Genome Biology and Evolution最新文献_第4页

Mixed Evidence that Dosage Sensitive Genes Drive Global Dosage Compensation in Flour Beetles. 混合证据表明剂量敏感基因驱动粉甲虫的全球剂量补偿。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-09-02 DOI: 10.1093/gbe/evag206

Shana H Pau, Balan Ramesh, Ryan R Bracewell, Jeffery P Demuth

{"title":"Mixed Evidence that Dosage Sensitive Genes Drive Global Dosage Compensation in Flour Beetles.","authors":"Shana H Pau, Balan Ramesh, Ryan R Bracewell, Jeffery P Demuth","doi":"10.1093/gbe/evag206","DOIUrl":"10.1093/gbe/evag206","url":null,"abstract":"Heteromorphic sex chromosomes create inherent gene dosage differences between males and females because one sex carries a single copy of the X chromosome while the other carries two. Many species have evolved mechanisms that equalize X-linked gene expression between the sexes and, in some cases, restore ancestral autosomal levels, a process known as dosage compensation. Although chromosome-wide compensation is common in male heterogametic (XY) insects, regulatory outcomes vary across taxa and sex chromosome systems, leaving the evolutionary forces shaping sex chromosome regulation unresolved. One hypothesis proposes that the extent to which genes are sensitive to changes in gene dose determines whether complete compensation evolves. We tested predictions of this insensitive sex chromosome hypothesis (ISCH) across five flour beetle species using comparative transcriptomics and genome-wide RNAi-derived measures of gene-by-gene sensitivity. Including an X-autosome fusion in Tribolium confusum allowed direct assessment of expression evolution following a transition from a diploid autosome to a hemizygous Neo-X. Across all five species, we detect complete chromosome-wide dosage compensation and balance between the sexes in somatic tissues, including the Neo-X region. Consistent with ISCH predictions, neither the ancestral Shared-X nor the Neo-X is depleted of genes that are sensitive to RNAi-based expression disruption. However, contrary to expectations, at the level of individual genes, we find little evidence that more sensitive genes exhibit reduced expression divergence. These results suggest that chromosome-wide compensation can be maintained by global regulatory mechanisms that persist through sex chromosome turnover, even when gene-by-gene constraints are weak. Understanding the molecular basis of these mechanisms remains a central challenge in sex chromosome evolution.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13547855/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148840134","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

Phylotranscriptomics Allows Distinguishing Major Gene Flow Events from Incomplete Lineage Sorting in Rapidly Diversifying Mimetic Orchids (Genus Ophrys). 系统转录组学允许在快速分化的拟兰（Ophrys属）中区分主要基因流事件和不完全谱系分选。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-09-02 DOI: 10.1093/gbe/evag202

Lucas Vandenabeele, Anaïs Gibert, Pascaline Salvado, Roselyne Buscail, Christel Llauro, Michèle Laudié, Hervé Philippe, Joris A M Bertrand

{"title":"Phylotranscriptomics Allows Distinguishing Major Gene Flow Events from Incomplete Lineage Sorting in Rapidly Diversifying Mimetic Orchids (Genus Ophrys).","authors":"Lucas Vandenabeele, Anaïs Gibert, Pascaline Salvado, Roselyne Buscail, Christel Llauro, Michèle Laudié, Hervé Philippe, Joris A M Bertrand","doi":"10.1093/gbe/evag202","DOIUrl":"10.1093/gbe/evag202","url":null,"abstract":"Ophrys orchids (or bee orchids) provide an outstanding example of a plant adaptive radiation. Over the last 5 million years, this genus has diversified into hundreds of taxa as a result of its unconventional pollination strategy, known as \"sexual swindling\". However, the rapid and substantial diversification of this genus, combined with its capacity for hybridization and large genome size, poses significant challenges in addressing its systematics. We used phylotranscriptomics as a genome complexity reduction technique to infer the phylogenetic relationships among Ophrys main lineages. More than seven thousand gene trees enabled us to determine the relative contributions of gene flow and incomplete lineage sorting (ILS) in Ophrys evolution. First, we propose a new phylogenetic hypothesis for the genus with an unprecedented resolution that largely confirms the relationships between the main Ophrys lineages, but also provides new insights within each subgenera. By combining phylogenetic network inference with introgression analyzes based on gene tree topologies and branch lengths, we then show that the numerous phylogenetic incongruences among gene tree topologies result from a pervasive background of ILS, over which stand out several well-supported, ancient and potentially adaptive gene flow events between lineages. These major gene flow events provide a new perspective on the evolution of the Ophrys genus and its pollination, questioning previous hypotheses inferred without considering its reticulate evolution, and providing a better understanding of discrepancies observed among previous phylogenetic studies of the genus.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"18 9","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13554809/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148911789","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

A Chromosome-scale Assembly for the Genome of Southern Corn Rootworm, Diabrotica Undecimpunctata. 南方玉米根虫（Diabrotica decimpunctata）基因组的染色体尺度组装。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-09-02 DOI: 10.1093/gbe/evag226

Brad S Coates, Scott M Geib, Luke R Tembrock, Ana Vélez, Monica Poelchau, Christopher Childers, Ana Childers, Amanda Cooksey, Kevin Hackett, Sheina B Sim

{"title":"A Chromosome-scale Assembly for the Genome of Southern Corn Rootworm, Diabrotica Undecimpunctata.","authors":"Brad S Coates, Scott M Geib, Luke R Tembrock, Ana Vélez, Monica Poelchau, Christopher Childers, Ana Childers, Amanda Cooksey, Kevin Hackett, Sheina B Sim","doi":"10.1093/gbe/evag226","DOIUrl":"10.1093/gbe/evag226","url":null,"abstract":"Diabrotica undecimpunctata ssp. howardi, the southern corn rootworm or eastern 12-spotted cucumber beetle, is a generalist insect herbivore that causes damage and yield loss to several crops in North America, including maize. Unresolved phylogenetic relationships within and among D. undecimpunctata subspecies are impacting current quarantine policies. We report the chromosome-level haploid genome assembly, icDiaUnde3, constructed using HiFi and Hi-C read data from a single male D. undecimpunctata collected and identified as subspecies howardi based on geographic location and morphology. The primary 1.74 Gbp assembly contains 11 chromosome-length scaffolds representing 9 autosomes, a single X chromosome, and a supernumerary (B) chromosome (scaffold N50 = 162.8 Mb and L50 = 5). Ab initio and evidence-based structural reference sequence (RefSeq) annotations predicted 18,959 protein-coding genes, in which 99.2% of the 1,367 Benchmark Universal Single-Copy Orthologs from Insecta were complete. Repeat elements occupy 1.26 Gbp (72.33%) of the icDiaUnde3 assembly, with nearly 36% predicted to be retroelements. Alignment of whole chromosomes from icDiaUnde3 with those previously assembled from Diabrotica spp. predicted 2 and 6 autosomal inversions with D. balteata and D. virgifera, respectively. The mitochondrial genome had an annotated gene order and orientation conserved among beetles. The icDiaUnde3 reference genome assembly is a vital resource for taxonomic, comparative, and functional studies to enhance sustainable crop production.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13617350/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148955876","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

Whole-Genome Sequencing Revealed Local Genetic Differences and Multi-Layered Genetic Structure in Asian Brown Bear (Ursus arctos) Populations. 全基因组测序揭示了亚洲棕熊（Ursus arctos）种群的局部遗传差异和多层遗传结构。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-09-02 DOI: 10.1093/gbe/evag214

Yu Endo, Naoki Osada, Tsutomu Mano, Alexei V Abramov, Ryuichi Masuda

{"title":"Whole-Genome Sequencing Revealed Local Genetic Differences and Multi-Layered Genetic Structure in Asian Brown Bear (Ursus arctos) Populations.","authors":"Yu Endo, Naoki Osada, Tsutomu Mano, Alexei V Abramov, Ryuichi Masuda","doi":"10.1093/gbe/evag214","DOIUrl":"10.1093/gbe/evag214","url":null,"abstract":"A multi-layered genetic structure shaped by multiple demographic events across different time periods has been well documented in some species. However, evaluating this pattern remains challenging in many wide-ranging wildlife because genome-wide datasets with broad geographic coverage are still scarce. Brown bears are genetically differentiated among regional populations, but the genomic data are still limited and the demographic events remain incompletely understood. Here, we generated whole-genome resequencing data from brown bears in Asian local populations previously reported to show significant variation and combined these data with ancient samples for population genomic analyses. Our results support previously reported demographic events, such as the early divergence of Central Asian populations. Furthermore, we found genetic differences among Asian brown bear populations, suggesting that population-specific demographic histories occurring at different times have contributed to their unique genetic characteristics. In the Central and West Asian populations, divergence times estimated from autosomal genomes differed by hundreds of thousands of years from those inferred from mitochondrial DNA and Y-chromosomal DNA haplotypes, suggesting that gene flow continued after regional dispersal. In addition, the Y-chromosomal phylogeny and ƒ4 statistics indicated genetic differentiation between the Kazakhstan and Tibetan populations, likely resulting from male-biased introgression into the Tibetan population. Finally, the Hokkaido and Etorofu (Iturup) populations retained alleles derived from hybridization with polar bears, likely due to the limited impact of post-Last Glacial Maximum population expansion. These findings indicate that the genetic variation among brown bear populations is shaped by multiple demographic events occurring at different times, resulting in a multi-layered genetic structure.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13584206/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148840076","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 First Highly Contiguous Genome Assembly for the Western Bluebird (Sialia mexicana). 西部蓝鸟（Sialia mexicana）的第一个高度连续的基因组组装。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-09-02 DOI: 10.1093/gbe/evag219

Carlos W Esperanza, Haley K Gee, Renée A Duckworth, Andrea D Schreier

{"title":"The First Highly Contiguous Genome Assembly for the Western Bluebird (Sialia mexicana).","authors":"Carlos W Esperanza, Haley K Gee, Renée A Duckworth, Andrea D Schreier","doi":"10.1093/gbe/evag219","DOIUrl":"10.1093/gbe/evag219","url":null,"abstract":"The western bluebird (Sialia mexicana) is a secondary cavity-nesting thrush that has experienced historical population declines, local extirpations, and more recent recoveries associated with nest box programs. Despite these regional successes, recent eBird estimates suggest continued range-wide declines and substantial geographic variation in population trajectories, making this species a useful system for future studies of demographic change, connectivity, and conservation genomics. However, genomic resources for western bluebirds remain limited, and no reference genome currently exists for any species in the genus Sialia. Here, we present the first high-quality de novo reference genome for S. mexicana. Using PacBio HiFi long-read sequencing from an adult female, we generated a highly contiguous, phased 1.3 Gb nuclear assembly with a contig N50 of 24.8 Mb and high BUSCO completeness of 98.3%. We annotated the nuclear genome using transcriptomic and protein evidence, identifying 16,656 protein-coding genes and 26,060 transcripts/protein isoforms. We also assembled a complete ∼16 kb mitochondrial genome from Illumina short-read data. This reference genome provides a foundational resource for future studies of population structure, genetic diversity, connectivity, demographic history, and adaptation in western bluebirds and related taxa.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13548056/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148827646","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

Comparing ARG Inference Methods Under Transmission of Reproductive Success: Tree Imbalance Matters. 比较生殖成功传递下的ARG推理方法：树木不平衡的影响。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-09-02 DOI: 10.1093/gbe/evag215

Fanny Pouyet, Ferdinand Petit, Jérémy Guez, Léo Planche, Evelyne Heyer, Bruno Toupance, Flora Jay, Frédéric Austerlitz

{"title":"Comparing ARG Inference Methods Under Transmission of Reproductive Success: Tree Imbalance Matters.","authors":"Fanny Pouyet, Ferdinand Petit, Jérémy Guez, Léo Planche, Evelyne Heyer, Bruno Toupance, Flora Jay, Frédéric Austerlitz","doi":"10.1093/gbe/evag215","DOIUrl":"10.1093/gbe/evag215","url":null,"abstract":"Inferring coalescent trees from genomic data has become a major subject in population genetics, particularly with the recent advances in tree sequence reconstruction methods. However, it remains unclear how well these methods perform for imbalanced genealogies. Such imbalances can arise from processes such as cultural transmission of reproductive success (CTRS) or positive selection. Using simulated genomic data, we benchmarked three major software packages, SINGER, Relate, and tsinfer, by comparing the imbalance of reconstructed trees by these methods with that of the true simulated trees, for three indices that quantify this imbalance. The three methods performed well under scenarios yielding balanced trees. However, their accuracy declined as imbalance increased. Performances also varied with mutation rate, recombination rate, and sample size. This study opens possibilities for applying these methods to infer CTRS or positive selection in large-scale genomic datasets, using simulation-based inference such as approximate Bayesian computation.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13548055/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148818294","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

Same Sex Chromosomes With Independent Origins in Haplochromine Cichlids. 单倍体慈鲷中具有独立起源的同性染色体。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-09-02 DOI: 10.1093/gbe/evag223

Sophie Helen Smith, Zuzana Musilova, Astrid Böhne

{"title":"Same Sex Chromosomes With Independent Origins in Haplochromine Cichlids.","authors":"Sophie Helen Smith, Zuzana Musilova, Astrid Böhne","doi":"10.1093/gbe/evag223","DOIUrl":"10.1093/gbe/evag223","url":null,"abstract":"Elucidating theories of sex chromosome evolution requires approaches that allow fine scale delimitations of sex-determining regions within a phylogenetic context. This can address whether shared sex chromosomes across related species are due to shared ancestry, or whether genetic sex-determining regions have repeatedly evolved. Haplochromine cichlids, as one of the most successful fish lineages on Earth, have been a focal study system of sex chromosome research, both because of their rapid rate of sex chromosome turnover and the repeated emergence of certain sex chromosomes across the lineage. Here, we newly describe sex chromosomes in members of the earliest branch of the modern haplochromines, the Tropheini, based on whole-genome sequencing data, using a combination of SNP- and kmers-based methods. We show that despite the repeated co-options of ancestral chromosomes LG5 and LG7 in these species, the origins of these sex chromosomes are independent. Investigation of gene functions, allele differences, and sex-biased gene expression within the discovered sex-linked regions provides no evidence that sexual antagonism has driven the repeated evolution of a region on LG5 that overlaps between four of these species. By comparing the sex-determining regions on LG5 and LG7 across haplochromines, we show that a common origin is unlikely, and that while sex chromosomes themselves may be shared between several Haplochromini, the sex-determining genes or mechanism likely differ. This study paves the way to explore newly emerging theories of sex chromosome evolution, such as the role of chromosomal fusion or recombination patterns across the genome.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13563295/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148905926","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

Weak but Repeated Patterns of Co-Introgression of Nuclear OXPHOS Genes and Mitochondrial DNA in Iberian Wall Lizards. 伊比利亚壁蜥核OXPHOS基因和线粒体DNA的弱但重复的共渗模式。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-09-02 DOI: 10.1093/gbe/evag228

Mathias Laizé, João Pedro Marques, Philippe Geniez, Gabriel Mochales-Riaño, Antigoni Kaliontzopoulou, Aline Muyle, Catarina Pinho, Pierre-André Crochet

{"title":"Weak but Repeated Patterns of Co-Introgression of Nuclear OXPHOS Genes and Mitochondrial DNA in Iberian Wall Lizards.","authors":"Mathias Laizé, João Pedro Marques, Philippe Geniez, Gabriel Mochales-Riaño, Antigoni Kaliontzopoulou, Aline Muyle, Catarina Pinho, Pierre-André Crochet","doi":"10.1093/gbe/evag228","DOIUrl":"10.1093/gbe/evag228","url":null,"abstract":"In this study, we took advantage of the previously reported instances of mitochondrial DNA (mtDNA) capture in the Podarcis Iberian group, a speciose group of Iberian wall lizards, to test the hypothesis that nuclear genes from the OXPHOS (oxidative phosphorylation) chain can co-introgress with the mitochondria as an evolutionary response to mitigate the costs of mitonuclear incompatibilities. Using dense population sampling and transcriptome data, we generated capture-sequence datasets for nuclear OXPHOS chain genes (nucOXPHOS), random nuclear loci (nucControl) and the complete mitochondrial genome. Phylogenetic analyses of nuclear and mitochondrial genes confirmed two previously identified events of mitochondrial introgression in the Podarcis Iberian group and revealed two new cases. Three of these cases have led to complete local mtDNA replacements, where the introgressed mitotypes have replaced the native ones in several populations, and involve a currently unknown and presumably extinct donor species, so-called \"ghost lineage.\" Detecting introgression from ghost lineages, whose genomes are not accessible, remains challenging. To overcome this issue, we designed or adapted several tests aimed at detecting differential signals of introgression between our nucOXPHOS and nucControl gene sets. One of these tests, based on the effects of introgression on branch lengths in phylogenetic trees, uncovered a weak but consistently significant signal of partial co-introgression of nucOXPHOS genes compared to the genomic background (represented by the nucControl gene set) in three out of four cases of mtDNA introgression.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599021/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148944611","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

Interspecies Exchange of Mobile Genetic Elements During a Plant Disease Outbreak. 植物病害爆发期间可移动遗传元素的种间交换。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-09-02 DOI: 10.1093/gbe/evag192

Daria Evseeva, Yann Pecrix, Marek Kucka, Catrin Weiler, Carolin Franzl, Markéta Vlková-Žlebková, Elena Colombi, Yingguang Frank Chan, Stéphane Poussier, Emmanuel Wicker, Honour C McCann

{"title":"Interspecies Exchange of Mobile Genetic Elements During a Plant Disease Outbreak.","authors":"Daria Evseeva, Yann Pecrix, Marek Kucka, Catrin Weiler, Carolin Franzl, Markéta Vlková-Žlebková, Elena Colombi, Yingguang Frank Chan, Stéphane Poussier, Emmanuel Wicker, Honour C McCann","doi":"10.1093/gbe/evag192","DOIUrl":"10.1093/gbe/evag192","url":null,"abstract":"Outbreak sequencing provides insight into the origin and evolutionary processes acting on emerging pathogens. Sequencing a historic multihost outbreak of Ralstonia spp. in Martinique shows the outbreak was caused by two lineages that diverged at separate times from mainland populations. One lineage (Ralstonia pseudosolanacearum I-18) was originally introduced from Asia to South America, where it became well established prior to its dissemination to Martinique, where it retains a signature of specialization on solanaceous hosts. The novel lineage first identified during the outbreak (Ralstonia solanacearum IIB-4NPB) arose from a mainland population endemic to the Americas prior to its arrival in Martinique, where host-range expansion was observed. In contrast to minor changes in secreted effector protein repertoires, the emergent R. solanacearum IIB-4NPB acquired a novel integrative and conjugative element (ICERsoRUN1145). After identifying all Ralstonia spp. ICEs and mapping their spatial and phylogenetic distribution among Ralstonia spp. sampled during the outbreak, we found closely related ICEs circulating in mainland populations of R. pseudosolanacearum, indicating likely exchange between introduced and endemic Ralstonia spp. The family of ICEs in Ralstonia (ICERs) has a conserved bipartite structure and display a striking pattern of functional specialization in each cargo gene insertion hotspot: the first hotspot is a target for metabolic gene acquisition, and the second is a target for defense element acquisition. This work provides unparalleled phylogenetic and spatial resolution of an unusual outbreak and highlights the role of horizontal transfer in shaping the ecological success of an emerging pathogen.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13540745/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148630384","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

Identification and Classification of Expressed Orphan Genes, Spurious Orphan Genes, and Conserved Genes in the Human Gut Microbiome. 人类肠道微生物组中表达孤儿基因、假孤儿基因和保守基因的鉴定和分类。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-09-02 DOI: 10.1093/gbe/evag211

Chen Chen, Nikolaos Vakirlis, Rens Holmer, Dick de Ridder, Anne Kupczok

{"title":"Identification and Classification of Expressed Orphan Genes, Spurious Orphan Genes, and Conserved Genes in the Human Gut Microbiome.","authors":"Chen Chen, Nikolaos Vakirlis, Rens Holmer, Dick de Ridder, Anne Kupczok","doi":"10.1093/gbe/evag211","DOIUrl":"10.1093/gbe/evag211","url":null,"abstract":"Orphan genes (OGs)-genes lacking detectable homologs outside a species-are widespread in microbial genomes and are thought to contribute to their adaptation and molecular innovation. However, not all predicted OGs may represent novel functional coding sequences. False positive OGs, also called spurious OGs, can arise from gene prediction errors. We reason that OGs lacking detectable expression are more likely to be spurious. To test this, we combined large-scale metatranscriptomic profiling of the human gut microbiome with machine learning to distinguish expressed OGs from spurious ones and compare them with conserved genes (CGs) found in multiple species. Using nearly 5,000 metatranscriptome libraries, we identified ∼218,000 OGs supported by expression evidence, while ∼330,000 predicted OGs lacked detectable expression and were classified as spurious. We extracted 154 features for sequence, structural, and evolutionary properties for each gene and trained XGBoost classifiers while accounting for genomic representation. The models achieved an area under the receiver operating characteristic curve (AUC) of 0.82 in distinguishing expressed OGs from spurious OGs and an AUC of 0.93 in distinguishing expressed OGs from CGs. Interpretation based on SHAP (SHapley Additive exPlanations) revealed clear biological signals. Particularly, expressed orphans were present in more genomes than spurious ones, and expressed OGs were shorter than CGs. This work improves OG discovery and suggests that expressed OGs differ systematically from CGs and spurious OGs in sequence composition, structural constraints, and evolutionary signals.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13554803/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148808346","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