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Inferring the demographic history of aye-ayes (Daubentonia madagascariensis) from high-quality, whole-genome, population-level data.
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2025-01-03 DOI: 10.1093/gbe/evae281
John W Terbot Ii, Vivak Soni, Cyril J Versoza, Susanne P Pfeifer, Jeffrey D Jensen
{"title":"Inferring the demographic history of aye-ayes (Daubentonia madagascariensis) from high-quality, whole-genome, population-level data.","authors":"John W Terbot Ii, Vivak Soni, Cyril J Versoza, Susanne P Pfeifer, Jeffrey D Jensen","doi":"10.1093/gbe/evae281","DOIUrl":"https://doi.org/10.1093/gbe/evae281","url":null,"abstract":"<p><p>The nocturnal aye-aye, Daubentonia madagascariensis, is one of the most elusive lemurs on the island of Madagascar. The timing of its activity and arboreal lifestyle has generally made it difficult to obtain accurate assessments of population size using traditional census methods. Therefore, alternative estimates provided by population genetic inference are essential for yielding much needed information for conservation measures and for enabling ecological and evolutionary studies of this species. Here, we utilize genomic data from 17 individuals-including 5 newly sequenced, high-coverage genomes-to estimate this history. Essential to this estimation are recently published annotations of the aye-aye genome which allow for variation at putatively neutral genomic regions to be included in the estimation procedures, and regions subject to selective constraints, or in linkage to such sites, to be excluded owing to the biasing effects of selection on demographic inference. By comparing a variety of demographic estimation tools to develop a well-supported model of population history, we find strong support for two demes, separating northern Madagascar from the rest of the island. Additionally, we find that the aye-aye has experienced two severe reductions in population size. The first occurred rapidly, approximately 3,000 to 5,000 years ago, and likely corresponded with the arrival of humans to Madagascar. The second occurred over the past few decades and is likely related to substantial habitat loss, suggesting that the species is still undergoing population decline and remains at great risk for extinction.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142921502","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
Evolutionary and Functional Analysis of Monoamine Oxidase F (MAO F): A Novel Member of the MAO Gene Family.
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2025-01-03 DOI: 10.1093/gbe/evae280
Gianluca Merello Oyarzún, Montserrat Olivares-Costa, Lorenzo Basile, Tammy P Pástor, Pablo Mendoza-Soto, Luis Padilla-Santiago, Gonzalo A Mardones, Claudia Binda, Juan C Opazo
{"title":"Evolutionary and Functional Analysis of Monoamine Oxidase F (MAO F): A Novel Member of the MAO Gene Family.","authors":"Gianluca Merello Oyarzún, Montserrat Olivares-Costa, Lorenzo Basile, Tammy P Pástor, Pablo Mendoza-Soto, Luis Padilla-Santiago, Gonzalo A Mardones, Claudia Binda, Juan C Opazo","doi":"10.1093/gbe/evae280","DOIUrl":"https://doi.org/10.1093/gbe/evae280","url":null,"abstract":"<p><p>The monoamine oxidase (MAO) gene family encodes for enzymes that perform the oxidative deamination of monoamines, a process required to degrade norepinephrine, serotonin, dopamine, and other amines. While mammalian MAO enzymes, MAO A and MAO B, have been extensively studied, the molecular properties of the other family members are only partly uncovered. This study aims to explore the evolution of monoamine oxidases, emphasizing understanding the MAO gene repertoire among vertebrates. Our analyses show that the duplication that gave rise to MAO A and MAO B occurred in the ancestor of tetrapods, between 408 and 352 million years ago. Non-tetrapod jawed vertebrates possess the ancestral preduplicative condition of MAO A/B. Our results also identified a new family member, MAO F, in non-tetrapod jawed vertebrates. Thus, most jawed vertebrates possess a repertoire of two MAO genes, MAO A and MAO B in tetrapods and MAO A/B and MAO F in non-tetrapod jawed vertebrates, representing different MAO gene lineages. Jawless vertebrates possess the ancestral condition of a single copy gene, MAO A/B/F. Enzymatic assays conducted on the MAO recombinant enzymes of the Indo-Pacific tarpon show that both proteins, MAO A/B and MAO F, have enzymatic and molecular properties more similar to human MAO A, with the former featuring a strikingly higher activity rate when compared to all other MAO enzymes. Our analyses underscore the importance of scanning the tree of life for new gene lineages to understand phenotypic diversity and gain detailed insights into their function.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142921500","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
Bacterial growth temperature as a horizontally acquired polygenic trait.
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-12-26 DOI: 10.1093/gbe/evae277
Anne A Farrell, Camilla L Nesbø, Olga Zhaxybayeva
{"title":"Bacterial growth temperature as a horizontally acquired polygenic trait.","authors":"Anne A Farrell, Camilla L Nesbø, Olga Zhaxybayeva","doi":"10.1093/gbe/evae277","DOIUrl":"https://doi.org/10.1093/gbe/evae277","url":null,"abstract":"<p><p>Evolutionary events leading to organismal preference for a specific growth temperature, as well as genes whose products are needed for a proper function at that temperature, are poorly understood. Using 64 bacteria from phylum Thermotogota as a model system, we examined how optimal growth temperature changed throughout Thermotogota history. We inferred that Thermotogota's last common ancestor was a thermophile and that some Thermotogota evolved the mesophilic and hyperthermophilic lifestyles secondarily. By modeling gain and loss of genes throughout Thermotogota history and by reconstructing their phylogenies, we demonstrated that adaptations to lower and higher growth temperature involve both the acquisition of necessary genes and loss of unnecessary genes. Via a pangenome-wide association study, we correlated presence/absence of 68 genes with specific optimal growth temperature intervals. While some of these genes are poorly characterized, most are involved in metabolism of amino acids, nucleotides, carbohydrates, and lipids, as well as in signal transduction and regulation of transcription. Most of the 68 genes have a history of horizontal gene transfer with other bacteria and archaea that often grow at similar temperatures, suggesting that parallel acquisitions of genes likely promote independent adaptations of different Thermotogota species to specific growth temperatures.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142894002","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
CAT-PMSF improves phylogenetic modelling under maximum likelihood and resolves Tardigrada within Panarthropoda, as the sister of Arthropoda plus Onychophora.
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-12-23 DOI: 10.1093/gbe/evae273
Mattia Giacomelli, Matteo Vecchi, Roberto Guidetti, Lorena Rebecchi, Philip C J Donoghue, Jesus Lozano-Fernandez, Davide Pisani
{"title":"CAT-PMSF improves phylogenetic modelling under maximum likelihood and resolves Tardigrada within Panarthropoda, as the sister of Arthropoda plus Onychophora.","authors":"Mattia Giacomelli, Matteo Vecchi, Roberto Guidetti, Lorena Rebecchi, Philip C J Donoghue, Jesus Lozano-Fernandez, Davide Pisani","doi":"10.1093/gbe/evae273","DOIUrl":"https://doi.org/10.1093/gbe/evae273","url":null,"abstract":"<p><p>Tardigrada, the water bears, are microscopic animals with walking appendages, that are members of Ecdysozoa, the clade of moulting animals that also includes Nematoda (round worms), Nematomorpha (horsehair worms), Priapulida (penis worms), Kinorhyncha (mud dragons), Loricifera (loricated animals), Arthropoda (insects, spiders centipedes, crustaceans and their allies) and Onychophora (velvet worms). The phylogenetic relationships within Ecdysozoa are still unclear, with analyses of molecular and morphological data yielding incongruent results. Here we use CAT-posterior mean site frequencies (CAT-PMSF), a new method to export dataset-specific mixture models (CAT-Poisson and CAT-GTR) parameterized using Bayesian methods to maximum likelihood software. We developed new maximum-likelihood based model adequacy tests using parametric bootstrap and show that CAT-PMSF describes across-site compositional heterogeneity better than other across-site compositionally heterogeneous models currently implemented in maximum likelihood software. CAT-PMSF suggests that tardigrades are members of Panarthropoda, a lineage including also Arthropoda and Onychophora. Within Panarthropoda, our results favour Tardigrada sister to Onychophora plus Arthropoda (the Lobopodia hypothesis). Our results illustrate the power of CAT-PMSF to model across-site compositionally heterogeneous datasets in the maximum likelihood framework and clarify the relationships of Tardigrada and the Ecdysozoa.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142881699","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
Investigating the impact of whole genome duplication on transposable element evolution in teleost fishes.
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-12-23 DOI: 10.1093/gbe/evae272
Rittika Mallik, Dustin J Wcisel, Thomas J Near, Jeffrey A Yoder, Alex Dornburg
{"title":"Investigating the impact of whole genome duplication on transposable element evolution in teleost fishes.","authors":"Rittika Mallik, Dustin J Wcisel, Thomas J Near, Jeffrey A Yoder, Alex Dornburg","doi":"10.1093/gbe/evae272","DOIUrl":"https://doi.org/10.1093/gbe/evae272","url":null,"abstract":"<p><p>Transposable elements (TEs) can make up more than 50% of any given vertebrate's genome, with substantial variability in TE composition among lineages. TE variation is often linked to changes in gene regulation, genome size, and speciation. However, the role that genome duplication events have played in generating abrupt shifts in the composition of the mobilome over macroevolutionary timescales remains unclear. We investigated the degree to which the teleost genome duplication (TGD) shaped the diversification trajectory of the teleost mobilome. We integrate a new high coverage genome of Polypterus bichir with data from over 100 publicly available actinopterygian genomes to assess the macroevolutionary implications of genome duplication events on TE evolution in teleosts. Our results provide no evidence for a substantial shift in mobilome composition following the TGD event. Instead, the diversity of the teleost mobilome appears to have been shaped by a history of lineage specific shifts in composition that are not correlated with commonly evoked drivers of diversification such as body size, water column usage, or latitude. Collectively, these results provide additional evidence for an emerging perspective that TGD did not catalyze bursts of diversification and innovation in the actinopterygian mobilome.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142881868","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
Convergent evolution has led to the loss of claw proteins in snakes and worm lizards.
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-12-19 DOI: 10.1093/gbe/evae274
Karin Brigit Holthaus, Julia Steinbinder, Attila Placido Sachslehner, Leopold Eckhart
{"title":"Convergent evolution has led to the loss of claw proteins in snakes and worm lizards.","authors":"Karin Brigit Holthaus, Julia Steinbinder, Attila Placido Sachslehner, Leopold Eckhart","doi":"10.1093/gbe/evae274","DOIUrl":"https://doi.org/10.1093/gbe/evae274","url":null,"abstract":"<p><p>The evolution of cornified skin appendages, such as hair, feathers and claws, is closely linked to the evolution of proteins that establish the unique mechanical stability of these epithelial structures. We hypothesized that the evolution of the limbless body anatomy of the Florida worm lizard (Rhineura floridana) and the concomitant loss of claws had led to the degeneration of genes with claw-associated functions. To test this hypothesis, we investigated the evolution of three gene families implicated in epithelial cell architecture, namely type I keratins, type II keratins and genes of the epidermal differentiation complex (EDC) in R. floridana in comparison to other squamates. We report that the orthologs of mammalian hair and nail keratins have undergone pseudogenization in R. floridana. Likewise, the EDC genes tentatively named EDYM1 and EDCCs have been lost in R. floridana. The aforementioned genes are conserved in various lizards with claws, but not in snakes. Proteomic analysis of the cornified claws of the bearded dragon (Pogona vitticeps) confirmed that type I and type II hair keratin homologs, EDYM1 and EDCCs are protein components of claws in squamates. We conclude that the convergent evolution of a limbless body was associated with the convergent loss of claw keratins and differentiation genes in squamates.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142853625","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
Chromosome-level Genome Assembly and Annotation of the Arctic Moss Ptychostomum knowltonii.
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-12-10 DOI: 10.1093/gbe/evae268
Changling Ma, Xuping Zhou, Dan Huang, Li Zhang, Yifeng Yao, Yang Liu, Shanshan Dong, Tao Peng
{"title":"Chromosome-level Genome Assembly and Annotation of the Arctic Moss Ptychostomum knowltonii.","authors":"Changling Ma, Xuping Zhou, Dan Huang, Li Zhang, Yifeng Yao, Yang Liu, Shanshan Dong, Tao Peng","doi":"10.1093/gbe/evae268","DOIUrl":"https://doi.org/10.1093/gbe/evae268","url":null,"abstract":"<p><p>The polar regions host a diverse array of moss species that have evolved to thrive extreme environments. These mosses exhibit remarkable adaptations, including tolerance to freezing temperatures, desiccation, and ultraviolet radiation. Despite their ecological significance, genomic data on these organisms are still limited, impeding our understanding of their evolutionary history and adaptive mechanisms in the context of climate change. In this study, we present the first chromosome-scale genome assembly and annotation of the Arctic moss Ptychostomum knowltonii. The assembled genome is 408.8 Mb in size, anchored to 12 pseudochromosomes, with a scaffold N50 of 32.61 Mb. Repetitive elements account for 56.24% of the genome. The genome contains 28,014 protein-coding genes, with a BUSCO completeness of 96.20%. This genomic resource will enable future comparative genomic studies, enhancing our understanding of how polar mosses may respond to a warming climate and shedding light on their evolutionary trajectories in persistently extreme environments.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142806813","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
De Novo Long-Read Genome Assembly and Annotation of the Mosquito Gut-Dwelling Fungus, Smittium minutisporum. 蚊子肠栖真菌 Smittium minutisporum 的全新长读基因组组装和注释。
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-12-04 DOI: 10.1093/gbe/evae259
Anusha Prakash, Yan Wang
{"title":"De Novo Long-Read Genome Assembly and Annotation of the Mosquito Gut-Dwelling Fungus, Smittium minutisporum.","authors":"Anusha Prakash, Yan Wang","doi":"10.1093/gbe/evae259","DOIUrl":"10.1093/gbe/evae259","url":null,"abstract":"<p><p>Mosquito guts host a variety of microbes, yet fungi are often overlooked. Smittium (Harpellales, Zoopagomycota) comprises numerous species that are obligate symbionts residing in the hindgut of mosquito larvae. Despite their association with pathogen-bearing vectors, these fungal symbionts remain understudied, largely due to the lack of high-quality genome resources. This limitation has impeded a deeper understanding of their genome biology and adaptive strategies in relation to their mosquito hosts, which may hold significant epidemiological implications. To address this gap, we generated the first reference-quality genome assembly for this group of fungi, using PacBio HiFi long-reads for an axenic culture of Smittium minutisporum, originally isolated from the eastern treehole mosquito, Aedes triseriatus. The genome assembly consists of 53 contigs, spanning a total length of 32.5 Mb, and is predicted to encode 8,254 protein-coding genes, with repetitive regions constituting 25.22% of the genome. Notably, despite being highly contiguous and gap free, the Benchmarking Universal Single-Copy Ortholog analysis suggests a completeness score of 71.8%, implying unusual genome features, possibly shaped by adaptation and specialization within the mosquito gut. This high-quality genome resource will be invaluable for advancing our understanding of mosquito gut-dwelling fungi, their natural history, and their cryptic symbiosis with insect hosts.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11630075/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695472","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
Selfing Shapes Fixation of a Mutant Allele Under Flux Equilibrium. 自交形成了通量平衡下突变等位基因的固定。
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-12-04 DOI: 10.1093/gbe/evae261
Yu Xiao, Yan-Wen Lv, Zi-Yun Wang, Chao Wu, Zi-Han He, Xin-Sheng Hu
{"title":"Selfing Shapes Fixation of a Mutant Allele Under Flux Equilibrium.","authors":"Yu Xiao, Yan-Wen Lv, Zi-Yun Wang, Chao Wu, Zi-Han He, Xin-Sheng Hu","doi":"10.1093/gbe/evae261","DOIUrl":"10.1093/gbe/evae261","url":null,"abstract":"<p><p>Sexual reproduction with alternative generations in a life cycle is an important feature in eukaryotic evolution. Partial selfing can regulate the efficacy of purging deleterious alleles in the gametophyte phase and the masking effect in heterozygotes in the sporophyte phase. Here, we develop a new theory to analyze how selfing shapes fixation of a mutant allele that is expressed in the gametophyte or the sporophyte phase only or in two phases. In an infinitely large population, we analyze a critical selfing rate beyond which the mutant allele tends to be fixed under equilibrium between irreversible mutation and selection effects. The critical selfing rate varies with genes expressed in alternative phases. In a finite population with partial self-fertilization, we apply Wright's method to calculate the fixation probability of the mutant allele under flux equilibrium among irreversible mutation, selection, and drift effects and compare it with the fixation probability derived from diffusion model under equilibrium between selection and drift effects. Selfing facilitates fixation of the deleterious allele expressed in the gametophyte phase only but impedes fixation of the deleterious allele expressed in the sporophyte phase only. Selfing facilitates or impedes fixation of the deleterious allele expressed in two phases, depending upon how phase variation in selection occurs in a life cycle. The overall results help to understand the adaptive strategy that sexual reproductive plant species evolve through the joint effects of partial selfing and alternative generations in a life cycle.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142828332","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
Complex Genomic Landscape of Inversion Polymorphism in Europe's Most Destructive Forest Pest. 欧洲最具破坏性森林害虫反转多态性的复杂基因组图谱。
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-12-04 DOI: 10.1093/gbe/evae263
Anastasiia Mykhailenko, Piotr Zieliński, Aleksandra Bednarz, Fredrik Schlyter, Martin N Andersson, Bernardo Antunes, Zbigniew Borowski, Paal Krokene, Markus Melin, Julia Morales-García, Jörg Müller, Zuzanna Nowak, Martin Schebeck, Christian Stauffer, Heli Viiri, Julia Zaborowska, Wiesław Babik, Krystyna Nadachowska-Brzyska
{"title":"Complex Genomic Landscape of Inversion Polymorphism in Europe's Most Destructive Forest Pest.","authors":"Anastasiia Mykhailenko, Piotr Zieliński, Aleksandra Bednarz, Fredrik Schlyter, Martin N Andersson, Bernardo Antunes, Zbigniew Borowski, Paal Krokene, Markus Melin, Julia Morales-García, Jörg Müller, Zuzanna Nowak, Martin Schebeck, Christian Stauffer, Heli Viiri, Julia Zaborowska, Wiesław Babik, Krystyna Nadachowska-Brzyska","doi":"10.1093/gbe/evae263","DOIUrl":"10.1093/gbe/evae263","url":null,"abstract":"<p><p>In many species, polymorphic genomic inversions underlie complex phenotypic polymorphisms and facilitate local adaptation in the face of gene flow. Multiple polymorphic inversions can co-occur in a genome, but the prevalence, evolutionary significance, and limits to complexity of genomic inversion landscapes remain poorly understood. Here, we examine genome-wide genetic variation in one of Europe's most destructive forest pests, the spruce bark beetle Ips typographus, scan for polymorphic inversions, and test whether inversions are associated with key traits in this species. We analyzed 240 individuals from 18 populations across the species' European range and, using a whole-genome resequencing approach, identified 27 polymorphic inversions covering ∼28% of the genome. The inversions vary in size and in levels of intra-inversion recombination, are highly polymorphic across the species range, and often overlap, forming a complex genomic architecture. We found no support for mechanisms such as directional selection, overdominance, and associative overdominance that are often invoked to explain the presence of large inversion polymorphisms in the genome. This suggests that inversions are either neutral or maintained by the combined action of multiple evolutionary forces. We also found that inversions are enriched in odorant receptor genes encoding elements of recognition pathways for host plants, mates, and symbiotic fungi. Our results indicate that the genome of this major forest pest of growing social, political, and economic importance harbors one of the most complex inversion landscapes described to date and raise questions about the limits of intraspecific genomic architecture complexity.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142828330","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
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