Genome Biology and Evolution最新文献

{"title":"The first de novo HiFi genome assemblies for three clownfish-hosting sea anemone species (Anthozoa: Actiniaria).","authors":"Aurélien De Jode, Benjamin M Titus","doi":"10.1093/gbe/evaf064","DOIUrl":"https://doi.org/10.1093/gbe/evaf064","url":null,"abstract":"<p><p>The symbiosis between clownfish and giant tropical sea anemones (Order Actiniaria) is one of the most iconic on the planet. Distributed on tropical reefs, 28 species of clownfishes form obligate mutualistic relationships with 10 nominal species of venomous sea anemones. Our understanding of the symbiosis is limited by the fact that most research has been focused on the clownfishes. Chromosome scale reference genomes are available for all clownfish species, yet only short reads based reference genomes are available for five speciesof host sea anemones. Recent studies have shown that the clownfish-hosting sea anemones belong to three distinct clades of sea anemones that have evolved symbiosis with clownfishes independently. Here we present the first high quality long read assemblies for three species of clownfish-hosting sea anemones belonging to each of these clades: Entacmaea quadricolor, Stichodactyla haddoni, Radianthus doreensis. PacBio HiFi sequencing yielded 1,597,562, 3,101,773, and 1,918,148 million reads for E. quadricolor, S. haddoni, and R. doreensis, respectively. All three assemblies were highly contiguous and complete with N50 values above 4Mb and BUSCO completeness above 95% on the Metazoa dataset. Genome structural annotation with BRAKER3 predicted 20,454, 18,948 and 17,056 protein coding genes in E. quadricolor, S. haddoni and R. doreeensis genome, respectively. These new resources will form the basis of comparative genomic analyses that will allow us to deepen our understanding of this mutualism from the host perspective.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811178","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":"Population genomics of Aspergillus sojae is shaped by the food environment.","authors":"Kimberly L Acevedo, Elizabeth Eaton, Julia Leite, Shu Zhao, Katherine Chacon-Vargas, Colin M McCarthy, Dasol Choi, Samuel O'Donnell, Emile Gluck-Thaler, Jae-Hyuk Yu, John G Gibbons","doi":"10.1093/gbe/evaf067","DOIUrl":"https://doi.org/10.1093/gbe/evaf067","url":null,"abstract":"<p><p>Traditional fermented foods often contain specialized microorganisms adapted to their unique environments. For example, the filamentous mold Aspergillus oryzae, used in saké fermentation, has evolved to thrive in starch-rich conditions compared to its wild ancestor, Aspergillus flavus. Similarly, Aspergillus sojae, used in soybean-based fermentations like miso and shochu, is hypothesized to have been domesticated from Aspergillus parasiticus. Here, we examined the effects of long-term A. sojae use in soybean fermentation on population structure, genome variation, and phenotypic traits. We analyzed 17 A. sojae and 24 A. parasiticus genomes (23 of which were sequenced for this study), alongside phenotypic traits of 9 isolates. A. sojae formed a distinct, low-diversity population, suggesting a recent clonal expansion. Interestingly, a population of A. parasiticus was more closely related to A. sojae than other A. parasiticus populations. Genome comparisons revealed loss-of-function mutations in A. sojae, notably in biosynthetic gene clusters encoding secondary metabolites, including the aflatoxin cluster. Interestingly though, A. sojae harbored a partial duplication of a siderophore biosynthetic cluster. Phenotypic assays showed A. sojae lacked aflatoxin production, while it was variable in A. parasiticus isolates. Additionally, certain A. sojae strains exhibited larger colony diameters under miso-like salt conditions. These findings support the hypothesis that A. parasiticus is the progenitor of A. sojae and that domestication significantly reduced genetic diversity. Future research should explore how wild and food-associated strains influence sensory attributes and microbial community dynamics in fermented soy products.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802888","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-level assemblies of the allohexaploid genomes of Conyza sumatrensis and Conyza bonariensis.","authors":"Anthony Côrtes Gomes, Jacob Montgomery, André Lucas Simões Araujo, Sarah Morran, Luan Cutti, Eric Patterson, Sofia Marques Hill, Maor Matzrafi, Anil Shrestha, Aldo Merotto, Fatemeh Abdollahi, David R Nelson, Victor Llaca, Kevin Fengler, Camila Ferreira de Pinho, Todd A Gaines","doi":"10.1093/gbe/evaf065","DOIUrl":"https://doi.org/10.1093/gbe/evaf065","url":null,"abstract":"<p><p>Conyza sumatrensis and Conyza bonariensis are two important hexaploid weed species that impact crop production systems across the globe. Here, we report reference genome assemblies for both species. The sequenced accession of C. sumatrensis is resistant to multiple herbicides and was collected from the state of Paraná in Brazil, while the accession of C. bonariensis was collected from California, USA. Genomic long read data was used along with optical mapping data to assemble the C. sumatrensis genome to a single haplome at chromosome-level contiguity. The same approach was used along with chromatin contact mapping data to phase the haplotypes of C. bonariensis and generate two chromosome-level haplome assemblies. Subgenome specific sequences were identified and used to classify the three subgenomes within each assembly. The assemblies are highly complete based on the presence of conserved single copy orthologs and telomeres, and the size of these assemblies agree with previous flow cytometry estimates. Full length transcript sequencing along with gene models from other Asteraceae members were used to predict gene models within each assembly. The genomic resources reported here will be useful for investigations into evolutionary and ecological questions around weed invasion and management for these two species.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143779422","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":"Demographic history, genetic load, and the efficacy of selection in the globally invasive mosquito Aedes aegypti.","authors":"Tyler V Kent, Daniel R Schrider, Daniel R Matute","doi":"10.1093/gbe/evaf066","DOIUrl":"https://doi.org/10.1093/gbe/evaf066","url":null,"abstract":"<p><p>Aedes aegypti is the main vector species of yellow fever, dengue, Zika and chikungunya. The species is originally from Africa but has experienced a spectacular expansion in its geographic range to a large swath of the world, the demographic effects of which have remained largely understudied. In this report, we examine whole-genome sequences from 6 countries in Africa, North America, and South America to investigate the demographic history of the spread of Ae. aegypti into the Americas and its impact on genomic diversity and deleterious genetic load. In the Americas, we observe patterns of strong population structure consistent with relatively low (but probably non-zero) levels of gene flow but occasional long-range dispersal and/or recolonization events. We also find evidence that the colonization of the Americas has resulted in introduction bottlenecks. However, while each sampling location shows evidence of a past population contraction and subsequent recovery, our results suggest that the bottlenecks in America have led to a reduction in genetic diversity of only ∼35% relative to African populations, and the American samples have retained high levels of genetic diversity (expected heterozygosity of ∼0.02 at synonymous sites). We additionally find that American populations of aegypti have experienced only a minor reduction in the efficacy of selection, with evidence for both an accumulation of deleterious alleles and some purging of strongly deleterious alleles. These results exemplify how an invasive species can expand its range with remarkable genetic resilience in the face of strong eradication pressure.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143779758","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":"A Class of Allopolyploidy Showing High Duplicate Retention and Continued Homoeologous Exchanges.","authors":"Abbey Coppage, Esha Bhatnagar, Mitali Joshi, Mustafa Siddiqui, Logan McRae, Gavin C Conant","doi":"10.1093/gbe/evaf054","DOIUrl":"10.1093/gbe/evaf054","url":null,"abstract":"<p><p>We describe four ancient polyploidy events where the descendant taxa retain many more duplicated gene copies than has been seen in other paleopolyploidies of similar ages. Using POInT (the Polyploidy Orthology Inference Tool), we modeled the evolution of these four events, showing that they do not represent recent independent polyploidies despite the rarity of shared gene losses. We find that these events have elevated rates of interlocus gene conversion and that these gene conversion events are spatially clustered in the genomes. Regions of gene conversion also show very low synonymous divergence between the corresponding paralogous genes. We suggest that these genomes have experienced a delay in the return to a diploid state after their polyploidies. Under this hypothesis, homoeologous exchanges between the duplicated regions created by the polyploidy persist to this day, explaining the high rates of duplicate retention. Genomes with these characteristics arguably represent a new class of paleopolyploid taxa because they possess evolutionary patterns distinct from the more common and well-known paradigm of the rapid loss of many of the duplicated pairs created by polyploidy.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11965797/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656807","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 History Across Timescales in an Urban Archipelago.","authors":"Emma K Howell, Lauren E Nolfo-Clements, Bret A Payseur","doi":"10.1093/gbe/evaf048","DOIUrl":"10.1093/gbe/evaf048","url":null,"abstract":"<p><p>Contemporary patterns of genetic variation reflect the cumulative history of a population. Population splitting, migration, and changes in population size leave genomic signals that enable their characterization. Existing methods aimed at reconstructing these features of demographic history are often restricted in their temporal resolution, leaving gaps about how basic evolutionary parameters change over time. To illustrate the prospects for extracting insights about dynamic population histories, we turn to a system that has undergone dramatic changes on both geological and contemporary timescales-an urbanized, near-shore archipelago. Using whole genome sequences, we employed both common and novel summaries of variation to infer the demographic history of three populations of endemic white-footed mice (Peromyscus leucopus) in Massachusetts' Boston Harbor. We find informative contrasts among the inferences drawn from these distinct patterns of diversity. While demographic models that fit the joint site frequency spectrum (jSFS) coincide with the known geological history of the Boston Harbor, patterns of linkage disequilibrium reveal collapses in population size on contemporary timescales that are not recovered by our jSFS-derived models. Historical migration between populations is also absent from best-fitting models for the jSFS, but rare variants show unusual clustering along the genome within individual mice, a novel pattern that is reproduced by simulations of recent migration. Together, our findings indicate that these urban archipelago populations have been shaped by both ancient geological processes and recent human influence. More broadly, our study demonstrates that the temporal resolution of demographic history can be extended by examining multiple facets of genomic variation.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11968337/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143663357","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 Bacterial Operons into Eukaryote Genomes.","authors":"Roman Kogay, Yuri I Wolf, Eugene V Koonin","doi":"10.1093/gbe/evaf055","DOIUrl":"10.1093/gbe/evaf055","url":null,"abstract":"<p><p>In prokaryotes, functionally linked genes are typically clustered into operons, which are transcribed into a single mRNA, providing for the coregulation of the production of the respective proteins, whereas eukaryotes generally lack operons. We explored the possibility that some prokaryotic operons persist in eukaryotic genomes after horizontal gene transfer (HGT) from bacteria. Extensive comparative analysis of prokaryote and eukaryote genomes revealed 33 gene pairs originating from bacterial operons, mostly encoding enzymes of the same metabolic pathways, and represented in distinct clades of fungi or amoebozoa. This amount of HGT is about an order of magnitude less than that observed for the respective individual genes. These operon fragments appear to be relatively recent acquisitions as indicated by their narrow phylogenetic spread and low intron density. In 20 of the 33 horizontally acquired operonic gene pairs, the genes are fused in the respective group of eukaryotes so that the encoded proteins become domains of a multifunctional protein ensuring coregulation and correct stoichiometry. We hypothesize that bacterial operons acquired via HGT initially persist in eukaryotic genomes under a neutral evolution regime and subsequently are either disrupted by genome rearrangement or undergo gene fusion which is then maintained by selection.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11965790/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143663351","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: Ancestral Sequence Reconstruction as a Tool to Detect and Study De Novo Gene Emergence.","authors":"","doi":"10.1093/gbe/evaf059","DOIUrl":"10.1093/gbe/evaf059","url":null,"abstract":"","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"17 4","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11965980/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143772016","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":"Genes Encoding Intracellular Signaling Proteins in Animals Originated Along with Metazoa and Chordata: Chance or Necessity?","authors":"Floriane Picolo, Jérémie Bardin, Michel Laurin, Benoît Piégu, Philippe Monget","doi":"10.1093/gbe/evaf034","DOIUrl":"https://doi.org/10.1093/gbe/evaf034","url":null,"abstract":"<p><p>In this work, we investigate whether the construction of signaling pathways during evolution follows a deterministic law through a study of the eventual link between age of appearance in the tree of life and position in the signaling pathway of genes involved in these pathways. We use the 47 human signaling pathways described in the Kyoto Encyclopedia of Genes and Genomes and investigate the orthologs of these genes in 315 animal species plus a yeast taxon, representing 15 large clades. Many genes appear on two key branches: those between the last common ancestor of Opisthokonta and Metazoa and between Deuterostomia and Chordata. We look for a link between the age of appearance of an upstream A gene and that of its downstream B partner. We observe that for all the interactions of two partners, only 20.6% of the corresponding genes arose simultaneously in the tree of life, 40.7% being called \"backward\" (i.e. B appearing before A) and 38.7% \"forward\" (A appearing before B). For 16 of the 47 pathways, there is a positive correlation between the age rank difference between interacting partner genes and the position of the corresponding proteins in the pathway: the more upstream a protein is involved in the pathway, the greater the rank difference is (the correlation, positive or negative, is not significant for 30 pathways). For the sole insulin signaling pathway, this correlation is negative. Moreover, by permutation test, we find that 14 of the 47 observed pathway contained larger modules (subset respecting a homogeneous appearance pattern) than expected by chance alone. Finally, for 20 of the 47 pathways, the construction scenario appears to be random, as these pathways do not validate any of our statistical tests (permutation tests on interaction direction and module sizes as well as correlation test on pathway position and age rank). Given that only 14.9% of the tests are significant and that significant effects are different among pathways, we conclude that there is no deterministic rule in the establishment of the pathways herein studied or that the patterns have been obscured by subsequent transformations.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"17 4","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811179","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":"Genomic Insights into Fertilization: Tracing PLCZ1 Orthologs Across Amphibian Lineages.","authors":"Rachel E Bainbridge, Joel C Rosenbaum, Paushaly Sau, Anne E Carlson","doi":"10.1093/gbe/evaf052","DOIUrl":"10.1093/gbe/evaf052","url":null,"abstract":"<p><p>Fertilization triggers a cascade of events, including a rise in egg cytosolic calcium that marks the onset of embryonic development. In mammals and birds, this critical process is mediated by the sperm-derived phospholipase C zeta (PLCζ), which is pivotal in releasing calcium from the endoplasmic reticulum in the egg and initiating embryonic activation. Intriguingly, Xenopus laevis, a key model organism in reproductive biology, lacks an annotated PLCZ1 gene, prompting questions about its calcium release mechanism during fertilization. Using bioinformatics and RNA sequencing of adult X. laevis testes, we investigated the presence of a PLCZ1 ortholog in amphibians. While we identified PLCZ1 homologs in 25 amphibian species, including 14 previously uncharacterized orthologs, we found none in X. laevis or its close relative, Xenopus tropicalis. Additionally, we found no compensatory expression of other PLC isoforms in these species. Synteny analysis revealed a PLCZ1 deletion in species within the Pipidae family and another intriguing deletion of potential sperm factor PLCD4 in the mountain slow frog, Nanorana parkeri. Our findings indicate that the calcium release mechanism in frog eggs involves a signaling pathway distinct from the PLCζ-mediated process observed in mammals.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11965574/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143663308","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}