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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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11652729/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Exploring the Allelic Diversity of the Self-Incompatibility Gene Across Natural Populations in Petunia (Solanaceae). 探索矮牵牛(茄科)自然种群中自交不亲和基因的等位基因多样性。
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-12-04 DOI: 10.1093/gbe/evae270
Taiga Maenosono, Kazuho Isono, Takanori Kuronuma, Miho Hatai, Kaori Chimura, Ken-Ichi Kubo, Hisashi Kokubun, Julián Alejandro Greppi, Hitoshi Watanabe, Koichi Uehara, Takashi Tsuchimatsu
{"title":"Exploring the Allelic Diversity of the Self-Incompatibility Gene Across Natural Populations in Petunia (Solanaceae).","authors":"Taiga Maenosono, Kazuho Isono, Takanori Kuronuma, Miho Hatai, Kaori Chimura, Ken-Ichi Kubo, Hisashi Kokubun, Julián Alejandro Greppi, Hitoshi Watanabe, Koichi Uehara, Takashi Tsuchimatsu","doi":"10.1093/gbe/evae270","DOIUrl":"10.1093/gbe/evae270","url":null,"abstract":"<p><p>Self-incompatibility (SI) is a genetic mechanism to prevent self-fertilization and thereby promote outcrossing in hermaphroditic plant species through discrimination of self and nonself-pollen by pistils. In many SI systems, recognition between pollen and pistils is controlled by a single multiallelic locus (called the S-locus), in which multiple alleles (called S-alleles) are segregating. Because of the extreme level of polymorphism of the S-locus, identification of S-alleles has been a major issue in many SI studies for decades. Here, we report an RNA-seq-based method to explore allelic diversity of the S-locus by employing the long-read sequencing technology of the Oxford Nanopore MinION and applied it for the gametophytic SI system of Petunia (Solanaceae), in which the female determinant is a secreted ribonuclease called S-RNase that inhibits the elongation of self-pollen tubes by degrading RNA. We developed a method to identify S-alleles by the search of S-RNase sequences, using the previously reported sequences as queries, and found in total 62 types of S-RNase including 45 novel types. We validated this method through Sanger sequencing and crossing experiments, confirming the sequencing accuracy and SI phenotypes corresponding to genotypes. Then, using the obtained sequence data together with polymerase chain reaction-based genotyping in a larger sample set of 187 plants, we investigated the diversity, frequency, and the level of shared polymorphism of S-alleles across populations and species. The method and the dataset obtained in Petunia will be an important basis for further studying the evolution of S-RNase-based gametophytic SI systems in natural populations.</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/PMC11670801/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823908","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
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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11652730/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Transcriptome and Evolutionary Analysis of Pseudotrichomonas keilini, a Free-Living Anaerobic Eukaryote. 自由生活的厌氧真核生物keilini假毛滴虫的转录组和进化分析。
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-12-04 DOI: 10.1093/gbe/evae262
Hend Abu-Elmakarem, Stephen J Taerum, Celine Petitjean, Michael Kotyk, Christopher Kay, Ivan Čepička, David Bass, Gillian H Gile, Tom A Williams
{"title":"Transcriptome and Evolutionary Analysis of Pseudotrichomonas keilini, a Free-Living Anaerobic Eukaryote.","authors":"Hend Abu-Elmakarem, Stephen J Taerum, Celine Petitjean, Michael Kotyk, Christopher Kay, Ivan Čepička, David Bass, Gillian H Gile, Tom A Williams","doi":"10.1093/gbe/evae262","DOIUrl":"10.1093/gbe/evae262","url":null,"abstract":"<p><p>The early evolution of eukaryotes and their adaptations to low-oxygen environments are fascinating open questions in biology. Genome-scale data from novel eukaryotes, and particularly from free-living lineages, are the key to answering these questions. The Parabasalia are a major group of anaerobic eukaryotes that form the most speciose lineage of Metamonada. The most well-studied are parasitic parabasalids, including Trichomonas vaginalis and Tritrichomonas foetus, but very little genome-scale data are available for free-living members of the group. Here, we sequenced the transcriptome of Pseudotrichomonas keilini, a free-living parabasalian. Comparative genomic analysis indicated that P. keilini possesses a metabolism and gene complement that are in many respects similar to its parasitic relative T. vaginalis and that in the time since their most recent common ancestor, it is the T. vaginalis lineage that has experienced more genomic change, likely due to the transition to a parasitic lifestyle. Features shared between P. keilini and T. vaginalis include a hydrogenosome (anaerobic mitochondrial homolog) that we predict to function much as in T. vaginalis and a complete glycolytic pathway that is likely to represent one of the primary means by which P. keilini obtains ATP. Phylogenomic analysis indicates that P. keilini branches within a clade of endobiotic parabasalids, consistent with the hypothesis that different parabasalid lineages evolved toward parasitic or free-living lifestyles from an endobiotic, anaerobic, or microaerophilic common ancestor.</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/PMC11635102/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142828333","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
Expression of Random Sequences and de novo Evolved Genes From the Mouse in Human Cells Reveals Functional Diversity and Specificity. 小鼠随机序列和新生进化基因在人类细胞中的表达揭示了功能多样性和特异性。
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-12-04 DOI: 10.1093/gbe/evae175
Silvia Aldrovandi, Johana Fajardo Castro, Kristian Ullrich, Amir Karger, Victor Luria, Diethard Tautz
{"title":"Expression of Random Sequences and de novo Evolved Genes From the Mouse in Human Cells Reveals Functional Diversity and Specificity.","authors":"Silvia Aldrovandi, Johana Fajardo Castro, Kristian Ullrich, Amir Karger, Victor Luria, Diethard Tautz","doi":"10.1093/gbe/evae175","DOIUrl":"10.1093/gbe/evae175","url":null,"abstract":"<p><p>Proteins that emerge de novo from noncoding DNA could negatively or positively influence cellular physiology in the sense of providing a possible adaptive advantage. Here, we employ two approaches to study such effects in a human cell line by expressing random sequences and mouse de novo genes that lack homologs in the human genome. We show that both approaches lead to differential growth effects of the cell clones dependent on the sequences they express. For the random sequences, 53% of the clones decreased in frequency, and about 8% increased in frequency in a joint growth experiment. Of the 14 mouse de novo genes tested in a similar joint growth experiment, 10 decreased, and 3 increased in frequency. When individually analysed, each mouse de novo gene triggers a unique transcriptomic response in the human cells, indicating mostly specific rather than generalized effects. Structural analysis of the de novo gene open reading frames (ORFs) reveals a range of intrinsic disorder scores and/or foldability into alpha-helices or beta sheets, but these do not correlate with their effects on the growth of the cells. Our results indicate that de novo evolved ORFs could easily become integrated into cellular regulatory pathways, since most interact with components of these pathways and could therefore become directly subject to positive selection if the general conditions allow this.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"16 12","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11635099/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142812754","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
Adaptation During the Shift from Entomopathogen to Endosymbiont Is Accompanied by Gene Loss and Intensified Selection. 从昆虫病原体到内共生体的转变过程中,伴随着基因的丢失和选择的加强。
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-12-04 DOI: 10.1093/gbe/evae251
Chris M Ward, Cristobal A Onetto, Anthony R Borneman
{"title":"Adaptation During the Shift from Entomopathogen to Endosymbiont Is Accompanied by Gene Loss and Intensified Selection.","authors":"Chris M Ward, Cristobal A Onetto, Anthony R Borneman","doi":"10.1093/gbe/evae251","DOIUrl":"10.1093/gbe/evae251","url":null,"abstract":"<p><p>Fungi have been found to be associated with many insect species, with some species transitioning to reside within insects as symbionts. However, the evolutionary pressures and genomic consequences associated with this transition are not well understood. Pathogenic fungi of the genus Ophiocordyceps have undergone multiple, independent transitions from pathogen to endosymbiont lifestyles, where they reside within the fatty tissues of infected soft-scale insects transgenerationally without killing their hosts. To gain an understanding of the genomic adaptations underlying this life history shift, long-read sequencing was utilized to assemble the genomes of both the soft-scale insect Parthenolecanium corni and its Ophiocordyceps endosymbiont from a single insect. Assembly and metagenomic-based binning produced a highly contiguous genome for Pa. corni and a chromosome-level assembly for the Ophiocordyceps endosymbiont. The endosymbiont genome was characterized by 524 gene loss events compared to free-living pathogenic Ophiocordyceps relatives, with predicted roles in hyphal growth, cell wall integrity, metabolism, gene regulation, and toxin production. Contrasting patterns of selection were observed between the nuclear and mitochondrial genomes specific to the endosymbiont lineage. Intensified selection was most frequently observed across orthologs in the nuclear genome, whereas selection on most mitochondrial genes was found to be relaxed. Scans for positive selection were enriched within the fatty acid metabolism pathway with endosymbiont specific selection within three adjacent enzymes catalyzing the conversion of acetoacetate to acetyl-coenzyme A, suggesting that the endosymbiont lineage is under selective pressure to effectively exploit the lipid rich environment of the insect fat bodies in which it is found.</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/PMC11632363/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675658","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
Evidence for a Novel X Chromosome in Termites. 白蚁中新X染色体的证据。
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-12-04 DOI: 10.1093/gbe/evae265
Roxanne Fraser, Ruth Moraa, Annika Djolai, Nils Meisenheimer, Sophie Laube, Beatriz Vicoso, Ann Kathrin Huylmans
{"title":"Evidence for a Novel X Chromosome in Termites.","authors":"Roxanne Fraser, Ruth Moraa, Annika Djolai, Nils Meisenheimer, Sophie Laube, Beatriz Vicoso, Ann Kathrin Huylmans","doi":"10.1093/gbe/evae265","DOIUrl":"10.1093/gbe/evae265","url":null,"abstract":"<p><p>Termites, together with cockroaches, belong to the Blattodea. They possess an XX/XY sex determination system which has evolved from an XX/X0 system present in other Blattodean species, such as cockroaches and wood roaches. Little is currently known about the sex chromosomes of termites, their gene content, or their evolution. We here investigate the X chromosome of multiple termite species and compare them with the X chromosome of cockroaches using genomic and transcriptomic data. We find that the X chromosome of the termite Macrotermes natalensis is large and differentiated showing hall marks of sex chromosome evolution such as dosage compensation, while this does not seem to be the case in the other two termite species investigated here where sex chromosomes may be evolutionary younger. Furthermore, the X chromosome in M. natalensis is different from the X chromosome found in the cockroach Blattella germanica indicating that sex chromosome turn-over events may have happened during termite evolution.</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/PMC11662285/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142806817","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
De Novo Genome Assembly and Annotation for the Synanthropic Webbing Clothes Moth (Tineola bisselliella): A Globally Distributed, Economically Important Pest. 一种全球分布的重要的经济害虫——同生织带衣蛾(Tineola bisselliella)的基因组组装和注释。
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-12-04 DOI: 10.1093/gbe/evae266
Jasmine D Alqassar, Hannah E Aichelman, Isabel A Novick, Sean P Mullen
{"title":"De Novo Genome Assembly and Annotation for the Synanthropic Webbing Clothes Moth (Tineola bisselliella): A Globally Distributed, Economically Important Pest.","authors":"Jasmine D Alqassar, Hannah E Aichelman, Isabel A Novick, Sean P Mullen","doi":"10.1093/gbe/evae266","DOIUrl":"10.1093/gbe/evae266","url":null,"abstract":"<p><p>Tineola bisselliella, the webbing clothes moth, is an economically important, globally distributed synanthropic pest species and member of the basal moth lineage Tineidae. These moths are facultatively keratinophagous, and their larvae can cause extensive damage, particularly to clothing, textiles, and museum specimens. Despite the economic and phylogenetic importance of T. bisselliella, there is a lack of quality genomic resources for this, or for other species within the Tineidae family. The T. bisselliella genome assembly presented here consists of 30 pseudochromosomes (29 autosomes and 1 Z chromosome) produced using synteny alignment of a preliminary contig-level assembly (256 contigs) to a closely related species, Tinea pellionella. The resulting final pseudochromosome-level assembly is 243.630 Mb and has an N50 length of 8.708 Mb. The assembly is highly contiguous and has similar or improved quality compared to other available Tineidae genomes, with 93.1% (91.8% single copy and 1.3% duplicated) of lepidopteran orthologs complete and present. Annotation of the pseudochromosome-level genome assembly with the transcriptome we produced ultimately yielded 11,259 annotated genes. Synteny alignments between the T. bisselliella genome assembly and other Tineidae genomes revealed evidence for numerous small rearrangements with high synteny conservation. In contrast, a synteny alignment performed between T. bisselliella and Melitaea cinxia, which is thought to have retained the ancestral karyotype (n = 31), revealed a fusion of the ancestral autosome 30 and Z chromosome that led to a reduction in T. bisselliella karyotype size. The reference quality annotated genome for T. bisselliella presented here will advance our understanding of the evolution of the lepidopteran karyotype by providing a chromosome-level genome for this basal moth lineage and provide future insights into the mechanisms underlying keratin digestion in T. bisselliella.</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/PMC11662235/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142806814","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
Neo-Sex Chromosome Evolution in Treehoppers Despite Long-Term X Chromosome Conservation. 尽管长期X染色体保存,树跳鸟的新性染色体进化。
IF 3.2 2区 生物学
Genome Biology and Evolution Pub Date : 2024-12-04 DOI: 10.1093/gbe/evae264
Daniela H Palmer Droguett, Micah Fletcher, Ben T Alston, Sarah Kocher, Diogo C Cabral-de-Mello, Alison E Wright
{"title":"Neo-Sex Chromosome Evolution in Treehoppers Despite Long-Term X Chromosome Conservation.","authors":"Daniela H Palmer Droguett, Micah Fletcher, Ben T Alston, Sarah Kocher, Diogo C Cabral-de-Mello, Alison E Wright","doi":"10.1093/gbe/evae264","DOIUrl":"10.1093/gbe/evae264","url":null,"abstract":"<p><p>Sex chromosomes follow distinct evolutionary trajectories compared to the rest of the genome. In many cases, sex chromosomes (X and Y or Z and W) significantly differentiate from one another resulting in heteromorphic sex chromosome systems. Such heteromorphic systems are thought to act as an evolutionary trap that prevents subsequent turnover of the sex chromosome system. For old, degenerated sex chromosome systems, chromosomal fusion with an autosome may be one way that sex chromosomes can \"refresh\" their sequence content. We investigated these dynamics using treehoppers (hemipteran insects of the family Membracidae), which ancestrally have XX/X0 sex chromosomes. We assembled the most complete reference assembly for treehoppers to date for Umbonia crassicornis and employed comparative genomic analyses of 12 additional treehopper species to analyze X chromosome variation across different evolutionary timescales. We find that the X chromosome is largely conserved, with one exception being an X-autosome fusion in Calloconophora caliginosa. We also compare the ancestral treehopper X with other X chromosomes in Auchenorrhyncha (the clade containing treehoppers, leafhoppers, spittlebugs, cicadas, and planthoppers), revealing X conservation across more than 300 million years. These findings shed light on chromosomal evolution dynamics in treehoppers and the role of chromosomal rearrangements in sex chromosome evolution.</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/PMC11662286/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142828331","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
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