Genome Biology and Evolution最新文献

{"title":"Chromosome-Level Genome Assembly of the Heptageniid Mayfly Parafronurus youi (Ephemeroptera), and Its Annotation.","authors":"Ran Li, Ze-Kai Wang, Dong-Kai Liu, Ying-Xue Zhang, Xiao-Yu Li, Hai-Xin Li","doi":"10.1093/gbe/evaf027","DOIUrl":"10.1093/gbe/evaf027","url":null,"abstract":"<p><p>As a group of winged insects (Pterygota) retaining many primitive characteristics, genomic research on mayflies remains highly limited, posing challenges to the study of their origin and evolution. In this study, we present the first chromosome-level genome assembly of the Chinese endemic mayfly Parafronurus youi utilizing Illumina short-read, PacBio long-read, and Hi-C sequencing technologies. The high-quality genome is 412.90 Mb in size with 99.07% of the sequences anchored to 11 chromosomes (ranging from 24.88 to 45.89 Mb). Genome annotation predicted 15,647 protein-coding genes with an average length of 9,934.7 bp, of which 85.9% were functionally annotated in the UniProtKB database. Repetitive elements accounted for 32.83% of the genome, including 27.33% transposable elements and 4.07% simple repeats. This study not only enriches genomic resources for mayflies but also establishes a foundation for investigating molecular mechanisms underlying ecological adaptation and evolutionary traits, contributing to the conservation of freshwater ecosystems.</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/PMC11882360/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143482979","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":"Genetic Origins of the Kiritimati Population from Central-Eastern Micronesia.","authors":"Maximilian Larena, Afifa Enam Chowdhury, Ma Junaliah Tuazon Kels, Kai Tätte, Mait Metspalu, Carina M Schlebusch, Ralph Garcia-Bertrand, Rene J Herrera","doi":"10.1093/gbe/evaf046","DOIUrl":"10.1093/gbe/evaf046","url":null,"abstract":"<p><p>The migration of Austronesian-speaking populations through Oceania has intrigued researchers for decades. The Kiribati islands, situated along the boundaries of Micronesia and Polynesia, provide a crucial link in this migration. We analyzed the genome-wide data of the Kiritimati population of Kiribati to uncover their genetic origins and connections with other Oceanian groups. Our study reveals that the Kiritimati population primarily exhibits Remote Oceanian-related ancestry associated with ancient Lapita and present-day Polynesian populations. In addition, our identity-by-descent analysis identifies populations from the coastal southern Philippines as their closest relatives in Island Southeast Asia. The genetic links between Kiritimati, ancient Lapita, and modern Polynesians underscore the shared ancestry and continuous gene flow across these regions. This genetic continuity and ongoing links are supported by linguistic and cultural evidence, illustrating a complex history of migration and admixture in Oceania.</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/PMC11937891/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143596736","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 Breeding Sex Ratio Interacts With Demographic History to Shape Comparative Patterns of Variation on the X Chromosome and the Autosomes.","authors":"William J Spurley, Bret A Payseur","doi":"10.1093/gbe/evaf035","DOIUrl":"10.1093/gbe/evaf035","url":null,"abstract":"<p><p>In many populations, unequal numbers of females and males reproduce each generation. This imbalance in the breeding sex ratio shapes patterns of genetic variation on the sex chromosomes and the autosomes in distinct ways. Despite recognition of this phenomenon, effects of the breeding sex ratio on some aspects of variation remain unclear, especially for populations with nonequilibrium demographic histories. To address this gap in the field, we used coalescent simulations to examine relative patterns of variation at X-linked loci and autosomal loci in populations spanning the range of breeding sex ratio with historical changes in population size. Shifts in breeding sex ratio away from 1:1 reduce nucleotide diversity and the number of unique haplotypes and increase linkage disequilibrium and the frequency of the most common haplotype, with contrasting effects on X-linked loci and autosomal loci. Strong population bottlenecks transform relationships among the breeding sex ratio, the site frequency spectrum, and linkage disequilibrium, while relationships among the breeding sex ratio, nucleotide diversity, and haplotype characteristics are broadly conserved. Our findings indicate that evolutionary interpretations of variation on the X chromosome should consider the combined effects of the breeding sex ratio and demographic history. The genomic signatures we report could be used to reconstruct these fundamental population parameters from genomic data in natural populations.</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/PMC11913216/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143556679","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-Wide Selection Scans in Mexican Indigenous Populations Reveal Recent Signatures of Pathogen and Diet Adaptation.","authors":"Maria Fernanda Miron-Toruno, Enrique Morett, Israel Aguilar-Ordonez, Austin W Reynolds","doi":"10.1093/gbe/evaf043","DOIUrl":"10.1093/gbe/evaf043","url":null,"abstract":"<p><p>Whole-genome scans for natural selection signatures across Mexican indigenous populations remain underrepresented in the literature. Here, we conducted the first comparative analysis of genetic adaptation in Mexican indigenous populations using whole-genome sequencing data from 76 individuals representing 27 different ethnic groups in Mexico. We divided the cohort into northern, central, and southern populations and identified signals of natural selection within and across populations. We find evidence of adaptation to pathogenic environments in all our populations, including significant signatures in the Duffy blood group gene in central Mexican indigenous populations. Despite each region exhibiting unique local adaptation profiles, selection signatures on ARHGAP15, VGLL4, LINGO2, SYNDIG1, and TFAP2B were common to all populations. Our results also suggest that selection signatures falling within enhancers or promoters are usually connected to noncoding features, with notable exceptions like ARHGAP15 and GTDC1. This paper provides new evidence on the selection landscape of Mexican indigenous populations and lays the foundation for additional work on Mexican phenotypic characterization.</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/PMC11954594/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604681","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":"Inferring the Selective History of CNVs Using a Maximum Likelihood Model.","authors":"Seyed Amir Malekpour, Ata Kalirad, Sina Majidian","doi":"10.1093/gbe/evaf050","DOIUrl":"10.1093/gbe/evaf050","url":null,"abstract":"<p><p>Copy number variations (CNVs)-structural variations generated by deletion and/or duplication that result in a change in DNA dosage-are prevalent in nature. CNVs can drastically affect the phenotype of an organism and have been shown to be both involved in genetic disorders and be used as raw material in adaptive evolution. Unlike single-nucleotide variations, the often large and varied effects of CNVs on phenotype hinders our ability to infer their selective advantage based on the population genetics data. Here, we present a likelihood-based approach, dubbed PoMoCNV (POlymorphism-aware phylogenetic MOdel for CNVs), that estimates the evolutionary parameters such as mutation rates among different copy numbers and relative fitness loss per copy deletion at a genomic locus based on population genetics data. As a case study, we analyze the genomics data of 40 strains of Caenorhabditis elegans, representing four different populations. We take advantage of the data on chromatin accessibility to interpret the mutation rate and fitness of copy numbers, as inferred by PoMoCNV, specifically in open or closed chromatin loci. We further test the reliability of PoMoCNV by estimating the evolutionary parameters of CNVs for mutation-accumulation experiments in C. elegans with varying levels of genetic drift.</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/PMC11950529/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656922","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":"A Broad Genome Survey Reveals Widespread Presence of Secretoglobin Genes in Squamate and Archosaur Reptiles that Flowered into Diversity in Mammals.","authors":"Robert C Karn, Christina M Laukaitis","doi":"10.1093/gbe/evaf024","DOIUrl":"10.1093/gbe/evaf024","url":null,"abstract":"<p><p>Secretoglobins (SCGBs) are a superfamily of small, dimeric, cytokine-like proteins found originally in the reproductive tracts and airways of mammals. Most SCGB research has focused on respiratory diseases in humans and laboratory animal models but knowledge of their biological functions is sparse. We report here a broad survey of Scgbs, the genes that encode SCGBs, in animal genomes. We tested the view that they are uniquely mammalian in origin and distribution, hoping that understanding their distribution would shed light on their evolutionary history and perhaps point to putative biological functions. Rather than being uniquely mammalian, we found many different SCGBs in turtles, crocodilians, lizards, and birds, suggesting they existed in the Carboniferous Period (∼320 MYA) when the sauropsids evolved in the amniote lineage. We identified no SCGBs in amphibians or fishes, suggesting that this characteristic originated in an amniote ancestor. Amniotes include sauropsid and synapsid lineages, and three subfamilies of SCGBs (SCGB2A, SCGB3A, and SCGB1C) are found in both sauropsid and synapsid lineages. Uteroglobin (SCGB1A), the first identified SCGB protein, is uniquely mammalian, having appeared in monotremes. The SCGB subfamilies including androgen-binding proteins (SCGB1B and SCGB2B) are first seen in metatherians. This complex distribution suggests that there is an as-yet-undiscovered basic function of SCGBs shared by all amniotes.</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/PMC11884772/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143413949","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":"Tracing the Origin and Evolution of the Fungal Mycophenolic Acid Biosynthesis Pathway.","authors":"Baptiste Bidon, Hajar Yaakoub, Arnaud Lanoue, Antoine Géry, Virginie Séguin, Florent Magot, Claire Hoffmann, Vincent Courdavault, Jean-Philippe Bouchara, Jean-Pierre Gangneux, Jens C Frisvad, Antonis Rokas, Gustavo H Goldman, Gilles Nevez, Solène Le Gal, Domenico Davolos, David Garon, Nicolas Papon","doi":"10.1093/gbe/evaf039","DOIUrl":"10.1093/gbe/evaf039","url":null,"abstract":"<p><p>Like bacteria and plants, fungi produce a remarkable diversity of small molecules with potent activities for human health known as natural products or secondary metabolites. One such example is mycophenolic acid, a powerful immunosuppressant drug that is administered daily to millions of transplant recipients worldwide. Production of mycophenolic acid is restricted to a very limited number of filamentous fungi, and little is known about its biosynthetic modalities. It is therefore a particular challenge to improve our knowledge of the biosynthesis of this valuable natural compound, as this would contribute to a better understanding of the specialized metabolism of fungi and could also lead to the identification of new fungal producers for the supply of immunosuppressants. Here, we were interested in deciphering the origin and evolution of the fungal mycophenolic acid biosynthetic pathway. Large-scale analyses of fungal genomic resources led us to identify several new species that harbor a gene cluster for mycophenolic acid biosynthesis. Phylogenomic analysis suggests that the mycophenolic acid biosynthetic gene cluster originated early in a common ancestor of the fungal family Aspergillaceae but was repeatedly lost and it is now present in a narrow but diverse set of filamentous fungi. Moreover, a comparison of the inosine 5'-monophosphate dehydrogenase protein sequences that are the target of the mycophenolic acid drug as well as analysis of mycophenolic acid production and susceptibility suggest that all mycophenolic acid fungal producers are resistant to this toxic compound, but that this resistance is likely to be based on different molecular mechanisms. Our study provides new insight into the evolution of the biosynthesis of the important secondary metabolite mycophenolic acid in fungi.</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/PMC11934065/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143572773","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":"Amino Acid Properties, Substitution Rates, and the Nearly Neutral Theory.","authors":"Jennifer E James, Martin Lascoux","doi":"10.1093/gbe/evaf025","DOIUrl":"10.1093/gbe/evaf025","url":null,"abstract":"<p><p>Do the properties of amino acids affect their rates of substitution? The neutral theory predicts that greater selective constraint leads to slower rates of evolution; similarly, we expect amino acids that are more different from each other to have lower rates of exchange because such changes are most likely to affect protein structure and function. Here, we test these predictions, using substitution rates estimated from empirical amino acid exchangeability matrices. To measure degree of amino acid difference, we focused on two physicochemical properties, charge and size, uncorrelated metrics that are known to have important implications for protein structure and function. We find that for both charge and size, amino acid pairs with large differences had lower rates of substitution. We also found that amino acids that differed in both properties had the lowest rates of substitution, suggesting that both physicochemical properties are under selective constraint. Mutation properties, such as the number of mutations or the number of transitions as opposed to transversions separating amino acid pairs, were also important predictors of substitution rates. The relationship between amino acid substitution rates and differences in their physiochemical properties holds across several taxonomically restricted datasets. This finding suggests that purifying selection affects amino acid substitution rates in a similar manner across taxonomic groups with different effective population sizes.</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/PMC11884779/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143457769","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":"Nanopore Sequencing of Amoebophrya Species Reveals Novel Collection of Bacteria Putatively Associated With Karlodinium veneficum.","authors":"Daniela Tizabi, Russell T Hill, Tsvetan Bachvaroff","doi":"10.1093/gbe/evaf022","DOIUrl":"10.1093/gbe/evaf022","url":null,"abstract":"<p><p>The dinoflagellate parasite Amoebophrya sp. ex Karlodinium veneficum plays a major role in controlling populations of the toxic bloom-forming dinoflagellate K. veneficum and is one of the few cultured representatives of Marine Alveolate Group II. The obligate parasitic nature of this Amoebophrya spp. precludes isolation in culture, and therefore, genomic characterization of this parasite relies on metagenomic sequencing. Whole-genome sequencing of an Amoebophrya sp. ex K. veneficum-infected culture using Nanopore long reads revealed a diverse community of novel bacteria as well as several species previously reported to be associated with algae. In sum, 39 metagenome-assembled genomes were assembled, and less than half of these required binning of multiple contigs. Seven were abundant but of unknown genera, 13 were identifiable at the generic level by BLAST (8 of which were apparently complete single-contig genomes), and the remaining 19 comprised less abundant (individually accounting for <2% of the total bacterial reads in the culture) and often rarer and/or novel species. Attempts to culture strains identified through sequencing revealed that only two of these bacterial isolates were readily amenable to cultivation, stressing the importance of a dual culture- and sequencing-based approach for robust community analysis. Functional annotations of metagenome-assembled genomes are presented here to support the characterization of a microbial community associated with K. veneficum and/or Amoebophrya sp. ex K. veneficum cultured from the Chesapeake Bay and give preliminary insights into the nature of the associations these bacteria have with this parasite-host complex.</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/PMC11890096/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143407081","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":"Differential Gene Expression and Unbalanced Homeolog Expression Bias in 4 Million-Year-Old Allopolyploids of Nicotiana Section Repandae.","authors":"Talieh Ostovar, Jacob B Landis, Elizabeth W McCarthy, Nicolas Sierro, Amy Litt","doi":"10.1093/gbe/evaf029","DOIUrl":"10.1093/gbe/evaf029","url":null,"abstract":"<p><p>Allopolyploidy, a phenomenon prevalent in angiosperms involving hybridization and whole-genome duplication, results in species with multiple subgenomes, altering genome structure and gene expression, leading to novel phenotypes. Allopolyploids often experience unbalanced homeolog expression bias, the preferential expression of homeologs from one of the two progenitor genomes. To explore the consequences of allopolyploidy and unbalanced homeolog expression bias, we investigate global gene expression and the fate of homeologs in Nicotiana (Solanaceae). We focus on Nicotiana section Repandae, including three allotetraploid species, Nicotiana nudicaulis, N. repanda, and N. stocktonii, derived from diploid progenitors N. sylvestris and N. obtusifolia ∼4.3 Ma. We identify genes with differential expression and investigate expression of candidate genes for flower size variation. Our results show expression differences with the allopolyploids intermediate between the two progenitor species, with a slight bias toward N. obtusifolia. Moreover, we demonstrate unbalanced homeolog expression bias toward the N. obtusifolia subgenome across developmental stages in the allopolyploids, with a stronger bias in N. nudicaulis. In contrast, unbalanced homeolog expression bias shifts toward N. sylvestris for flower size genes in N. nudicaulis, showing that genes involved in particular phenotypes can display different patterns of unbalanced homeolog expression than the overall transcriptome. We also see differential expression of several known flower size genes across corolla developmental stages. Our results highlight the role of unbalanced homeolog expression bias in shaping the evolutionary trajectory of Nicotiana species and provide a foundation for future research into the ecological and evolutionary implications of allopolyploidy in flowering plants.</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/PMC11890095/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143457771","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}