Genome Biology and Evolution最新文献_第3页

Population genetics of active transposable elements: overdispersion arises naturally from transposition-deletion-selection balance. 活跃转座因子的群体遗传学：过度分散自然产生于转座-缺失-选择平衡。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-10-01 DOI: 10.1093/gbe/evag244

Adekanmi Daniel Omole, Peter Czuppon

{"title":"Population genetics of active transposable elements: overdispersion arises naturally from transposition-deletion-selection balance.","authors":"Adekanmi Daniel Omole, Peter Czuppon","doi":"10.1093/gbe/evag244","DOIUrl":"https://doi.org/10.1093/gbe/evag244","url":null,"abstract":"Active transposable element (TE) families often show overdispersion (variance greater than the mean), which is in contrast to the predictions of classical Poisson-based models and related theories built on the same approximation. To address this gap, we develop a diploid stochastic model of TE dynamics under free recombination, based on a biparental Moran model with transposition, excision, purifying selection, and derive mean and variance dynamics of TE copy numbers at two stages of the life cycle: before and after transposition and excision. %which accounts for higher-order moments; the right-skewed, and heavy-tailed distribution of TE copy numbers. We show that overdispersion arises naturally through transposition generating positive linkage disequilibrium between TE insertion sites with the disequilibrium persisting even under free recombination. The higher the transposition rate, the stronger the resulting overdispersion. Underdispersion and Poisson-like variation are instead stage-dependent: neither is expected after transposition and excision, while both remain possible beforehand, governed by the curvature of the fitness function. We further show that maintaining positive equilibrium copy numbers, and thus sustaining overdispersion, requires the net transposition rate to remain below roughly 0.5 insertions per copy per generation, a constraint satisfied by observed natural populations to maintain genome stability. A qualitative comparison with the DPGP3 Zambian Drosophila melanogaster dataset, focusing on TE insertions in high-recombination euchromatic regions %and using 19 retained TE families across 164 strains, shows that most TE families are overdispersed and that many also exhibit the predicted right-skewness and excess-kurtosis patterns, which are predicted by our model. These results identify overdispersion as a natural outcome of active TE dynamics and provide a mechanistic framework for understanding the full distribution of TE copy numbers in highly recombining regions.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149108680","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

Signals of Natural Selection across Regions of Low Recombination in Wild Populations of the Purple Sea Urchin, Strongylocentrotus purpuratus. 紫海胆野生种群低重组区自然选择信号

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-10-01 DOI: 10.1093/gbe/evag232

Csenge Petak, Daniel E Sadler, Melissa H Pespeni, Joaquin C B Nunez

{"title":"Signals of Natural Selection across Regions of Low Recombination in Wild Populations of the Purple Sea Urchin, Strongylocentrotus purpuratus.","authors":"Csenge Petak, Daniel E Sadler, Melissa H Pespeni, Joaquin C B Nunez","doi":"10.1093/gbe/evag232","DOIUrl":"10.1093/gbe/evag232","url":null,"abstract":"Structural variants (SVs) are increasingly recognized as important components of genetic architecture. Yet our understanding of the evolutionary forces maintaining SVs in natural populations is limited. Chromosomal inversions in particular can facilitate local adaptation in populations with high gene flow, including many marine species. The purple sea urchin (Strongylocentrotus purpuratus) is a powerful system to study these dynamics due to its high gene flow, lack of population structure, and broad latitudinal range. We analyzed whole genome sequence data from 137 individuals sampled across seven populations to identify regions of low recombination using scans for elevated linkage disequilibrium and genetic differentiation. Such regions may arise from structural variants, including chromosomal inversions. We identified nine regions showing signatures of reduced recombination, including three way genotype clustering, long range linkage, and hanging bridge patterns frequently associated with inversion polymorphisms. The regions were polymorphic within locations and along the species range with three loci showing concordant signatures of balancing and spatially heterogeneous selection based on enrichment of outliers and distinct patterns of allelic age. Additionally, these loci showed enrichment for genes associated with biomineralization and development. Our results provide the first evidence for regions of low recombination in the purple sea urchin genome, several of which display genomic signatures consistent with structural variants such as chromosomal inversions. These findings add to growing evidence that regions of reduced recombination constitute an important component of standing genetic variation in natural populations and may play a key role in adaptation to heterogeneous environments.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13646828/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148944573","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

Evolutionary Consequences of Repeated Loss of Distyly in Linum. 羊草中菊科植物重复丧失的进化后果。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-10-01 DOI: 10.1093/gbe/evag234

Zoé Postel, Panagiotis-Ioannis Zervakis, Marco Fracassetti, Aleksandra Losvik, Matias Wanntorp, Lucile Soler, Allison Churcher, Aelys M Humphreys, Tanja Slotte

{"title":"Evolutionary Consequences of Repeated Loss of Distyly in Linum.","authors":"Zoé Postel, Panagiotis-Ioannis Zervakis, Marco Fracassetti, Aleksandra Losvik, Matias Wanntorp, Lucile Soler, Allison Churcher, Aelys M Humphreys, Tanja Slotte","doi":"10.1093/gbe/evag234","DOIUrl":"10.1093/gbe/evag234","url":null,"abstract":"The breakdown of distyly, a polymorphism that promotes disassortative pollination between two floral morphs, is often assumed to increase self-fertilization, reducing the efficacy of selection and challenging long-term species persistence. We tested whether repeated losses of distyly in Linum were associated with genomic signatures of selfing by 1) testing for relaxed selective pressure in homostylous relative to distylous lineages, and 2) by characterizing population genomic patterns of the homostylous Linum leonii in comparison to its distylous close relative Linum perenne. We generated whole-genome sequences and target-capture data from sixteen Linum species, and additionally built a high-quality genome assembly and acquired population-level whole-genome sequencing data for L. leonii (n = 20). We reconstructed plastome phylogenies, estimated selective pressure for chloroplast and nuclear genes, inferred ancestral floral morph states, and tested for signatures of selfing in homostylous lineages. Compared to theoretical expectations, results were mixed, with partial identification of relaxed selective pressure in homostyles. Population genomic analyses of L. leonii revealed a moderate selfing rate of 0.32, suggesting that loss of distyly was associated with mixed mating rather than selfing, contrary to previous results on loss of distyly. Reduced nucleotide diversity and evidence for relaxed selection efficacy in L. leonii were instead consistent with a historical bottleneck. In Linum, the genomic consequences are more heterogeneous than generally assumed, and likely depend on species-specific evo-demographic history. This study highlights the complex evolutionary dynamics associated with the breakdown of distyly and emphasizes the need for comparative population genomic studies to clarify how such transitions shape evolutionary processes.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13669628/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149037759","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

Repeated domestication shaped the evolution of grain amaranth in Mesoamerica. 在中美洲，反复的驯化形成了粒状苋菜的进化。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-09-30 DOI: 10.1093/gbe/evag243

Roger Antonio Sulub-Tun, Akanksha Singh, Rolando Cifuentes-Velásquez, Markus G Stetter, Ivonne Sánchez-Del Pino

{"title":"Repeated domestication shaped the evolution of grain amaranth in Mesoamerica.","authors":"Roger Antonio Sulub-Tun, Akanksha Singh, Rolando Cifuentes-Velásquez, Markus G Stetter, Ivonne Sánchez-Del Pino","doi":"10.1093/gbe/evag243","DOIUrl":"https://doi.org/10.1093/gbe/evag243","url":null,"abstract":"Grain amaranths are nutritious pseudocereals that have been domesticated in the Andes and Mesoamerica. The three grain amaranth species were probably domesticated independently from Amaranthus hybridus in different geographical regions. Although the domestication process across the three grain amaranths has been partially elucidated, the history within each domesticated species remains vastly unknown. Therefore, we study the origin and domestication history of A. cruentus within Mesoamerica. We reveal a high genetic diversity and distinct histories of subgroups, using whole genome sequencing of 138 accessions belonging to A. cruentus and its closely related species (A. hypochondriacus) along with the wild relative A. hybridus mainly from the South of Mexico and Guatemala. We identified three genetic groups of A. cruentus. Amaranthus cruentus group 1, representing the center of Mexico, A. cruentus group 2 mostly from Guatemala, and A. cruentus group 3, including individuals dispersed across Mexico, but distinct from group 1. Compared to A. hybridus, A. cruentus group 3 exhibited the lowest genetic differentiation. It had the highest genetic diversity among the A. cruentus groups. We find gene flow between A. cruentus group 1 and A. hybridus indicating the ongoing interbreeding between wild and domesticated amaranth in its domestication center. Our results suggest that A. cruentus was probably first domesticated in central Mexico and secondary population in Guatemala, where this species is most widely preferred and cultivated today. Our findings help elucidate the complex history of grain amaranth in the Americas and underline the non-linear nature of domestication.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149108696","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

Identifying patterns of selection at synonymous sites in a Pseudomonas phylogeny. 鉴定假单胞菌系统发育中同义位点的选择模式。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-09-29 DOI: 10.1093/gbe/evag241

Luz Angela Alonso-Morales, Susan F Bailey, Nicolas Rodrigue, Rees Kassen

{"title":"Identifying patterns of selection at synonymous sites in a Pseudomonas phylogeny.","authors":"Luz Angela Alonso-Morales, Susan F Bailey, Nicolas Rodrigue, Rees Kassen","doi":"10.1093/gbe/evag241","DOIUrl":"https://doi.org/10.1093/gbe/evag241","url":null,"abstract":"A growing body of evidence suggests that synonymous substitutions, DNA sequence changes that do not alter the encoded amino acid and so should be selectively neutral, can be under strong selection. Yet our ability to identify putative non-neutral synonymous substitutions from comparative sequence data is limited. Here, we use Bayesian stochastic character mapping to contrast substitution rates and patterns for each position along two bacterial genes, followed by hierarchical clustering on principal components (HCPC) and consensus clustering to robustly identify synonymous sites showing signatures of selection. Specifically, we compare gtsB from Pseudomonas fluorescens, known from experimental studies to harbour synonymous mutations with strongly beneficial fitness effects, with a more conserved gene in the same operon, gtsD. We find that synonymous four-fold degenerate sites can vary from highly constrained, characterized by low rates and constrained patterns of substitution comparable to neighboring nonsynonymous second codon positions, to weakly constrained, exhibiting high rates and diverse patterns of substitution indicative of weak purifying selection characteristic of nearly neutrally evolving sites. Highly constrained sites account for 8% and 7.5% of the four-fold degenerate sites in gtsB and gtsD, respectively, and include some positions previously characterized through experiments as beneficial, suggesting they are sites that experience non-neutral selection. Patterns of codon usage, protein structure, or local sequence motifs do not explain the variation in substitution patterns between constrained and unconstrained sites. Combined, our site-specific approach suggests non-neutral synonymous mutations can occur at an appreciable frequency and may often contribute to adaptation.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149080516","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

Species-specific loss of genetic diversity and inbreeding following agricultural intensification. 农业集约化后物种特有的遗传多样性丧失和近交。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-09-24 DOI: 10.1093/gbe/evag235

Zachary J Nolen, Patrycja Jamelska, Ana Sofia Torres Lara, Niklas Wahlberg, Anna Runemark

{"title":"Species-specific loss of genetic diversity and inbreeding following agricultural intensification.","authors":"Zachary J Nolen, Patrycja Jamelska, Ana Sofia Torres Lara, Niklas Wahlberg, Anna Runemark","doi":"10.1093/gbe/evag235","DOIUrl":"https://doi.org/10.1093/gbe/evag235","url":null,"abstract":"Land-use change driven by agricultural intensification is a major contributor to insect declines globally. As a result of population decline and subdivision, species lose genetic diversity, reducing adaptive potential and increasing genetic load. We examine how genetic diversity has changed over the past century in three focal and five additional Polyommatinae butterfly species in Sweden by sequencing specimens from museum collections. Based on 59 historical and 90 contemporary genomes, we document a 6% decline in heterozygosity in the grassland specialist Cyaniris semiargus, driven by division into small, isolated populations. In contrast, generalist Polyommatus icarus and heathland specialist Plebejus argus have maintained genetic diversity and connectivity. Reduced heterozygosity in Cy. semiargus reflects increases in runs of homozygosity, increasing the homozygosity of derived mutations at missense and conserved positions. While genomic erosion is currently relatively mild, it is expected to lag demographic change. We infer that demographic decline in Cy. semiargus is considerably larger than declines in genetic diversity to date. We use simulations to demonstrate that only mild losses of genetic diversity are expected at the early stages of demographic decline, leaving populations with substantial genetic extinction debt. We detect similar reductions in genetic diversity in two of five additional species, underscoring the need for restoring habitat connectivity and gene flow to limit further genomic erosion in specialist grassland insects. This study illustrates how incorporation of genetic monitoring into conservation planning can identify where demographic decline has left populations with a genetic extinction debt even after they stabilize.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149037778","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

High levels of mitotic gene conversion are needed to effectively purge deleterious mutations in asexual organisms. 高水平的有丝分裂基因转换需要有效清除无性生物中的有害突变。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-09-08 DOI: 10.1093/gbe/evag224

Dominik Kopčak, Matthew Hartfield

{"title":"High levels of mitotic gene conversion are needed to effectively purge deleterious mutations in asexual organisms.","authors":"Dominik Kopčak, Matthew Hartfield","doi":"10.1093/gbe/evag224","DOIUrl":"https://doi.org/10.1093/gbe/evag224","url":null,"abstract":"Self-fertilisation and asexual reproduction are both hypothesised to cause long-term extinction due to inefficient selection against deleterious mutations. Self-fertilisation can counter these effects through creating homozygous genotypes and purging deleterious mutations. Although complete asexuality lacks meiotic gene exchange, mitotic gene conversion creates homozygous regions that could limit deleterious mutation accumulation in an analogous manner. We compare mutation accumulation in self-fertilising and facultative sexual populations subject to mitotic gene conversion, and quantify the efficacy of purging in the latter. We first show analytically that purging is most effective with high levels of asexuality and gene conversion, and when deleterious mutations are recessive. We further show using simulations that, when mitotic gene conversion becomes sufficiently high in obligate asexuals, there is a reduction in the mutation count and a jump in homozygosity, reflecting purging. However, this mechanism is not necessarily as efficient at purging under high self-fertilisation, and elevated rates of mitotic gene conversion seem to be needed for widespread purging compared to empirical estimates. If gene conversion rates are allowed to evolve, then elevated rates that increase mean fitness can arise, but only if there is sufficient variance in the gene conversion rate. Conversely, if gene conversion rates are already high and rates are not constrained then they will slightly decrease, reducing mean fitness.","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148911710","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

Changes in Alternative Splicing are Associated with Insecticide Response and Resistance. 选择性剪接的变化与杀虫剂反应和抗性有关。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-09-02 DOI: 10.1093/gbe/evag227

Christine A Tabuloc, Sergio Hidalgo, Curtis R Carlson, Hongtao Zhang, Frank G Zalom, Joanna C Chiu

{"title":"Changes in Alternative Splicing are Associated with Insecticide Response and Resistance.","authors":"Christine A Tabuloc, Sergio Hidalgo, Curtis R Carlson, Hongtao Zhang, Frank G Zalom, Joanna C Chiu","doi":"10.1093/gbe/evag227","DOIUrl":"10.1093/gbe/evag227","url":null,"abstract":"Alternative splicing (AS) promotes phenotypic plasticity to adverse conditions by altering the transcripts of genes directly involved in adaptation to those conditions. Whether changes in AS occur in a few select genes or at a larger scale is unclear. Insect pests are regularly exposed to xenobiotic stress from insecticide applications and thus develop resistance. Here, we used a genome-wide approach to show that the fruit pest Drosophila suzukii, resistant to multiple insecticides, exhibits aberrant splicing in many classes of genes, including those involved in general stress response and processes previously implicated in insecticide resistance, such as metabolic and cuticular pathways. Our results suggest that resistance is not simply a consequence of broad, transcriptome-wide increases in AS events. Instead, the specific classes of genes that are differentially spliced are better determinants of insecticide resistance. Furthermore, we observe that sublethal insecticide exposure promotes AS events even in the absence of substantial differential gene expression. Based on our results, we propose that genetic accommodation could have led to the development of insecticide resistance in D. suzukii, in which repeated insecticide exposure alters the regulation of environmentally induced AS events, ultimately leading to genetic assimilation. This leads to elevated AS of specific transcripts, a phenomenon normally induced by insecticide exposure, potentially becoming genetically encoded and constitutively expressed, even in the absence of insecticide exposure. In summary, this study provides insights into the role of AS in enabling insects to diversify genome function to survive acute insecticide treatment and to develop xenobiotic resistance upon prolonged exposure.","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/PMC13587830/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148918952","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

Genomic Evidence of Early-Diverging Domesticated Lineages in Norwegian Farmhouse Yeast. 挪威农家乐酵母早期分化驯化谱系的基因组证据。

IF 3.3 2区生物学

Genome Biology and Evolution Pub Date : 2026-09-02 DOI: 10.1093/gbe/evag220

Michael Dondrup, Atle Ove Martinussen, Lisa Karine Haugland, Jonas Brandenburg, Oya Inanli, Abdelhameed Elameen, David Dolan, Sushma Nagaraja Grellscheid, Snorre B Hagen, Hannes Schroeder, Tor Myking, Hans Geir Eiken

{"title":"Genomic Evidence of Early-Diverging Domesticated Lineages in Norwegian Farmhouse Yeast.","authors":"Michael Dondrup, Atle Ove Martinussen, Lisa Karine Haugland, Jonas Brandenburg, Oya Inanli, Abdelhameed Elameen, David Dolan, Sushma Nagaraja Grellscheid, Snorre B Hagen, Hannes Schroeder, Tor Myking, Hans Geir Eiken","doi":"10.1093/gbe/evag220","DOIUrl":"10.1093/gbe/evag220","url":null,"abstract":"The use of Saccharomyces cerevisiae to ferment alcoholic beverages is an ancient tradition, with genetic evidence indicating origins in Neolithic Asia, although the domestication process of the species is not fully understood. Kveik is a group of traditional yeasts used in farmhouse brewing in western Norway preserved through generations of rural brewing practice. While recent studies have highlighted the distinctiveness of kveik, its precise phylogenetic position, genetic diversity, and domestication history remain unclear. We performed whole-genome sequencing on 64 isolates from 25 traditional brewing cultures from Western Norway selected using cultural heritage criteria and generated telomere-to-telomere assemblies for selected strains. Phylogenomic and population genetic analyses reveal that kveik strains form a paraphyletic and early-diverging group with respect to other domesticated S. cerevisiae strains. Most strains exhibit low diversity among isolates from the same brewing culture, strong geographic clustering, and little evidence of gene flow or admixture. Mitochondrial genomes and Ty1 retrotransposon profiles corroborate this distinct lineage history. We further show that previously reported signals of gene flow between kveik and Asian fermentation strains are likely artifacts caused by population structure and selection. Divergence time estimates suggest that the common ancestor of beer, kveik, and other liquid-phase fermenting strains originated from ancestral populations 4,000 to 8,000 years ago. Our genomic resource sheds light on yeast evolution and domestication. Kveik likely comprises some of the oldest domesticated lineages in continuous use until today, connecting intangible cultural heritage to an early genetic origin.","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/PMC13616522/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148827596","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