demographic history for the species in the last 100,000 years. The genetic variation analysis revealed that major components of B. insularis venom appear to be evolving largely under natural selection processes rather than genetic drift as expected for an insular species. PLA2s and CTLs are under balancing selection, whereas SVMPs and SVSPs are under positive selection. The CNV suggests recent duplication events in SVMPs and CTLs and deletion events in SVSPs and PLA2s. The demographic history indicates a stable population size over the last 10,000 years, suggesting that B. insularis is both genetically and demographically healthy. Altogether, we provide a genomic resource to better understand the differentiation of an iconic snake and evidence that selection has driven the evolution of diverse venom genes over short evolutionary timescales in an insular species.
The Chromosome-Scale Genome Assembly of the Redlip Blenny, Ophioblennius macclurei (Blenniidae).
Kulikov N, Joffroy K, Bonacolta AM … +2 more , Del Campo J, Irisarri I
Genome Biol Evol · 2026 Jan · PMID 41378738 · Full text
We present a high-quality, chromosome-scale genome assembly for the redlip blenny Ophioblennius macclurei (family Blenniidae). The assembly was generated using a combination of Oxford Nanopore long-read sequencing, Illum...
We present a high-quality, chromosome-scale genome assembly for the redlip blenny Ophioblennius macclurei (family Blenniidae). The assembly was generated using a combination of Oxford Nanopore long-read sequencing, Illumina short-read data, and Hi-C scaffolding technology. The assembled genome is 529.6 Mb in size, with a scaffold N50 of 23.7 Mb and a GC content of 43.49%. BUSCO analysis recovered 97.06% of expected genes in the scaffolded assembly and 89.2% from the annotated proteome. Automatic genome annotation identified a total of 18,927 protein-coding genes. This genome provides a valuable resource for understanding the diversity and evolutionary history of Ophioblennius and the fish family Blenniidae.
To Migrate or not to Migrate? Exploring the Genomic Basis of Partial Migratory Behavior in Bats.
Peralta DM, Jaramillo-Correa JP, Hernández-Rosales HS … +4 more , Túnez JI, Gasca-Pineda J, Medellín RA, Eguiarte LE
Genome Biol Evol · 2025 Nov · PMID 41355052 · Full text
Migration is a widespread phenomenon in animals that involves the synchronized movement of numerous individuals across habitats. While migratory traits appear to be environmentally triggered, evidence also points to a st...
Migration is a widespread phenomenon in animals that involves the synchronized movement of numerous individuals across habitats. While migratory traits appear to be environmentally triggered, evidence also points to a still poorly understood genetically regulated mechanism. The study of both the genomic architecture of migration and the degree of similarity across migrating taxa is a recurrent topic in evolutionary biology. Here, we investigated the genomic basis of migration in a flying mammal, the lesser long-nosed bat (Leptonycteris yerbabuenae), a nectar-feeding bat with a partially migratory behavior. Each year, the migrant group of females travels north from central Mexico to give birth in the Sonoran Desert, while the resident females remain and give birth in central Mexico. Using RAD-seq, we detected a demographic decline in this species during the Last Glacial Maximum and found that resident and migratory females form a single genetic cluster. Nevertheless, we identified 10 divergent genomic regions enriched with highly differentiated SNPs (FST values three or more orders of magnitude above the mean). Seven of such regions bear signatures of balancing selection and contain genes that have been identified in other migrating animals; such genes are qualitatively enriched for nervous system-related functions, potentially linked to circadian cycle, orientation, and navigation. Given that the migratory behavior is supposed to have originated recently in L. yerbabuenae (i.e., 10 to 20 Ka), we hypothesize that strong diversifying selection is operating in specific regions of the genome, while the rest is homogenized by the effect of males, which mate indistinctively with females from both groups.
Assessing the Impact of Whole Genome Duplication on Gene Expression and Regulation During Arachnid Development.
Aase-Remedios ME, Leite DJ, Janssen R … +1 more , McGregor AP
Genome Biol Evol · 2025 Nov · PMID 41351246 · Full text
Whole genome duplication (WGD) generates a new genetic material that can contribute to the evolution of developmental processes and phenotypic diversification. A WGD occurred in an ancestor of arachnopulmonates (spiders,...
Whole genome duplication (WGD) generates a new genetic material that can contribute to the evolution of developmental processes and phenotypic diversification. A WGD occurred in an ancestor of arachnopulmonates (spiders, scorpions, and their relatives), which provides an important independent comparison to WGDs in other animal lineages. After WGD, arachnopulmonates retained many duplicated copies (ohnologues) of developmental genes including clusters of homeobox genes, many of which have been inferred to have undergone subfunctionalization. However, there has been little systematic analysis of gene regulatory sequences and comparison of the expression of ohnologues versus their single-copy orthologues between arachnids. Here, we compare the regions of accessible chromatin and gene expression of ohnologues and single-copy genes during three embryonic stages between an arachnopulmonate arachnid, the spider Parasteatoda tepidariorum, and a nonarachnopulmonate arachnid, the harvestman Phalangium opilio. We found that the expression of each spider ohnologue was lower than their single-copy orthologues in the harvestman suggesting subfunctionalization. However, this was not reflected in a reduction in the number of peaks of accessible chromatin because both spider ohnologues and single-copy genes had more peaks than the orthologous harvestman genes. We also found that the number of peaks of accessible chromatin was higher in the late embryonic stage associated with activation of genes expressed later during embryogenesis in both species. Taken together, our study provides a genome-wide comparison of gene regulatory sequences and embryonic gene expression in arachnids and thus new insights into the impact of the arachnopulmonate WGD.
Ancestral Chromosome-Level Assemblies Reveal Posthybridization Genome Evolution in the New Mexico Whiptail Lizard (Aspidoscelis neomexicanus).
Ho DV, Odell A, Tormey D … +9 more , Deimler N, Patterson V, Tsuchiya D, Klabacka RL, Schnittker RR, Baumann DP, Neaves WB, Barley AJ, Baumann P
Genome Biol Evol · 2025 Nov · PMID 41346306 · Full text
Unisexual species of whiptail lizards in the genus Aspidoscelis arose by interspecific hybridization. They reproduce clonally through parthenogenesis and are thought to maintain the fixed heterozygosity that resulted fro...
Unisexual species of whiptail lizards in the genus Aspidoscelis arose by interspecific hybridization. They reproduce clonally through parthenogenesis and are thought to maintain the fixed heterozygosity that resulted from their hybrid origin by avoiding recombination between homeologous chromosomes. In the absence of chromosome-level assemblies for the sexual progenitor species, questions relating to the long-term consequences of clonal reproduction have remained largely unanswered. Here, we present chromosome-level genome assemblies for A. marmoratus and A. arizonae, the parental species of the unisexual A. neomexicanus. Using these references, we have analyzed whole-genome sequencing data from both wild and laboratory-reared A. neomexicanus individuals as well as newly generated F1 hybrids. Our analysis identified population-specific losses of heterozygosity affecting multiple syntenic chromosome pairs, demonstrating that homeologous chromosome pairing and recombination must occur at a low frequency and contribute to genome erosion in these unisexual lineages. The loss of heterozygosity patterns we observed further suggest that the genomes of unisexual lineages diverge over time more quickly than anticipated based on mutation accumulation alone. Our results establish genomic resources for Aspidoscelis and provide new insights into how genome structure can evolve in the absence of sexual reproduction.
Discovery and Evolutionary Analysis of a Novel Genus of Endogenous Pararetroviruses with Long Terminal Repeats.
Gao D, Tressel LG
Genome Biol Evol · 2025 Nov · PMID 41340553 · Full text
Despite being widespread in plants, endogenous pararetroviruses (EPRVs) are still poorly understood in barley and many other cereal crops. In this study, the barley reference genome was examined and a new EPRV was identi...
Despite being widespread in plants, endogenous pararetroviruses (EPRVs) are still poorly understood in barley and many other cereal crops. In this study, the barley reference genome was examined and a new EPRV was identified and named Hvu-EPRV. In contrast to all EPRVs identified thus far, Hvu-EPRV contains long terminal repeats (LTRs) which are similar to LTR retrotransposons. Homologous sequences of Hvu-EPRV were found in a wide range of plants, however, only those in 17 grasses belonging to the six tribes contain LTRs. The insertion times of nested LTR retrotransposons indicated that Hvu-EPRVs inserted into barley more than 2.37 million years ago, but the invasion and endogenization of Hvu-EPRV related elements in the grass family may be ancient, and horizontal transfers may have occurred between grasses. Phylogenetic analysis revealed that Hvu-EPRV and its homologs in grasses were grouped apart from all 13 reported genera of exogenous and EPRVs, thus the EPRVs in grasses represent a novel genus of the Caulimoviridae family named Idahovirus. Genome-wide comparisons of Hvu-EPRVs were conducted between the reference genome and other 84 genomes of cultivated and wild barley, three independent integration events were observed and suggested that the integrations likely occurred after the divergence between barley and its wild progenitor. This is the first time to identify EPRVs with LTRs and to detect their recent integrations, and this research provides new insights into the evolution of plant EPRVs and their invasion history in the grass family.
About
- Frequency
- Sun
- Papers found
- 200
- RSS feed
- Subscribe