Genome Biology and Evolution最新文献

{"title":"Plasmodium falciparum CyRPA Glycan Binding Does Not Explain Adaptation to Humans.","authors":"Paul M Sharp, Frederic Bibollet-Ruche, Beatrice H Hahn","doi":"10.1093/gbe/evaf016","DOIUrl":"10.1093/gbe/evaf016","url":null,"abstract":"<p><p>The human malaria parasite Plasmodium falciparum evolved from a parasite that infects gorillas, termed Plasmodium praefalciparum. The sialic acids on glycans on the surface of erythrocytes differ between humans and other apes. It has recently been shown that the P. falciparum cysteine-rich protective antigen (PfCyRPA) binds human sialoglycans as an essential step in the erythrocyte invasion pathway, while that of the chimpanzee parasite, Plasmodium reichenowi has affinities matching ape glycans. Two amino acid changes, at sites 154 and 209, were shown to be sufficient to switch glycan binding preferences and inferred to reflect adaptation of P. falciparum to humans. However, we show that sites 154 and 209 are identical in P. falciparum and P. praefalciparum, with no other differences located in or near the CyRPA glycan binding sites. Thus, the gorilla precursor appears to have already been preadapted to bind human sialoglycans.</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/PMC11797028/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143046409","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-Scale Assembly of Capsella orientalis, Maternal Progenitor of Cosmopolitan Allotetraploid C. bursa-pastoris.","authors":"Alexandra M Kasianova, Vladislav D Mityukov, Dmitry A German, Artem S Kasianov, Aleksey A Penin, Maria D Logacheva","doi":"10.1093/gbe/evaf009","DOIUrl":"10.1093/gbe/evaf009","url":null,"abstract":"<p><p>The genus Capsella serves as a model for understanding speciation, hybridization, and genome evolution in plants. Here, we present a chromosome-scale genome assembly of Capsella orientalis, the maternal progenitor of a cosmopolitan allotetraploid C. bursa-pastoris. Using nanopore sequencing and data on chromatin contacts (Hi-C), we assembled the genome into eight pseudo-chromosomes with high contiguity, evidenced by a benchmarking universal single-copy orthologs (BUSCO) completeness score of 99.3%. Comparative analysis with C. rubella and C. bursa-pastoris revealed overall synteny, except for 2 Mb inversion on chromosome 4 of C. rubella. Comparative genome analysis highlighted the conservation of gene content and structural integrity in the C. orientalis-derived subgenome of C. bursa-pastoris, with the exception of a 1.8 Mb region absent in O subgenome but present in C. orientalis. The genome annotation includes 27,675 protein-coding genes, with most exhibiting one-to-one orthology with Arabidopsis thaliana. Notably, 2,155 genes showed no similarity to A. thaliana ones. These results establish a robust genomic resource for C. orientalis, facilitating future studies on polyploid evolution, gene regulation, and species divergence within Capsella.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"17 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11783323/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143064931","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-Scale Genomes of the Flightless Caterpillar Hunter Beetles Calosoma tepidum and Calosoma wilkesii From British Columbia (Coleoptera: Carabidae).","authors":"Jérémy Gauthier, Mickael Blanc, Emmanuel F A Toussaint","doi":"10.1093/gbe/evae247","DOIUrl":"10.1093/gbe/evae247","url":null,"abstract":"<p><p>The giant ground beetle genus Calosoma (Coleoptera, Carabidae) comprises ca. 120 species distributed worldwide. About half of the species in this genus are flightless due to a process of wing reduction likely resulting from the colonization of remote habitats such as oceanic islands, highlands, and deserts. This clade is emerging as a new model to study the genomic basis of wing evolution in insects. In this framework, we present the de novo assemblies and annotations of two Calosoma species genomes from British Columbia, Calosoma tepidum and Calosoma wilkesii. Combining PacBio HiFi and Hi-C sequencing, we produce high-quality reference genomes for these two species. Our annotation using long-read RNAseq and existing Coleoptera protein evidence identified a total of 21,976 genes for C. tepidum and 26,814 genes for C. wilkesii. Using synteny analyses, we provide an in-depth comparison of genomic architectures in these two species. We infer an overall pattern of chromosome-scale conservation between the two species, with only minor rearrangements within chromosomes. These new reference genomes represent a major step forward in the study of this group, providing high-quality references that open the door to different approaches such as comparative genomics or population scale resequencing to study the implications of flight evolution.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11702298/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643816","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":"CAT-Posterior Mean Site Frequencies Improves Phylogenetic Modeling Under Maximum Likelihood and Resolves Tardigrada as the Sister of Arthropoda Plus Onychophora.","authors":"Mattia Giacomelli, Matteo Vecchi, Roberto Guidetti, Lorena Rebecchi, Philip C J Donoghue, Jesus Lozano-Fernandez, Davide Pisani","doi":"10.1093/gbe/evae273","DOIUrl":"10.1093/gbe/evae273","url":null,"abstract":"<p><p>Tardigrada, the water bears, are microscopic animals with walking appendages that are members of Ecdysozoa, the clade of molting animals that also includes Nematoda (round worms), Nematomorpha (horsehair worms), Priapulida (penis worms), Kinorhyncha (mud dragons), Loricifera (loricated animals), Arthropoda (insects, spiders, centipedes, crustaceans, and their allies), and Onychophora (velvet worms). The phylogenetic relationships within Ecdysozoa are still unclear, with analyses of molecular and morphological data yielding incongruent results. Accounting for across-site compositional heterogeneity using mixture models that partition sites in frequency categories, CATegories (CAT)-based models, has been shown to improve fit in Bayesian analyses. However, CAT-based models such as CAT-Poisson or CAT-GTR (where CAT is combined with a General Time Reversible matrix to account for replacement rate heterogeneity) have proven difficult to implement in maximum likelihood. Here, we use CAT-posterior mean site frequencies (CAT-PMSF), a new method to export dataset-specific mixture models (CAT-Poisson and CAT-GTR) parameterized using Bayesian methods to maximum likelihood software. We developed new maximum likelihood-based model adequacy tests using parametric bootstrap and show that CAT-PMSF describes across-site compositional heterogeneity better than other across-site compositionally heterogeneous models currently implemented in maximum likelihood software. CAT-PMSF suggests that tardigrades are members of Panarthropoda, a lineage also including Arthropoda and Onychophora. Within Panarthropoda, our results favor Tardigrada as sister to Onychophora plus Arthropoda (the Lobopodia hypothesis). Our results illustrate the power of CAT-PMSF to model across-site compositionally heterogeneous datasets in the maximum likelihood framework and clarify the relationships between the Tardigrada and the Ecdysozoa.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11756273/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142881699","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Adaptation in the Alleyways: Candidate Genes Under Potential Selection in Urban Coyotes.","authors":"Samantha E S Kreling, Summer E Vance, Elizabeth J Carlen","doi":"10.1093/gbe/evae279","DOIUrl":"10.1093/gbe/evae279","url":null,"abstract":"<p><p>In the context of evolutionary time, cities are an extremely recent development. Although our understanding of how urbanization alters ecosystems is well developed, empirical work examining the consequences of urbanization on adaptive evolution remains limited. To facilitate future work, we offer candidate genes for one of the most prominent urban carnivores across North America. The coyote (Canis latrans) is a highly adaptable carnivore distributed throughout urban and nonurban regions in North America. As such, the coyote can serve as a blueprint for understanding the various pathways by which urbanization can influence the genomes of wildlife via comparisons along urban-rural gradients, as well as between metropolitan areas. Given the close evolutionary relationship between coyotes and domestic dogs, we leverage the well-annotated dog genome and highly conserved mammalian genes from model species to outline how urbanization may alter coyote genotypes and shape coyote phenotypes. We identify variables that may alter selection pressure for urban coyotes and offer suggestions of candidate genes to explore. Specifically, we focus on pathways related to diet, health, behavior, cognition, and reproduction. In a rapidly urbanizing world, understanding how species cope and adapt to anthropogenic change can facilitate the persistence of, and coexistence with, these species.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11775663/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142947726","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 and Recombination Fuel Ty4 Retrotransposon Evolution in Saccharomyces.","authors":"Jingxuan Chen, David J Garfinkel, Casey M Bergman","doi":"10.1093/gbe/evaf004","DOIUrl":"10.1093/gbe/evaf004","url":null,"abstract":"<p><p>Horizontal transposon transfer (HTT) plays an important role in the evolution of eukaryotic genomes; however, the detailed evolutionary history and impact of most HTT events remain to be elucidated. To better understand the process of HTT in closely related microbial eukaryotes, we studied Ty4 retrotransposon subfamily content and sequence evolution across the genus Saccharomyces using short- and long-read whole genome sequence data, including new PacBio genome assemblies for two Saccharomyces mikatae strains. We find evidence for multiple independent HTT events introducing the Tsu4 subfamily into specific lineages of Saccharomyces paradoxus, Saccharomyces cerevisiae, Saccharomyces eubayanus, Saccharomyces kudriavzevii and the ancestor of the S. mikatae/Saccharomyces jurei species pair. In both S. mikatae and S. kudriavzevii, we identified novel Ty4 clades that were independently generated through recombination between resident and horizontally transferred subfamilies. Our results reveal that recurrent HTT and lineage-specific extinction events lead to a complex pattern of Ty4 subfamily content across the genus Saccharomyces. Moreover, our results demonstrate how HTT can lead to coexistence of related retrotransposon subfamilies in the same genome that can fuel evolution of new retrotransposon clades via recombination.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11739139/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142947730","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":"Population Genomics of Japanese Macaques (Macaca fuscata): Insights Into Deep Population Divergence and Multiple Merging Histories.","authors":"Atsunori Higashino, Katsuki Nakamura, Naoki Osada","doi":"10.1093/gbe/evaf001","DOIUrl":"10.1093/gbe/evaf001","url":null,"abstract":"<p><p>The influence of long-term climatic changes such as glacial cycles on the history of living organisms has been a subject of research for decades, but the detailed population dynamics during the environmental fluctuations and their effects on genetic diversity and genetic load are not well understood on a genome-wide scale. The Japanese macaque (Macaca fuscata) is a unique primate adapted to the cold environments of the Japanese archipelago. Despite the past intensive research for the Japanese macaque population genetics, the genetic background of Japanese macaques at the whole-genome level has been limited to a few individuals, and the comprehensive demographic history and genetic differentiation of Japanese macaques have been underexplored. We conducted whole-genome sequencing of 64 Japanese macaque individuals from 5 different regions, revealing significant genetic differentiation and functional variant diversity across populations. In particular, Japanese macaques have low genetic diversity and harbor many shared and population-specific gene loss, which might contribute to population-specific phenotypes. Our estimation of population demography using phased haplotypes suggested that, after the strong population bottleneck shared among all populations around 400 to 500 kya, the divergence among populations initiated around 150 to 200 kya, but there has been the time with strong gene flow between some populations after the split, indicating multiple population split and merge events probably due to habitat fragmentation and fusion during glacial cycles. These findings not only present a complex population history of Japanese macaques but also enhance their value as research models, particularly in neuroscience and behavioral studies. This comprehensive genomic analysis sheds light on the adaptation and evolution of Japanese macaques, contributing valuable insights to both evolutionary biology and biomedical research.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"17 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11735745/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004434","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":"Evolutionary Genomics of Two Co-occurring Congeneric Fore Reef Coral Species on Guam (Mariana Islands).","authors":"Héctor Torrado, Dareon Rios, Karim Primov, David R Burdick, Bastian Bentlage, Sarah Lemer, David Combosch","doi":"10.1093/gbe/evae278","DOIUrl":"10.1093/gbe/evae278","url":null,"abstract":"<p><p>Population structure provides essential information for developing meaningful conservation plans. This is especially important in remote places, such as oceanic islands, where limited population sizes and genetic isolation can make populations more susceptible and self-dependent. In this study, we assess and compare the relatedness, population genetics and molecular ecology of two sympatric Acropora species, A. surculosa sensu Randall & Myers (1983) and A. cf. verweyi Veron & Wallace, 1984 around Guam, using genome-wide sequence data (ddRAD). We further contrast our findings with the results of a recent study on back reef A. cf. pulchra (Brook, 1891) to assess the impact of habitat, colony morphology, and phylogenetic relatedness on these basic population genetic characteristics and generate testable hypotheses for future studies. Both target species were found to have small effective population sizes, low levels of genetic diversity, and minimal population structure around Guam. Nonetheless, A. cf. verweyi had significantly higher levels of genetic diversity, some population structure as well as more clones, close relatives and putative loci under selection. Comparisons with A. cf. pulchra indicate a potentially significant impact by habitat on population structure and genetic diversity while colony morphology seems to significantly impact clonality. This study revealed significant differences in the basic population genetic makeup of two sympatric Acropora species on Guam. Our results suggest that colony morphology and habitat/ecology may have a significant impact on the population genetic makeup in reef corals, which could offer valuable insights for future management decisions in the absence of genetic data.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"17 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11746966/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004421","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 Has Led to the Loss of Claw Proteins in Snakes and Worm Lizards.","authors":"Karin Brigit Holthaus, Julia Steinbinder, Attila Placido Sachslehner, Leopold Eckhart","doi":"10.1093/gbe/evae274","DOIUrl":"10.1093/gbe/evae274","url":null,"abstract":"<p><p>The evolution of cornified skin appendages, such as hair, feathers, and claws, is closely linked to the evolution of proteins that establish the unique mechanical stability of these epithelial structures. We hypothesized that the evolution of the limbless body anatomy of the Florida worm lizard (Rhineura floridana) and the concomitant loss of claws had led to the degeneration of genes with claw-associated functions. To test this hypothesis, we investigated the evolution of three gene families implicated in epithelial cell architecture, namely type I keratins, type II keratins, and genes of the epidermal differentiation complex in R. floridana in comparison with other squamates. We report that the orthologs of mammalian hair and nail keratins have undergone pseudogenization in R. floridana. Likewise, the epidermal differentiation complex genes tentatively named EDYM1 and EDCCs have been lost in R. floridana. The aforementioned genes are conserved in various lizards with claws, but not in snakes. Proteomic analysis of the cornified claws of the bearded dragon (Pogona vitticeps) confirmed that type I and type II hair keratin homologs, EDYM1 and EDCCs, are protein components of claws in squamates. We conclude that the convergent evolution of a limbless body was associated with the convergent loss of claw keratins and differentiation genes in squamates.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11704414/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142853625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Novel High-Quality Amoeba Genomes Reveal Widespread Codon Usage Mismatch Between Giant Viruses and Their Hosts.","authors":"Anouk Willemsen, Alejandro Manzano-Marín, Matthias Horn","doi":"10.1093/gbe/evae271","DOIUrl":"10.1093/gbe/evae271","url":null,"abstract":"<p><p>The need for high-quality protist genomes has prevented in-depth computational and experimental studies of giant virus-host interactions. In addition, our current knowledge of host range is highly biased due to the few hosts used to isolate novel giant viruses. This study presents 6 high-quality amoeba genomes from known and potential giant virus hosts belonging to 2 distinct eukaryotic clades: Amoebozoa and Discoba. We employ their genomic data to investigate the predictability of giant virus host range. Using a combination of long- and short-read sequencing, we obtained highly contiguous and complete genomes of Acanthamoeba castellanii, Acanthamoeba griffini, Acanthamoeba terricola, Naegleria clarki, Vermamoeba vermiformis, and Willaertia magna, contributing to the collection of sequences for the eukaryotic tree of life. We found that the 6 amoebae have distinct codon usage patterns and that, contrary to other virus groups, giant viruses often have different and even opposite codon usage with their known hosts. Conversely, giant viruses with matching codon usage are frequently not known to infect or replicate in these hosts. Interestingly, analyses of integrated viral sequences in the amoeba host genomes reveal potential novel virus-host associations. Matching of codon usage preferences is often used to predict virus-host pairs. However, with the broad-scale analyses performed in this study, we demonstrate that codon usage alone appears to be a poor predictor of host range for giant viruses infecting amoeba. We discuss the potential strategies that giant viruses employ to ensure high viral fitness in nonmatching hosts. Moreover, this study emphasizes the need for more high-quality protist genomes. Finally, the amoeba genomes presented in this study set the stage for future experimental studies to better understand how giant viruses interact with different host species.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"17 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11702301/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142930151","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}