Genome Biology and Evolution最新文献

Comparative transcriptomics reveals an extracellular worm Argonaute as an ancestral regulator of LTR retrotransposons. 比较转录组学揭示了细胞外蠕虫Argonaute作为LTR反转录转座子的祖先调节因子。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-05-08 DOI: 10.1093/gbe/evag117

Isaac Martinez-Ugalde, Kyriaki Neophytou, Yenetzi Villagrana-Pacheco, Adriana Orrego Durañona, Lewis Stevens, Xiaochen Du, Rowan Bancroft, Jessica L Hall, Amy B Pedersen, Mark Blaxter, Amy H Buck, Cei Abreu-Goodger

{"title":"Comparative transcriptomics reveals an extracellular worm Argonaute as an ancestral regulator of LTR retrotransposons.","authors":"Isaac Martinez-Ugalde, Kyriaki Neophytou, Yenetzi Villagrana-Pacheco, Adriana Orrego Durañona, Lewis Stevens, Xiaochen Du, Rowan Bancroft, Jessica L Hall, Amy B Pedersen, Mark Blaxter, Amy H Buck, Cei Abreu-Goodger","doi":"10.1093/gbe/evag117","DOIUrl":"https://doi.org/10.1093/gbe/evag117","url":null,"abstract":"Safeguarding the genome from non-self elements is essential for development, reproduction, and ageing. One of the major threats to genomic integrity is transposable elements (TEs), which can be post-transcriptionally silenced through small RNAs (sRNAs) and argonaute proteins. Recent work suggests TE-derived sRNAs may also act as virulence factors in host-pathogen interactions. During infection, the intestinal parasite Heligmosomoides bakeri secretes a single argonaute protein (exWAGO) and a wide variety of TE-derived sRNAs. Although exWAGO is highly expressed, conserved, and secreted by parasitic nematodes, its function and sRNA guide preference remain unclear. Using comparative transcriptomics of the sRNAs bound to exWAGO within parasites of rodents, livestock and humans, and its orthologs in C. elegans, we found that exWAGO is capable of loading sRNAs produced from all classes of TEs in addition to some protein-coding and non-coding transcripts. However, our results suggest that the ancestral endogenous function of exWAGO was likely linked to LTR retrotransposon regulation. To understand how this relates to potential extracellular functions of exWAGO we also examined the sRNAs bound to exWAGO secreted by H. bakeri in both vesicular and non-vesicular forms. Extracellular exWAGO preferentially loads sRNA guides derived from non-autonomous and fragmented LTRs, suggesting the existence of adaptable reservoirs of regulatory sRNAs with potential roles in cross-species RNA communication. Together, our results show that exWAGO is part of an evolutionarily conserved pathway for LTR retrotransposon regulation, while preferentially utilising degenerated elements as sources of secreted sRNAs.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147837134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome of facultatively parthenogenetic harvester (Opiliones) indicates frequent mitonuclear sequence transfer and novel full-length insertions. 兼性孤雌生殖稻（Opiliones）基因组显示频繁的有丝核序列转移和新的全长插入。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-05-08 DOI: 10.1093/gbe/evag113

Sarah Stellwagen, Mercedes Burns

{"title":"Genome of facultatively parthenogenetic harvester (Opiliones) indicates frequent mitonuclear sequence transfer and novel full-length insertions.","authors":"Sarah Stellwagen, Mercedes Burns","doi":"10.1093/gbe/evag113","DOIUrl":"https://doi.org/10.1093/gbe/evag113","url":null,"abstract":"Facultative parthenogenesis and intra-population mixed ploidy (where individuals with differing ploidy exist within the same area) are rare in animals. However, these unique characteristics allow opportunities to investigate the relationship between sexual modality and genome structure. We have completed a genome assembly of the Japanese harvester (\"daddy-longlegs\") Leiobunum manubriatum, a species which reproduces sexually and asexually, and with mixed diploid and tetraploid populations. We combined Oxford Nanopore's MinION long-read sequencing platform with Dovetail Hi-C scaffolding to assemble the haploid genome for the diploid race, which is approximately 336 Mbp after collapsing heterozygous sequence. The assembly's completeness was measured using BUSCOs from Arthropoda (complete: 97.7%). We also searched raw sequence reads and the draft genome for nuclear mitochondrial DNA (numt) sequences. While only one complete mitochondrial genomic transfer was found in the draft genome, there are at least 12 complete numts across 9 reads within the raw sequencing data that were collapsed during the assembly process. The genome of the L. manubriatum diploid race is a valuable resource not only for opilionid research, but also for facilitating studies investigating the evolution of their unique reproductive mode and mixed ploidy. To our knowledge, this is the first published genome of a wild-derived facultative parthenogen. Future work will leverage this resource in comparative genomics and transcriptomics of L. manubriatum to understand the connection between ploidy and sexual strategy.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147837238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Population-level variability in genome-wide repressive histone marks in a fungal wheat pathogen. 小麦真菌病原菌全基因组抑制性组蛋白标记的群体水平变异。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-05-08 DOI: 10.1093/gbe/evag118

Leen Nanchira Abraham, Ana Margarida Sampaio, Suhani Bhattacharyya, Sabina Moser Tralamazza, Daniel Croll

{"title":"Population-level variability in genome-wide repressive histone marks in a fungal wheat pathogen.","authors":"Leen Nanchira Abraham, Ana Margarida Sampaio, Suhani Bhattacharyya, Sabina Moser Tralamazza, Daniel Croll","doi":"10.1093/gbe/evag118","DOIUrl":"https://doi.org/10.1093/gbe/evag118","url":null,"abstract":"Epigenetic modifications influence the expression of phenotypic traits by modulating gene expression and responses to environmental cues. In plant pathogens, the expression of virulence-associated genes is known to be regulated by epigenetic modifications and is considered a key adaptation for pathogens. Gene expression variation within pathogen species are regulated by extensive cis-regulatory polymorphism and insertion activities of transposable elements. However, whether pathogens vary in epigenetic profiles among members of the same species remains largely unexplored. Here, we focus on the major fungal wheat pathogen Zymoseptoria tritici and establish histone methylation profiles for 45 isolates of an extensively characterized wheat field population. We analyzed the facultative heterochromatin mark H3K27me3 thought to regulate effector and gene cluster loci in the genome. H3K27m3 coverage was increased in transposable element rich regions, with newly inserted retrotransposons contributing to epigenetic variation among pathogen genotypes. Nearly 20% of all genes showed within-population variation in H3K27me3 marks, which likely contributes to the substantial within-population variation in gene expression. Effector candidate genes and members of gene clusters showed higher than average H3K27me3 variation. Our study provides among the first insights into intra-species epigenetic variation of a fungal pathogen and opens avenues to recapitulate epigenetic mechanisms of pathogen adaptation.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147837157","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Reference genome assembly of a tetraploid accession of the tuber crop Tropaeolum tuberosum. 四倍体块茎作物Tropaeolum tuberosum的参考基因组组装。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-05-06 DOI: 10.1093/gbe/evag115

Daniela Ruiz-Mateus, Ina Scheffler, María Del Pilar Márquez-Cardona, Thomas Greb, Wilson Terán, Pascal Hunziker

{"title":"Reference genome assembly of a tetraploid accession of the tuber crop Tropaeolum tuberosum.","authors":"Daniela Ruiz-Mateus, Ina Scheffler, María Del Pilar Márquez-Cardona, Thomas Greb, Wilson Terán, Pascal Hunziker","doi":"10.1093/gbe/evag115","DOIUrl":"https://doi.org/10.1093/gbe/evag115","url":null,"abstract":"Tropaeolum tuberosum is a tuber-forming crop native to the Andes, valued for its nutritional content, pest resistance and adaptation to high-altitude environments. Despite its contribution to food security and sustainable agriculture, it remains an underutilized species with scarce genomic resources, limiting genetic and functional studies. To address this gap, we generated a reference genome assembly for a European ex situ tetraploid accession of T. tuberosum using PacBio HiFi sequencing. The assembly spans 1.3 Gb in 1,805 contigs (contigs N50 = 32.2 Mb, longest contig = 60 Mb) and recovers 87% of the estimated genome size. We assessed assembly completeness and accuracy using Benchmarking Universal Single-Copy Orthologs, which detected 98.5% complete genes (21.7% single-copy, 76.8% duplicated), 0.7% fragmented, and 0.7% missing, demonstrating near-complete gene space recovery consistent with a high-quality tetraploid genome. To evaluate transferability, we resequenced a field-collected Colombian genotype of economic relevance using Oxford Nanopore technology. Read mapping showed 99.7% of primary alignments to the reference (weighted mean coverage = 16.4×, 96.1% at ≥5×), confirming broad sequence conservation between accessions and validating the suitability of the ex situ reference as an anchor for in situ germplasm. Repetitive elements accounted for 71.3% of the genome. Using ANNEVO, we annotated 56,354 high-confidence protein-coding genes, achieving 98.3% complete BUSCOs, a PSAURON score of 97.2, and 90.5% taxonomic consistency with the rosid lineage (OMArk). This high-quality reference genome establishes a foundational resource for comparative genomics, population genomics and functional analyses on T. tuberosum, supporting future breeding and conservation of this important food resource.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147837152","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Recurrent Modular Assembly Drives Independent Origins of Group II Introns Encoding LAGLIDADG Homing Endonucleases. 循环模块组装驱动编码LAGLIDADG归巢内切酶的II组内含子的独立起源。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-05-06 DOI: 10.1093/gbe/evag114

Feng Liu, Shuangle Jin, Qingbao Du

{"title":"Recurrent Modular Assembly Drives Independent Origins of Group II Introns Encoding LAGLIDADG Homing Endonucleases.","authors":"Feng Liu, Shuangle Jin, Qingbao Du","doi":"10.1093/gbe/evag114","DOIUrl":"https://doi.org/10.1093/gbe/evag114","url":null,"abstract":"Group II introns are catalytic RNAs that typically mobilize with intron-encoded reverse transcriptase/maturase (RT/M) proteins, yet a small subset encodes LAGLIDADG homing endonucleases (LHEs). The evolutionary mechanisms underlying this atypical RNA-protein association remain poorly understood. Here, we analyze 753 LHE-encoding group II introns (group II-LHE introns) from green algae, fungi, and bacteria to investigate their origins and structural diversification. Our comparative analyses reveal that these introns are distributed across four deeply divergent RNA backbone subclasses (IIA1, IIB1, IIB2, IIC) and form 13 lineage-specific intron families. Secondary-structure reconstruction reveals a conserved catalytic core together with extensive family-specific remodeling, including variable LHE insertion sites, recurrent loss of branch-point adenosine, and differential retention of exon-recognition elements. Phylogenetic incongruence between the RNA backbone and LHE phylogenies supports multiple independent acquisitions rather than descent from a single ancestral composite element. These results demonstrate that LHE modules have been repeatedly recruited onto distinct group II intron scaffolds, highlighting recurrent modular assembly as a key mechanism in the evolution of RNA-protein mobile elements. Our study provides a unified framework for understanding the origin, diversification, and modular evolution of LHE-encoding group II introns.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147837150","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evidence for Non-optimal Codon Choice in Highly Transcribed Sex-Biased Genes of Drosophila melanogaster. 黑腹果蝇高度转录性别偏倚基因非最佳密码子选择的证据。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-05-01 DOI: 10.1093/gbe/evag093

Carrie A Whittle, Cassandra G Extavour

{"title":"Evidence for Non-optimal Codon Choice in Highly Transcribed Sex-Biased Genes of Drosophila melanogaster.","authors":"Carrie A Whittle, Cassandra G Extavour","doi":"10.1093/gbe/evag093","DOIUrl":"10.1093/gbe/evag093","url":null,"abstract":"Biases in synonymous codon use occur in many unicellular and multicellular organisms. Optimal codons, defined as those most commonly used in highly transcribed genes, are thought to arise from selection for cost-efficient translation, which would favor codons with abundant matching tRNAs. Such presumed selection is described as optimal codon choice. Non-optimal codons, defined as those least commonly used in highly transcribed genes, may in principle also play important roles, but the dynamics of their use remain understudied. Here, we examine non-optimal codon use using sex-biased genes expressed in the gonads of Drosophila melanogaster as a case study. We show that genes with sex-biased expression exhibit a preference for non-optimal codon use, especially testis-biased genes. Further, we show that the use of non-optimal codons is not random. Instead, specific non-optimal codons are favored, again especially in testis-biased genes. Non-optimal codon use is positively linked to elevated disorder of the encoded proteins. Remarkably, all 18 degenerate amino acids were associated with higher disorder when encoded by the identified primary non-optimal codon, than when encoded by its sister optimal codon. We hypothesize that selection may have promoted non-optimal codon choice for a subset of favored non-optimal codons to regulate translation. We discuss the putative roles of tRNA gene copy numbers, pleiotropy, and sex-biased expression in the evolution of this level of gene regulation.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13148536/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147672557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Characterization of Hairpin Loops and Cruciforms Across 118,019 Genomes Spanning the Tree of Life. 横跨生命之树的118019个基因组的发夹环和十字形特征。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-05-01 DOI: 10.1093/gbe/evag089

Nikol Chantzi, Camille Moeckel, Candace S Y Chan, Akshatha Nayak, Guliang Wang, Ioannis Mouratidis, Dionysios Chartoumpekis, Karen M Vasquez, Ilias Georgakopoulos-Soares

{"title":"Characterization of Hairpin Loops and Cruciforms Across 118,019 Genomes Spanning the Tree of Life.","authors":"Nikol Chantzi, Camille Moeckel, Candace S Y Chan, Akshatha Nayak, Guliang Wang, Ioannis Mouratidis, Dionysios Chartoumpekis, Karen M Vasquez, Ilias Georgakopoulos-Soares","doi":"10.1093/gbe/evag089","DOIUrl":"10.1093/gbe/evag089","url":null,"abstract":"Inverted repeats (IRs) can form alternative DNA secondary structures, including hairpins and cruciforms, which have a multitude of functional roles and have been associated with genomic instability. However, their prevalence across diverse organismal genomes remains only partially understood. Here, we examine the prevalence of perfect IRs, which do not have mismatches in their arms, across 118,019 complete organismal genomes. Our comprehensive analysis across taxonomic subdivisions reveals significant differences in the distribution, frequency, and biophysical properties of perfect IRs among these genomes. We identify a total of 33,558,920 perfect IRs and show a highly variable density across different organisms, with strikingly distinct patterns observed in Viruses, Bacteria, Archaea, and Eukaryota. We report IRs with perfect arms of extreme lengths, which can extend to hundreds of thousands of base pairs. Our findings reveal that Bacteria possess the highest IR density. Additionally, this study reveals the enrichment of IRs at transcription start and end sites in prokaryotes and Viruses and underscores their potential roles in gene regulation and genome organization. Analysis of intraspecies variation shows elevated substitution burden in IR spacers and relative conservation of IR arms, particularly near transcriptional terminators. Through a comprehensive overview of the distribution and characteristics of IRs in a wide array of organisms, this largest-scale analysis to date sheds light on the functional significance of perfect IRs, their contribution to genomic instability, and their evolutionary impact across the tree of life.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147618657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Reconstructing the Network of Horizontal Gene Exchange in Bacteria to Differentiate Direct and Indirect Transfers. 重建细菌水平基因交换网络，区分直接和间接转移。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-05-01 DOI: 10.1093/gbe/evag099

Michael Sheinman, Tommaso Stentella, Paul Etheimer, Florian Massip, Peter F Arndt

{"title":"Reconstructing the Network of Horizontal Gene Exchange in Bacteria to Differentiate Direct and Indirect Transfers.","authors":"Michael Sheinman, Tommaso Stentella, Paul Etheimer, Florian Massip, Peter F Arndt","doi":"10.1093/gbe/evag099","DOIUrl":"10.1093/gbe/evag099","url":null,"abstract":"Horizontal gene transfer (HGT) plays a central role in bacterial evolution. Yet, its large-scale dynamics and underlying network structure remain poorly characterized. We present a theoretical framework that models HGT as a continuous stochastic process over a network of bacterial genera and analyze its genomic footprint via the distribution of exact sequence matches shared across taxa-the match length distribution (MLD). We show that different evolutionary regimes imprint distinct statistical signatures on the MLD: single episodic gene transfer events yield exponential distributions, while continuous sustained HGT processes lead to power-law tails. The power-law exponent is analytically linked to the topology of the transfer network, distinguishing between intra-clade transfers and hub-mediated dissemination. Empirical MLDs derived from bacterial genomes recapitulate these predicted patterns. Moreover, we find that defining a genus-specific \"transferability\" parameter that governs pairwise HGT rates, and incorporating a high-transferability hub, accurately reproduces the observed data. Our approach provides a general framework for inferring hidden structure in genomic horizontal transfer processes, enabling quantitative analysis of microbial evolution.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13148533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147716558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Use of dN/dS Ratios to Investigate Types of Selection in Related Sexual and Asexual Lineages. 利用dN/dS比值研究相关有性和无性谱系的选择类型。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-05-01 DOI: 10.1093/gbe/evag096

Finn L Klemp, Elvira Hörandl, Mark Maraun, Stefan Scheu, Bastian Heimburger

{"title":"The Use of dN/dS Ratios to Investigate Types of Selection in Related Sexual and Asexual Lineages.","authors":"Finn L Klemp, Elvira Hörandl, Mark Maraun, Stefan Scheu, Bastian Heimburger","doi":"10.1093/gbe/evag096","DOIUrl":"10.1093/gbe/evag096","url":null,"abstract":"With the increasing availability of whole-genome assemblies, interest in the genomic consequences of diverse reproductive modes has grown. Reduced efficiency of selection in asexually reproducing species is often cited as a major consequence and is frequently investigated using the ratio of nonsynonymous to synonymous substitutions (dN/dS). However, many studies do not give sufficient attention to the fundamental differences between nonsexual reproductive modes, which likely have substantial effects on the efficiency of selection. We reviewed studies that compared dN/dS ratios of sexual and asexual relatives across 20 taxa. Asexual reproductive modes were classified into two categories: Meiosis without interchromosomal mixis (automixis and premeiotic doubling), i.e. modified meiosis that restores ploidy without outcrossing, and apomixis, i.e. production of unreduced eggs that develop without meiosis and without interchromosomal or intrachromosomal mixis. We further included two modes of reproduction which are not sexual and not strictly asexual, but may be seen as such at first glance: Fissiparity/clonal growth, i.e. the formation of new modules/ramets by splitting of somatic tissue without meiosis or mixis, and selfing, i.e. meiosis followed by fertilization of the gametes by the same individual. Consistent with theory, fissiparous lineages generally exhibited elevated dN/dS ratios, whereas automicts and apomicts showed no consistent pattern, even among taxa with identical reproductive modes. We discuss limitations of commonly used phylogenetic analyses using maximum likelihood (PAML) branch and branch-site models, which can obscure subtle differences, and propose different avenues to assess detection of selection. We propose that the heterogeneous patterns in asexual lineages reflect lineage-specific consequences of asexuality, model limitations, and our incomplete understanding of cytological mechanisms underlying different nonsexual reproductive modes.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13134044/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147672535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genomic Analysis of Megalocytivirus Genomes Reveals Widespread Recombination. 巨细胞病毒基因组的基因组分析揭示了广泛的重组。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-05-01 DOI: 10.1093/gbe/evag095

Polly I Hannaford, Lachlan Coff, Robyn N Hall, Jeffrey Go, Nicholas J G Moody, Robert Lanfear

{"title":"Genomic Analysis of Megalocytivirus Genomes Reveals Widespread Recombination.","authors":"Polly I Hannaford, Lachlan Coff, Robyn N Hall, Jeffrey Go, Nicholas J G Moody, Robert Lanfear","doi":"10.1093/gbe/evag095","DOIUrl":"10.1093/gbe/evag095","url":null,"abstract":"Megalocytiviruses are pathogens of global significance that can lead to substantial economic losses in aquaculture. Recombination among megalocytiviruses is typically assumed to be rare, although it has been relatively understudied. Here, we uncover widespread recombination within megalocytiviruses through the detailed analyses of 63 Megalocytivirus genomes, including two that are newly sequenced and assembled. We also identify a number of genes that megalocytiviruses have likely obtained from outside the family Iridoviridae (iridovirids). These results have serious implications for the biosecurity management of megalocytiviruses, as they indicate that Megalocytivirus strains could be misclassified based on traditional approaches, which target individual loci in the genome. We use this new knowledge of recombination to estimate updated phylogenetic trees of megalocytiviruses at the family-, genus-, and species-level. These trees show strong support for the designation of two novel species within the genus Megalocytivirus and highlight the difficulty of placing highly recombinant genomes in a single phylogenetic framework. We discuss the implications of our work for disease management and the importance of genome-wide recombination detection and phylogenomic analysis in the classification and genetic characterization of viruses.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147689747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0