Genome Biology and Evolution最新文献

{"title":"Tandem Repeats Provide Evidence for Convergent Evolution to Similar Protein Structures.","authors":"Erik S Wright","doi":"10.1093/gbe/evaf013","DOIUrl":"10.1093/gbe/evaf013","url":null,"abstract":"<p><p>Homology is a key concept underpinning the comparison of sequences across organisms. Sequence-level homology is based on a statistical framework optimized over decades of work. Recently, computational protein structure prediction has enabled large-scale homology inference beyond the limits of accurate sequence alignment. In this regime, it is possible to observe nearly identical protein structures lacking detectable sequence similarity. In the absence of a robust statistical framework for structure comparison, it is largely assumed similar structures are homologous. However, it is conceivable that matching structures could arise through convergent evolution, resulting in analogous proteins without shared ancestry. Large databases of predicted structures offer a means of determining whether analogs are present among structure matches. Here, I find that a small subset (∼2.6%) of Foldseek clusters lack sequence-level support for homology, including ∼1% of strong structure matches with template modeling score ≥ 0.5. This result by itself does not imply these structure pairs are nonhomologous, since their sequences could have diverged beyond the limits of recognition. Yet, strong matches without sequence-level support for homology are enriched in structures with predicted repeats that could induce spurious matches. Some of these structural repeats are underpinned by sequence-level tandem repeats in both matching structures. I show that many of these tandem repeat units have genealogies inconsistent with their corresponding structures sharing a common ancestor, implying these highly similar structure pairs are analogous rather than homologous. This result suggests caution is warranted when inferring homology from structural resemblance alone in the absence of sequence-level support for homology.</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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143033079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"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":"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":"https://doi.org/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 (LPMO) 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":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ZW sex chromosome differentiation in paleognathous birds is associated with mitochondrial effective population size but not mitochondrial genome size or mutation rate.","authors":"Brooke Weinstein, Zongji Wang, Qi Zhou, Scott William Roy","doi":"10.1093/gbe/evaf005","DOIUrl":"https://doi.org/10.1093/gbe/evaf005","url":null,"abstract":"<p><p>Eukaryotic genome size varies considerably, even among closely related species. The causes of this variation are unclear, but weak selection against supposedly costly \"extra\" genomic sequences has been central to the debate for over 50 years. The mutational hazard hypothesis, which focuses on the increased mutation rate to null alleles in superfluous sequences, is particularly influential, though challenging to test. This study examines the sex chromosomes and mitochondrial genomes of 15 flightless or semi-flighted paleognathous bird species. In this clade, the non-recombining portion of the W chromosome has independently expanded stepwise in multiple lineages. Given the shared maternal inheritance of the W chromosome and mitochondria, theory predicts that mitochondrial effective population size (Ne) should decrease due to increased Hill-Robertson Interference in lineages with expanded non-recombining W regions. Our findings support the extent of the non-recombining W region with three indicators of reduced selective efficiency: (1) the ratio of non-synonymous to synonymous nucleotide changes in the mitochondrion, (2) the probability of radical amino acid changes, and (3) the number of ancient, W-linked genes lost through evolution. Next, we tested whether reduced Ne affects mitochondrial genome size, as predicted by weak selection against genome expansion. We find no support for a relationship between mitochondrial genome size and expanded non-recombining W regions, nor with increased mitochondrial mutation rates (predicted to modulate selective costs). These results highlight the utility of non-recombining regions and mitochondrial genomes for studying genome evolution and challenge the general idea of a negative relation between the efficacy of selection and genome size.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","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":"https://doi.org/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 1-2 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":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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}