Genome Biology and Evolution最新文献_第2页

Host-Parasite Interactions Revisited: Evidence of Horizontal Transfer of a Transposable Element Between a Snail and Its Parasite. 寄主-寄生虫相互作用的重新审视：蜗牛和它的寄生虫之间转座因子水平转移的证据。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-05-01 DOI: 10.1093/gbe/evag107

Toby Brann, Fernanda Souza de Oliveira, Andrés Iriarte, Anna Victoria Protasio

{"title":"Host-Parasite Interactions Revisited: Evidence of Horizontal Transfer of a Transposable Element Between a Snail and Its Parasite.","authors":"Toby Brann, Fernanda Souza de Oliveira, Andrés Iriarte, Anna Victoria Protasio","doi":"10.1093/gbe/evag107","DOIUrl":"10.1093/gbe/evag107","url":null,"abstract":"In eukaryotes, horizontal gene transfer (HGT) often involves transposable elements (TEs), host-parasite relationships, aquatic environments, or any of them combined. Horizontal transfer of transposable elements is both impactful, owing to the subsequent transposition burst, and insightful, providing information on organisms' evolutionary history. The flatworm Schistosoma mansoni is a human parasite with two free-living aquatic stages (intercalated between a definitive human host and intermediate snail host) and has a sizable TE content. We aimed to identify and characterize potential instances of HGT leveraging new genomic resources available. Using the latest chromosome-scale genome assembly and available TE sequences for the S. mansoni genome, we identify that two TEs, named Perere-3 and Sr3, are putatively horizontally transferred. We demonstrate the presence of these TEs in the genomes of Schistosoma spp. intermediate hosts, most likely explained by HGT. Perere-3/Sr3 were also found across a wide range of additional organisms not susceptible to schistosome infection, including turtles, fish, and other mollusks. We propose that the patchy distribution of Perere-3/Sr3 across the phylogenetic tree is best explained by HGT. Our synonymous substitution calculations further support HGT, as divergence between schistosome and snail TE sequences is markedly lower than that observed for conserved orthologous genes. We propose that HGT is likely linked to schistosomes' parasitic nature as several snail species sharing the elements are susceptible to infection. However, the rationale for the presence of Perere-3/Sr3 in species beyond this relationship is unknown.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"18 5","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13155389/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147856147","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

Comparative Genomics of Transisthmian Damselfishes (Abudefduf saxatilis and A. troschelii). 跨峡豆鲷（Abudefduf saxatilis和A. troschelii）的比较基因组学。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-04-30 DOI: 10.1093/gbe/evag111

Claire B Tracy, Carlos F Arias, Eirlys Tysall, Marc P Hoeppner, Owen W McMillan, Oscar Puebla, Moisés A Bernal

{"title":"Comparative Genomics of Transisthmian Damselfishes (Abudefduf saxatilis and A. troschelii).","authors":"Claire B Tracy, Carlos F Arias, Eirlys Tysall, Marc P Hoeppner, Owen W McMillan, Oscar Puebla, Moisés A Bernal","doi":"10.1093/gbe/evag111","DOIUrl":"https://doi.org/10.1093/gbe/evag111","url":null,"abstract":"The uplift of the Central American Isthmus (CAI) represents a natural laboratory for the study of allopatric speciation in marine organisms. Several geminate species pairs of both vertebrates and invertebrates formed following the uplift of the CAI, including damselfishes of the Pomacentridae family. However, to date few studies have explored the genomic differences among trainsisthmian species in the Pacific and Atlantic Oceans. In this study we present genome assemblies for the transisthmian species pair consisting of the Sergeant Major Abudefduf saxatilis (Tropical Atlantic) and the Panamic Sergeant Major Abudefduf troschelii (Tropical Eastern Pacific) derived from PacBio long-read sequencing. The new genomes are near-chromosome level, and among the highest-quality genomes currently available for coral reef fishes. We show that large structural variants distinguish the two species, including a nine-megabase inversion in linkage group (putative chromosome) six. Additionally, we show through an analysis of demographic history that alleles within the two genomes have different coalescence time distributions, which may be due to different effective population sizes, population structures, and/or selection regimes in the two oceans. Finally, we highlight gene families that were significantly expanded or contracted between A. troschelii and A. saxatilis. Some of these are related to the environmental differences between the two oceans, including gamma crystallin M (crygm), which is linked to vision, and vitellogenin (vtg), which is associated with egg provisioning. These genomes set the stage for comparative analyses of genetic structure and selection on the marine organisms that originated with the formation of the CAI.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147814141","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

Archaic introgression shapes genetic variation at loci associated with DNA virus load in modern humans. 在现代人类中，古代基因渗入形成了与DNA病毒载量相关的基因座的遗传变异。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-04-28 DOI: 10.1093/gbe/evag110

Rutvi Rajpara, Sofiia Stefaniia Polishchuk, Danat Yermakovich, Michael Dannemann

{"title":"Archaic introgression shapes genetic variation at loci associated with DNA virus load in modern humans.","authors":"Rutvi Rajpara, Sofiia Stefaniia Polishchuk, Danat Yermakovich, Michael Dannemann","doi":"10.1093/gbe/evag110","DOIUrl":"https://doi.org/10.1093/gbe/evag110","url":null,"abstract":"Archaic introgression has shaped the modern human immune system, particularly components involved in RNA virus responses. In contrast, its contribution to DNA virus defense remains poorly understood. Here, we investigate the contribution of Neandertal- and Denisovan-introgressed haplotypes to viral load of five common DNA viruses in UK Biobank samples, using genome-wide association summary statistics. We identified 18 genome-wide significant associations, predominantly involving Epstein-Barr virus (EBV) and loci within the Major Histocompatibility Complex, including a Denisovan-like haplotype tightly linked to HLA-A*11:01. Notably, the archaic alleles of these haplotypes showed a directional bias toward increased viral loads. Focusing on two chromosome 17 haplotypes associated with higher EBV load, we identified phenotypic associations with blood cell traits and disease markers, as well as functional effects on immune-relevant genes, including GSDMB, ARRB2, and ALOX15. Allele frequency analysis of one of the chromosome 17 haplotypes revealed signatures of shifting modes of selection, possibly reflecting changes in pathogen landscapes over time. Our results suggest that archaic DNA systematically contributes to DNA virus immunity in modern humans, with effects distinct from previously described RNA virus associations. These findings provide novel evolutionary and functional insights into host-virus interactions and the role of archaic admixture in antiviral defense.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147769704","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

Diversity and distribution of the subtelomeric Y' elements across Saccharomyces cerevisiae strains. 酿酒酵母亚端粒Y′元件的多样性及分布。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-04-28 DOI: 10.1093/gbe/evag108

Liébaut Dudragne, Juliana Silva Bernardes, Zhou Xu

{"title":"Diversity and distribution of the subtelomeric Y' elements across Saccharomyces cerevisiae strains.","authors":"Liébaut Dudragne, Juliana Silva Bernardes, Zhou Xu","doi":"10.1093/gbe/evag108","DOIUrl":"https://doi.org/10.1093/gbe/evag108","url":null,"abstract":"The subtelomeric regions of eukaryotic chromosomes harbor repeated elements that contribute to genomic plasticity and adaptation. In Saccharomyces cerevisiae, the Y' elements represent a major class of subtelomeric repeats, yet their diversity and evolutionary dynamics remain incompletely characterized. Here, we analyzed Y' elements across 54 S. cerevisiae strains using high-quality telomere-to-telomere genome assemblies. We detected 893 high-confidence Y' elements, which we classified into 12 major clusters, revealing a broader structural diversity than previously described, including canonical short (∼5.2 kb) and long (∼6.7 kb) elements, intermediate-size classes (mid1 and mid2), and a novel family containing CA-rich repeats. Sequence analyses showed that open reading frames (ORFs), including those encoding the putative Y'-Help1 helicase, are highly conserved within clusters, suggesting selective maintenance of functional sequences. The distribution of Y' elements varied widely across strains and chromosome extremities, with some strains lacking Y' entirely and others, such as the clinical ADI isolate, carrying up to 149 copies. Interstitial telomeric sequences (ITSs) were variably associated with Y' elements and tandem Y' repeats, potentially facilitating recombination and amplification. Analysis of telomere length data further revealed that the presence of long Y' elements, but not Y' elements from other clusters, at the subtelomere is correlated with shorter telomeres at the same chromosome end. Our results provide the most comprehensive catalog of S. cerevisiae Y' elements to date, uncovering unexpected structural and sequence diversity, and a potentially functional role in telomere length regulation.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147769729","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

Adaptive P-element insertions in a long non-coding RNA are potential emerging piRNA clusters. 长链非编码RNA中的适应性p元件插入是潜在的新piRNA簇。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-04-28 DOI: 10.1093/gbe/evag109

Savana Hadjipanteli, Natalie Copeland, Nancy Marmolejo Bustamante, Maureen Nweke, Basabdatta Adhikari, Erin S Kelleher

{"title":"Adaptive P-element insertions in a long non-coding RNA are potential emerging piRNA clusters.","authors":"Savana Hadjipanteli, Natalie Copeland, Nancy Marmolejo Bustamante, Maureen Nweke, Basabdatta Adhikari, Erin S Kelleher","doi":"10.1093/gbe/evag109","DOIUrl":"10.1093/gbe/evag109","url":null,"abstract":"Transposable elements are genetic parasites whose mobilization throughout the genome is a major source of deleterious mutations. However, some TE insertions are beneficial because they improve host fitness. Adaptive TE insertions sometimes alter the function of adjacent genes by positively and negatively impacting their expression, or by altering their encoding proteins. Alternatively, individual TE insertions can also be adaptive because they occur in piRNA clusters and lead to piRNA-mediated silencing of transposition. In a recent laboratory evolution experiment, we discovered that the long non-coding RNA CR43651 is an adaptive insertion hot spot for P-element DNA transposons in Drosophila melanogaster. The functional effects of these insertions on P-element repression and CR43651 function were unknown. In this study, we examined the effects of CR43651 insertions on P-element transcriptional regulation, piRNA biogenesis, and viability. We determined that although CR43651 is not a canonical piRNA cluster, chromosomes containing antisense P-element insertions in CR43651 exhibit enhanced piRNA-like silencing in the stage of oogenesis when P-elements transpose, potentially explaining their adaptive benefit. We also discovered that the fitness benefit provided by P-element repression is offset by recessive viability effects of insertion chromosomes, potentially due to disrupted production of mir14, a miRNA produced from CR43651.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147769669","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

Trans-phylum single cell orthology reveals conserved ovarian cell states between sea urchin and human. 跨门单细胞形态学揭示了海胆和人类卵巢细胞状态的保守性。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-04-27 DOI: 10.1093/gbe/evag105

Daniel Li, Nathalie Oulhen, Gary M Wessel

{"title":"Trans-phylum single cell orthology reveals conserved ovarian cell states between sea urchin and human.","authors":"Daniel Li, Nathalie Oulhen, Gary M Wessel","doi":"10.1093/gbe/evag105","DOIUrl":"https://doi.org/10.1093/gbe/evag105","url":null,"abstract":"Oocytes are produced before birth in women and their abundance and quality decrease overtime until the loss of ovarian functions at menopause. In contrast, animals such as sea urchins retain stem cells that enable a continuous, high fecundity production of quality oocytes throughout their lifespan. We hypothesize that the somatic cells required for these two different adult ovarian functions are distinct. Comparing sea urchin adult ovaries with human fetal ovaries may reveal greater conservation, since they are both in a state of active oocyte production. Here, we present the first integration of the sea urchin adult ovary with the human fetal and adult ovary single cell RNA seq datasets. Using SAMap, the resulting integration demonstrates high conservation of cell states and gene expression in both the somatic cells (such as immune and muscle cells) and the germ cells of the ovary. Whereas multiple cell states change over time in the human ovary during its transition from fetal to adult stages, the sea urchin adult ovary instead represents an intermediate state that preserved most of the cell states characteristic of both the fetal and adult human ovary. Comparing reproductive strategies and ovarian function separated by 540 million years since their last common ancestor could lead to new approaches to treat human reproductive senescence. Our results highlight the potential of the sea urchin as a powerful comparative model that lacks reproductive senescence to better understand the cellular transitions underlying the aging human ovary.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147769741","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

Demographic History of Indigenous Populations in Mexico Explored Through Whole Mitogenome Analysis. 通过全有丝分裂基因组分析探索墨西哥土著人口的人口历史。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-04-24 DOI: 10.1093/gbe/evag102

Marlen Flores-Huacuja, Meradeth Snow, Jazmín Ramos-Madrigal, Cecilia Contreras-Cubas, Francisco Barajas-Olmos, Angélica González-Oliver, Elvia Mendoza-Caamal, Isabel Cicerón-Arellano, Federico Centeno-Cruz, Emilio J Córdova, Paulina Baca, Silvia Esperanza Flores-Martínez, Rocío Ortiz-López, Austin W Reynolds, Aleksandar David Kostic, José Rafael Villafan-Bernal, Carlos Galaviz-Hernández, Alejandra Guadalupe García-Zapién, Haydee Miranda-Ortíz, Blanca Patricia Lazalde-Ramos, Francisco Loeza-Becerra, Alessandra Carnevale, Héctor Rangel-Villalobos, Martha Sosa-Macías, Augusto Rojas-Martinez, Angélica Martínez-Hernández, Humberto García-Ortiz, Lorena Orozco

{"title":"Demographic History of Indigenous Populations in Mexico Explored Through Whole Mitogenome Analysis.","authors":"Marlen Flores-Huacuja, Meradeth Snow, Jazmín Ramos-Madrigal, Cecilia Contreras-Cubas, Francisco Barajas-Olmos, Angélica González-Oliver, Elvia Mendoza-Caamal, Isabel Cicerón-Arellano, Federico Centeno-Cruz, Emilio J Córdova, Paulina Baca, Silvia Esperanza Flores-Martínez, Rocío Ortiz-López, Austin W Reynolds, Aleksandar David Kostic, José Rafael Villafan-Bernal, Carlos Galaviz-Hernández, Alejandra Guadalupe García-Zapién, Haydee Miranda-Ortíz, Blanca Patricia Lazalde-Ramos, Francisco Loeza-Becerra, Alessandra Carnevale, Héctor Rangel-Villalobos, Martha Sosa-Macías, Augusto Rojas-Martinez, Angélica Martínez-Hernández, Humberto García-Ortiz, Lorena Orozco","doi":"10.1093/gbe/evag102","DOIUrl":"https://doi.org/10.1093/gbe/evag102","url":null,"abstract":"Mitochondrial DNA plays a key role in understanding the demographic history of human populations. Particularly in the Americas, nine widespread Native American specific mitochondrial lineages have been identified. Here we performed the whole mitogenome sequencing of 572 Indigenous individuals from 60 populations spanning the Mexican territory. To minimize the effects of European and African admixture, we focused on individuals with at least 90% Native American ancestry, estimated by ADMIXTURE. We identified all the five major Native American haplogroups clades, with A2 being the most prevalent (53.9%), followed by B2 (24.0%), C1 (17.6%), D1 (4.3%), and D4h3a (0.2%). We also identified 82 different subhaplogroup widespread across the country, revealing shared mtDNA haplogroups in populations from distant regions. Moreover, mitochondrial DNA variation in the Mexican Native populations is not structured by geography or linguistic affiliation, suggesting complex gene flow across regions. Demographic reconstructions based on whole mitogenomes showed an exponential increase the maternal Ne around 10 kya in all tested regions. All these findings suggest a mitochondrial genetic persistence through Mexico and possibly the Americas.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147769717","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

Examining the role of a chromosomal inversion in accumulating adaptive and barrier loci in a cold-adapted insect species. 检查染色体反转在冷适应昆虫物种中积累适应性和屏障基因座的作用。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-04-17 DOI: 10.1093/gbe/evag101

N Poikela, V Hoikkala, M G Ritchie, M Kankare

{"title":"Examining the role of a chromosomal inversion in accumulating adaptive and barrier loci in a cold-adapted insect species.","authors":"N Poikela, V Hoikkala, M G Ritchie, M Kankare","doi":"10.1093/gbe/evag101","DOIUrl":"https://doi.org/10.1093/gbe/evag101","url":null,"abstract":"Chromosomal inversions can play a crucial role in population adaptation and divergence by reducing gene flow and preserving adaptive allelic combinations between populations with different arrangements. However, demonstrating this empirically is challenging due to numerous interacting processes with similar genomic signatures affecting inversion evolution. In this study, we characterized a large (9.5Mb) polymorphic inversion in the cold-adapted and widely distributed species, Drosophila montana, using long- and short-read sequencing across several populations. The origin of this inversion predates the divergence of North American (NA) and Fennoscandian (North European) populations, suggesting it emerged in the ancestral D. montana population in the Rocky Mountains of NA. Despite the species' expansion across the northern hemisphere, this inversion has remained exclusive to the Rocky Mountains populations, where it is fixed in the southernmost high-elevation population and appears at lower frequencies in the more northern and lower-elevation populations. By independently mapping SNPs linked to climate adaptation and barriers to gene flow (barrier loci; identified through reduced migration rates), we found enrichment of both within the inversion, with barrier and adaptive regions partially overlapping. However, the inversion was not enriched for SNPs related to cold tolerance. These findings suggest that inversions may maintain associations between multiple adaptive and barrier loci, effectively coupling them, and that locally adaptive regions may act as barriers to gene flow. Our study provides empirical evidence that inversions can contribute to population adaptation and divergence by reducing gene flow, maintaining adaptive allelic combinations, and facilitating the coupling of different barriers to gene flow.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147698723","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

Cryptic diversity and impacts of domestication in the black soldier fly (Hermetia illucens) genome. 黑兵蝇（Hermetia illucens）基因组的隐多样性及其驯化影响。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-04-15 DOI: 10.1093/gbe/evag097

Tomas N Generalovic, Christoph Sandrock, Benjamin J Roberts, Joana I Meier, Martin Hauser, Ian A Warren, Miha Pipan, Richard Durbin, Chris D Jiggins

{"title":"Cryptic diversity and impacts of domestication in the black soldier fly (Hermetia illucens) genome.","authors":"Tomas N Generalovic, Christoph Sandrock, Benjamin J Roberts, Joana I Meier, Martin Hauser, Ian A Warren, Miha Pipan, Richard Durbin, Chris D Jiggins","doi":"10.1093/gbe/evag097","DOIUrl":"https://doi.org/10.1093/gbe/evag097","url":null,"abstract":"The black soldier fly (Hermetia illucens) is the main species in the developing global industry of insects as food and feed, but little is known about its natural diversity or the genetic basis of its domestication. We obtained whole genome sequences for 54 individuals from both wild and captive populations. We identified two major genetic clusters at least 3 million years divergent, revealing cryptic diversity within the species. Our study indicates that the most common populations used for commercial and academic applications are primarily derived from just one of these sampled lineages, likely originating from a wild North American progenitor. We find that captive populations show strong reductions in genetic diversity, consistent with genome-wide effects of population bottlenecks and drift associated with rearing in captivity. Some limited evidence of gene flow between divergent lineages was observed, as well as evidence of hybridisation from domesticated populations into the wild. Our study suggests that natural genetic diversity could provide important variation for industrial purposes in this novel agricultural species.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147689543","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

Comparative Genomics Provide Insight Into the Evolution of European Aphanomyces euteiches Strains. 比较基因组学提供了洞察欧洲隐菌株的进化。

IF 2.8 2区生物学

Genome Biology and Evolution Pub Date : 2026-04-01 DOI: 10.1093/gbe/evag066

Carol Kälin, Edoardo Piombo, David Manyara, Sofia Dubusc, Mukesh Dubey, Magnus Karlsson

{"title":"Comparative Genomics Provide Insight Into the Evolution of European Aphanomyces euteiches Strains.","authors":"Carol Kälin, Edoardo Piombo, David Manyara, Sofia Dubusc, Mukesh Dubey, Magnus Karlsson","doi":"10.1093/gbe/evag066","DOIUrl":"10.1093/gbe/evag066","url":null,"abstract":"Aphanomyces euteiches is an oomycete pathogen causing root rot in pea and other legumes, leading to devastating yield losses in pea production. Previously, three genetic groups of A. euteiches were identified in Europe based on simple sequence repeat markers. In this study, we determined the genome sequences of 68 European A. euteiches strains and performed a comparative genomic analysis with the aim to investigate the population genetic structure of A. euteiches, to delineate species boundaries and to identify gene families evolving under selection for gene gains or losses. Population genetic analysis based on genome-wide single nucleotide polymorphisms identified three genetic groups in Europe, where strains from Italy formed a distinct and genetically isolated group. Genealogical concordance phylogenetic species recognition analysis indicated that strains from Italy may represent a cryptic species. Aphanomyces strains differed in virulence on susceptible and partially resistant pea host genotypes, but virulence did not correlate with genetic groups. Analysis of virulence-related gene family evolution revealed a significant expansion of gene families acting in the detoxification of plant-derived secondary metabolites in plant-pathogenic Aphanomyces species. Moreover, the carbohydrate esterase family 1 (CE1) was significantly expanded in A. euteiches but not in the cryptic species represented by Italian strains. Modular structure analyses revealed exclusive presence of feruloyl esterase domains in CE1 homologs of plant-pathogenic Aphanomyces species, indicating a role in plant cell wall degradation.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13044513/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147463150","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