Genome Biology and Evolution最新文献

{"title":"A Short-Term View of Protein Sequence Evolution from Salmonella.","authors":"Joshua L Cherry","doi":"10.1093/gbe/evaf040","DOIUrl":"10.1093/gbe/evaf040","url":null,"abstract":"<p><p>Much of the study of protein sequence evolution is based on sequence changes inferred to have occurred in nature. The sequences compared for this purpose are usually sufficiently distant that purifying selection has had nearly its full effect and most of the changes inferred have been exposed to a variety of conditions. Here, I make use of large numbers of Salmonella genome sequences to study changes known to be of very recent origin because they are inferred from comparison of very closely related sequences. The effects of purifying selection are weak yet discernible on this short timescale: the ratio of nonsynonymous to synonymous changes is smaller than expected under selective neutrality, but only slightly so. Essential genes have lower rates of nonsynonymous change, as they do on a longer timescale, but much more of this association remains after controlling for expression level. Positive selection for nonsynonymous change is inferred for 151 genes. For nearly half of these, this is attributable to selection for loss of function. Other forms of positive selection inferred include selection for amino acid changes that make enzymes less sensitive to antibiotics and selection for activating changes to proteins involved in transcriptional regulation. Positively selected variants of many genes are likely favored only under unusual conditions and disfavored in the long term, making detection of the positive selection with more distant comparisons difficult or impossible. The short-term view provided by close comparisons complements the long-term view obtained from more distant comparisons such as those between species.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11925014/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143572771","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":"Horizontal Transfer of msp130 Genes and the Evolution of Metazoan Biocalcification.","authors":"Macie M Chess, Saoirse Foley, Charles A Ettensohn","doi":"10.1093/gbe/evaf028","DOIUrl":"10.1093/gbe/evaf028","url":null,"abstract":"<p><p>The formation of calcified skeletons is crucial for the development, physiology, and ecology of many marine metazoans. The evolutionary origins of the genetic toolkit required for biocalcification are widely debated. MSP130 proteins, originally identified through their expression specifically by sea urchin skeletal cells, have been hypothesized to have been acquired by metazoans from bacteria through horizontal gene transfer. Here, we provide support for a horizontal gene transfer-based origin of metazoan MSP130 proteins by conducting phylogenetic and in silico protein analyses utilizing high-quality genomes. We show that msp130 genes underwent duplications within almost all biocalcifying bilaterian phyla and identify highly conserved intron-exon junctions specific to bilaterian msp130 genes. The absence of MSP130 proteins in calcifying, nonbilaterian metazoans and other basal eukaryotes suggests that an ancestral msp130 gene underwent a horizontal gene transfer event that predates bilaterians, but not metazoans. We report striking structural similarities between bilaterian and bacterial MSP130 proteins, with each containing a seven-bladed, barrel-like motif that encompasses a choice-of-anchor domain, and identify highly conserved, predicted Ca2+-binding sites associated with the barrels. These findings point to a conserved, ancient function for MSP130 proteins in biocalcification and support the view that lateral transfer of bacterial genes supported the appearance of calcified animal skeletons.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11878542/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143440633","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":"Correction to: The Evolution of Temperature and Desiccation-Related Protein Families in Tardigrada Reveals a Complex Acquisition of Extremotolerance.","authors":"","doi":"10.1093/gbe/evaf018","DOIUrl":"10.1093/gbe/evaf018","url":null,"abstract":"","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"17 2","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11831363/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143440646","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":"Chromosome-Level Genome Assembly and Annotation of Corallium rubrum: A Mediterranean Coral Threatened by Overharvesting and Climate Change.","authors":"Jean-Baptiste Ledoux, Jessica Gomez-Garrido, Fernando Cruz, Francisco Camara Ferreira, Ana Matos, Xenia Sarropoulou, Sandra Ramirez-Calero, Didier Aurelle, Paula Lopez-Sendino, Natalie E Grayson, Bradley S Moore, Agostinho Antunes, Laura Aguilera, Marta Gut, Judit Salces-Ortiz, Rosa Fernández, Cristina Linares, Joaquim Garrabou, Tyler Alioto","doi":"10.1093/gbe/evae253","DOIUrl":"10.1093/gbe/evae253","url":null,"abstract":"<p><p>Reference genomes are key resources in biodiversity conservation. Yet, sequencing efforts are not evenly distributed across the tree of life raising concerns over our ability to enlighten conservation with genomic data. Good-quality reference genomes remain scarce in octocorals while these species are highly relevant targets for conservation. Here, we present the first annotated reference genome in the red coral, Corallium rubrum (Linnaeus, 1758), a habitat-forming octocoral from the Mediterranean and neighboring Atlantic, impacted by overharvesting and anthropogenic warming-induced mass mortality events. Combining long reads from Oxford Nanopore Technologies (ONT), Illumina paired-end reads for improving the base accuracy of the ONT-based genome assembly, and Arima Hi-C contact data to place the sequences into chromosomes, we assembled a genome of 532 Mb (20 chromosomes, 309 scaffolds) with contig and scaffold N50 of 1.6 and 18.5 Mb, respectively. Fifty percent of the sequence (L50) was contained in seven superscaffolds. The consensus quality value of the final assembly was 42, and the single and duplicated gene completeness reported by BUSCO was 86.4% and 1%, respectively (metazoa_odb10 database). We annotated 26,348 protein-coding genes and 34,548 noncoding transcripts. This annotated chromosome-level genome assembly, one of the first in octocorals and the first in Scleralcyonacea order, is currently used in a project based on whole-genome resequencing dedicated to the conservation and management of C. rubrum.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"17 2","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11803306/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143364447","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":"Phylogenetic Signal in Primate Tooth Enamel Proteins and its Relevance for Paleoproteomics.","authors":"Ricardo Fong-Zazueta, Johanna Krueger, David M Alba, Xènia Aymerich, Robin M D Beck, Enrico Cappellini, Guillermo Carrillo-Martin, Omar Cirilli, Nathan Clark, Omar E Cornejo, Kyle Kai-How Farh, Luis Ferrández-Peral, David Juan, Joanna L Kelley, Lukas F K Kuderna, Jordan Little, Joseph D Orkin, Ryan S Paterson, Harvinder Pawar, Tomas Marques-Bonet, Esther Lizano","doi":"10.1093/gbe/evaf007","DOIUrl":"10.1093/gbe/evaf007","url":null,"abstract":"<p><p>Ancient tooth enamel, and to some extent dentin and bone, contain characteristic peptides that persist for long periods of time. In particular, peptides from the enamel proteome (enamelome) have been used to reconstruct the phylogenetic relationships of fossil taxa. However, the enamelome is based on only about 10 genes, whose protein products undergo fragmentation in vivo and post mortem. This raises the question as to whether the enamelome alone provides enough information for reliable phylogenetic inference. We address these considerations on a selection of enamel-associated proteins that has been computationally predicted from genomic data from 232 primate species. We created multiple sequence alignments for each protein and estimated the evolutionary rate for each site. We examined which sites overlap with the parts of the protein sequences that are typically isolated from fossils. Based on this, we simulated ancient data with different degrees of sequence fragmentation, followed by phylogenetic analysis. We compared these trees to a reference species tree. Up to a degree of fragmentation that is similar to that of fossil samples from 1 to 2 million years ago, the phylogenetic placements of most nodes at family level are consistent with the reference species tree. We tested phylogenetic analysis on combinations of different enamel proteins and found that the composition of the proteome can influence deep splits in the phylogeny. With our methods, we provide guidance for researchers on how to evaluate the potential of paleoproteomics for phylogenetic studies before sampling valuable ancient specimens.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11878541/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004286","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":"Assembly and Annotation of the Tetraploid Salsola tragus (Russian Thistle) Genome.","authors":"John M Lemas, Eric L Patterson, Luan Cutti, Sarah Morran, Nicholas A Johnson, Jacob Montgomery, Fatemeh Abdollahi, David R Nelson, Victor Llaca, Kevin Fengler, Philip Westra, Todd A Gaines","doi":"10.1093/gbe/evaf014","DOIUrl":"10.1093/gbe/evaf014","url":null,"abstract":"<p><p>This report presents two phased chromosome-scale genome assemblies of allotetraploid Salsola tragus (2n = 4x = 36) and fills the current genomics resource gap for this species. Flow cytometry estimated 1C genome size was 1.319 Gb. PacBio HiFi reads were assembled and scaffolded with Hi-C chromatin contact mapping and Bionano optical mapping data. For annotation, a PacBio Iso-Seq library was generated from root, stem, leaf, and floral tissues followed by annotation using a modified Maker pipeline. The assembled haploid S. tragus genomes contained 18 chromosomes each, with 9 chromosomes assigned to subgenome A and 9 chromosomes to subgenome B. Each haplome assembly represented 95% of the total flow cytometry estimated genome size. Haplome 1 and haplome 2 contained 43,354 and 42,221 annotated genes, respectively. The availability of high-quality reference genomes for this economically important weed will facilitate future omics analysis of S. tragus and a better understanding of chenopod plants.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11797066/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143038063","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":"Massive Gene Loss in the Fungus Sporothrix epigloea Accompanied a Shift to Life in a Glucuronoxylomannan-based Gel Matrix.","authors":"Carmen C G Allen, David Díaz-Escandón, Sarah DeLong-Duhon, Gulnara Tagirdzhanova, Alejandro Huereca, Shauna Reckseidler-Zenteno, Andrew Forbes, Toby Spribille","doi":"10.1093/gbe/evaf015","DOIUrl":"10.1093/gbe/evaf015","url":null,"abstract":"<p><p>Fungi are well-known for their ability to both produce and catabolize complex carbohydrates to acquire carbon, often in the most extreme of environments. Glucuronoxylomannan (GXM)-based gel matrices are widely produced by fungi in nature and though they are of key interest in medicine and pharmaceuticals, their biodegradation is poorly understood. Though some organisms, including other fungi, are adapted to life in and on GXM-like matrices in nature, they are almost entirely unstudied, and it is unknown if they are involved in matrix degradation. Sporothrix epigloea is an ascomycete fungus that completes its life cycle entirely in the short-lived secreted polysaccharide matrix of a white jelly fungus, Tremella fuciformis. To gain insight into how S. epigloea adapted to life in this unusual microhabitat, we compared the predicted protein composition of S. epigloea to that of 21 other Sporothrix species. We found that the genome of S. epigloea is smaller than that of any other sampled Sporothrix, with widespread functional gene loss, including those coding for serine proteases and biotin synthesis. In addition, many predicted CAZymes degrading both plant and fungal cell wall components were lost while a lytic polysaccharide monooxygenase with no previously established activity or substrate specificity, appears to have been gained. Phenotype assays suggest narrow use of mannans and other oligosaccharides as carbon sources. Taken together, the results suggest a streamlined machinery, including potential carbon sourcing from GXM building blocks, facilitates the hyperspecialized ecology of S. epigloea in the GXM-like milieu.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11822852/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143046408","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 and Predictability of Gene Copy Numbers Associated with Diets in Mammals.","authors":"Kayla Wilhoit, Shun Yamanouchi, Bo-Jyun Chen, Yo Y Yamasaki, Asano Ishikawa, Jun Inoue, Wataru Iwasaki, Jun Kitano","doi":"10.1093/gbe/evaf008","DOIUrl":"10.1093/gbe/evaf008","url":null,"abstract":"<p><p>Convergent evolution, the evolution of the same or similar phenotypes in phylogenetically independent lineages, is a widespread phenomenon in nature. If the genetic basis for convergent evolution is predictable to some extent, it may be possible to infer organismic phenotypes and the capability of organisms to utilize new ecological resources based on genome sequence data. While repeated amino acid changes have been studied in association with convergent evolution, relatively little is known about the potential contribution of repeated gene copy number changes. In this study, we explore whether gene copy number changes of particular gene families are linked to diet shifts in mammals and assess whether trophic ecology can be inferred from the copy numbers of a specific set of gene families. Using 86 mammalian genome sequences, we identified 24 gene families with a trend toward higher copy numbers in herbivores, carnivores, and omnivores, even after phylogenetic corrections. We were able to confirm previous findings on genes such as amylase, olfactory receptors, and xenobiotic metabolism genes, and identify novel gene families whose copy numbers correlate with dietary patterns. For example, omnivores exhibited higher copy numbers of genes encoding regulators of translation. We also established a discriminant function based on the copy numbers of 13 gene families that can help predict trophic ecology to some extent. These findings highlight a possible association between convergent evolution and repeated copy number changes in specific gene families, suggesting the potential to develop a method for predicting animal ecology from genome sequence data.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11797053/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028634","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":"The Chromosome-level Genome of the Ctenophore Mnemiopsis leidyi A. Agassiz, 1865 Reveals a Unique Immune Gene Repertoire.","authors":"Vasiliki Koutsouveli, Montserrat Torres-Oliva, Till Bayer, Janina Fuß, Nora Grossschmidt, Angela M Marulanda-Gomez, Nadin Jensen, Diana Gill, Ruth A Schmitz, Lucía Pita, Thorsten B H Reusch","doi":"10.1093/gbe/evaf006","DOIUrl":"10.1093/gbe/evaf006","url":null,"abstract":"<p><p>Ctenophora are basal marine metazoans, the sister group of all other animals. Mnemiopsis leidyi is one of the most successful invasive species worldwide with intense ecological and evolutionary research interest. Here, we generated a chromosome-level genome assembly of M. leidyi with a focus on its immune gene repertoire. The genome was 247.97 Mb, with N50 16.84 Mb, and 84.7% completeness. Its karyotype was 13 chromosomes. In this genome and that of two other ctenophores, Bolinopsis microptera and Hormiphora californensis, we detected a high number of protein domains related to potential immune receptors. Among those, proteins containing Toll/interleukin-1 (TIR2) domain, NACHT domain, Scavenger Receptor Cystein-Rich (SRCR) domain, or C-type Lectin domain (CTLD) were abundant and presented unique domain architectures in M. leidyi. M. leidyi seems to lack bona fide Toll-like Receptors, but it does possess a repertoire of 15 TIR2 domain-containing genes. Besides, we detected a bona fide NOD-like receptor and 38 NACHT domain-containing genes. In order to verify the function of those domain-containing genes, we exposed M. leidyi to the pathogen Vibrio coralliilyticus. Among the differentially expressed genes, we identified potential immune receptors, including four TIR2 domain-containing genes, all of which were upregulated in response to pathogen exposure. To conclude, many common immune receptor domains, highly conserved across metazoans, are already present in Ctenophora. These domains have large expansions and unique architectures in M. leidyi, findings consistent with the basal evolutionary position of this group, but still might have conserved functions in immunity and host-microbe interaction.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11797021/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004417","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":"Functional Carbohydrate-Active Enzymes Acquired by Horizontal Gene Transfer from Plants in the Whitefly Bemisia tabaci.","authors":"Dominique Colinet, Mireille Haon, Elodie Drula, Mathilde Boyer, Sacha Grisel, Carole Belliardo, Georgios D Koutsovoulos, Jean-Guy Berrin, Etienne G J Danchin","doi":"10.1093/gbe/evaf012","DOIUrl":"10.1093/gbe/evaf012","url":null,"abstract":"<p><p>Carbohydrate-active enzymes involved in the degradation of plant cell walls and/or the assimilation of plant carbohydrates for energy uptake are widely distributed in microorganisms. In contrast, they are less frequent in animals, although there are exceptions, including examples of carbohydrate-active enzymes acquired by horizontal gene transfer from bacteria or fungi in several of phytophagous arthropods and plant-parasitic nematodes. Although the whitefly Bemisia tabaci is a major agricultural pest, knowledge of horizontal gene transfer-acquired carbohydrate-active enzymes in this phloem-feeding insect of the Hemiptera order (subfamily Aleyrodinae) is still lacking. We performed a comprehensive and accurate detection of horizontal gene transfer candidates in B. tabaci and identified 136 horizontal gene transfer events, 14 of which corresponding to carbohydrate-active enzymes. The B. tabaci horizontal gene transfer-acquired carbohydrate-active enzymes were not only of bacterial or fungal origin, but some were also acquired from plants. Biochemical analysis revealed that members of the glycoside hydrolase families 17 and 152 acquired from plants are functional beta-glucanases with different substrate specificities, suggesting distinct roles. These two carbohydrate-active enzymes are the first characterized glycoside hydrolase families 17 and 152 glucanases in an animal. We identified a lower number of horizontal gene transfer events in the related Aleyrodinae Trialeurodes vaporariorum, with only three horizontal gene transfer-acquired carbohydrate-active enzymes, including a glycoside hydrolase family 152 glucanase, with phylogenetic analysis suggesting a unique horizontal gene transfer event in the ancestor of the Aleyrodinae. Another glycoside hydrolase family 152 carbohydrate-active enzyme, most likely independently acquired from plants, was also identified in two plant cell-feeding insects of the Thysanoptera order, highlighting the importance of plant-acquired carbohydrate-active enzymes in the biology of piercing-sucking insects.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11800479/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143038192","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}