Genome Biology and Evolution最新文献

{"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}

{"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}

{"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}

{"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}

{"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}

{"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}

{"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}

{"title":"Convergent Evolution Associated with the Loss of Developmental Diapause May Promote Extended Lifespan in Bees.","authors":"Priscila K F Santos, Karen M Kapheim","doi":"10.1093/gbe/evae255","DOIUrl":"10.1093/gbe/evae255","url":null,"abstract":"<p><p>Diapause has long been proposed to play a significant role in the evolution of eusociality in Hymenoptera. Recent studies have shown that shifts in the diapause stage precede social evolution in wasps and bees; however, the genomic basis remains unknown. Given the overlap in molecular pathways that regulate diapause and lifespan, we hypothesized that the evolutionary loss of developmental diapause may lead to extended lifespan among adults, which is a prerequisite for the evolution of eusociality. To test whether the loss of prepupal diapause is followed by genomic changes associated with lifespan extension, we compared 27 bee genomes with or without prepupal diapause. Our results point to several potential mechanisms for lifespan extension in species lacking prepupal diapause, including the loss of the growth hormone PTTH and its receptor TORSO, along with convergent selection in genes known to regulate lifespan in animals. Specifically, we observed purifying selection of prolongevity genes and relaxed selection of antilongevity genes within the IIS/TOR pathway in species that have lost prepupal diapause. Changes in selection pressures on this pathway may lead to the evolution of new phenotypes, such as lifespan extension and altered responses to nutritional signals that are crucial for social 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/PMC11632380/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695471","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}

{"title":"Genome Streamlining: Effect of Mutation Rate and Population Size on Genome Size Reduction.","authors":"Juliette Luiselli, Jonathan Rouzaud-Cornabas, Nicolas Lartillot, Guillaume Beslon","doi":"10.1093/gbe/evae250","DOIUrl":"10.1093/gbe/evae250","url":null,"abstract":"<p><p>Genome streamlining, i.e. genome size reduction, is observed in bacteria with very different life traits, including endosymbiotic bacteria and several marine bacteria, raising the question of its evolutionary origin. None of the hypotheses proposed in the literature is firmly established, mainly due to the many confounding factors related to the diverse habitats of species with streamlined genomes. Computational models may help overcome these difficulties and rigorously test hypotheses. In this work, we used Aevol, a platform designed to study the evolution of genome architecture, to test 2 main hypotheses: that an increase in population size (N) or mutation rate (μ) could cause genome reduction. In our experiments, both conditions lead to streamlining but have very different resulting genome structures. Under increased population sizes, genomes lose a significant fraction of noncoding sequences but maintain their coding size, resulting in densely packed genomes (akin to streamlined marine bacteria genomes). By contrast, under an increased mutation rate, genomes lose both coding and noncoding sequences (akin to endosymbiotic bacteria genomes). Hence, both factors lead to an overall reduction in genome size, but the coding density of the genome appears to be determined by N×μ. Thus, a broad range of genome size and density can be achieved by different combinations of N and μ. Our results suggest that genome size and coding density are determined by the interplay between selection for phenotypic adaptation and selection for robustness.</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/PMC11666309/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142681680","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}

{"title":"Molecular Basis of Eusocial Complexity: The Case of Worker Reproductivity in Bees.","authors":"David C Prince, Anders Wirén, Timothy J Huggins, David H Collins, Tamas Dalmay, Andrew F G Bourke","doi":"10.1093/gbe/evae269","DOIUrl":"10.1093/gbe/evae269","url":null,"abstract":"<p><p>In eusocial insects, the molecular basis of worker reproductivity, including how it changes with eusocial complexity, remains relatively poorly understood. To address this, we used mRNA-seq to isolate genes differentially expressed between ovary-active and ovary-inactive workers in the intermediately eusocial bumblebee Bombus terrestris. By comparisons with data from the advanced eusocial honeybee Apis mellifera, which shows reduced worker reproductivity, we characterized gene expression differences associated with change in worker reproductivity as a function of eusocial complexity. By comparisons with genes associated with queen-worker caste development in B. terrestris larvae, we tested the behavioral-morphological caste homology hypothesis, which proposes co-option of genes influencing reproductive division of labor in adults in morphological caste evolution. We conducted comparisons having isolated genes expressed in B. terrestris worker-laid eggs to remove the potential confound caused by gene expression in eggs. Gene expression differences between the B. terrestris worker phenotypes were mainly in fat body and ovary, not brain. Many genes (86%) more highly expressed in ovary of ovary-active workers were also expressed in worker-laid eggs, confirming egg-expressed genes were potentially confounding. Comparisons across B. terrestris and A. mellifera, and with B. terrestris larvae, returned significant percentage overlaps in differentially expressed genes and/or enriched Gene Ontology terms, suggesting conserved gene functions underpin worker reproductivity as it declines with increasing eusocial complexity and providing support for the behavioral-morphological caste homology hypothesis. Therefore, within bees, both a degree of conserved gene use and gene co-option appear to underlie the molecular basis of worker reproductivity and morphological caste 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/PMC11670783/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142812736","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}