Genome Biology and Evolution最新文献

{"title":"Comparing Small and Large Genomes Within Monogonont Rotifers.","authors":"Jonathon E Mohl, Patrick D Brown, Aaron J Robbins, Philip Lavretsky, Rick Hochberg, Robert L Wallace, Elizabeth J Walsh","doi":"10.1093/gbe/evaf041","DOIUrl":"10.1093/gbe/evaf041","url":null,"abstract":"<p><p>Genome size is an important correlate of many biological features including body size, metabolic rate, and developmental rate and can vary due to a variety of mechanisms, including incorporation of repetitive elements, duplication events, or reduction due to selective constraints. Our ability to understand the causes of genome size variation is hampered by limited sampling of many nonmodel taxa, including monogonont rotifers. Here, we used high-throughput Nanopore sequencing and flow cytometry to estimate genome sizes of nine species of monogonont rotifers representing seven families, including three representatives of Superorder Gnesiotrocha. We annotated the genomes and classified the repetitive elements. We also compared genome size with two biological features: body size and metabolic rate. Body sizes were obtained from the literature and our estimates. Oxygen consumption was used as a proxy for metabolic rate and was determined using a respirometer. We obtained similar genome size estimates from genome assemblies and flow cytometry, which were positively correlated with body size and size-specific respiration rate. Importantly, we determined that genome size variation is not due to increased numbers of repetitive elements or large regions of duplication. Instead, we observed higher numbers of predicted proteins as genome size increased, but currently many have no known function. Our results substantially expand the taxonomic scope of available genomes for Rotifera and provide opportunities for addressing genetic mechanisms underlying evolutionary and ecological processes in the phylum.</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/PMC11954553/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143572772","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: De Novo Genome Assembly Highlights the Role of Lineage-Specific Gene Duplications in the Evolution of Venom in Fea's Viper (Azemiops feae).","authors":"","doi":"10.1093/gbe/evaf033","DOIUrl":"10.1093/gbe/evaf033","url":null,"abstract":"","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"17 3","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11906395/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143624307","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 Haplotype-resolved Chromosome-scale Genome Assembly and Annotation for the Leafcutter Ant, Acromyrmex octospinosus.","authors":"Gaurav Agavekar, Yoshihiko Suzuki, Miyuki Suenaga, Miguel Pacheco-Leiva, Michael Hiller, Adrián A Pinto-Tomas, Eugene Myers, Evan P Economo","doi":"10.1093/gbe/evaf047","DOIUrl":"10.1093/gbe/evaf047","url":null,"abstract":"<p><p>Leafcutter ants are ecologically important insects that cultivate fungal gardens for sustenance, playing crucial roles in Neotropical ecosystems. Due to their ecological and evolutionary significance, high-quality genomic assemblies for the species in this fascinating group can provide a foundation for understanding their evolution. Here, we present a chromosome-scale, haplotype-resolved genome assembly for Acromyrmex octospinosus, a common leafcutter ant species broadly distributed in the Neotropics. Using PacBio HiFi sequencing (99x coverage) and Hi-C scaffolding (51x coverage), we generated both haplotype-resolved assemblies (312-314 Mb) and a haplotype-collapsed assembly (320 Mb), each containing 19 chromosomes. One hundred percent of the assembly is anchored to chromosome-level scaffolds, and the assemblies exhibit high contiguity (contig N50: 6.13-8.28 Mb), base accuracy (QV 61.5-61.8), and gene completeness (BUSCO scores: 98.3% to 98.4%). Synteny analysis between haplotypes revealed high concordance (96.0% to 96.8%) with minor structural variations, consistent with expectations for a diploid individual. Combining transcriptomic and homology-based protein evidence with ab initio predictions, we annotated 12,123 genes, achieving a near-complete BUSCO gene completeness of 99.6%. The high-quality assemblies significantly enhance the current genomic resources available for leafcutter ants, providing a foundation for future comparative genomic studies within Acromyrmex and across fungus-farming ants.</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/PMC11926981/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604679","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":"Hematophagy Generates a Convergent Genomic Signature in Mosquitoes and Sandflies.","authors":"Julien Devilliers, Ben Warren, Ezio Rosato, Charalambos P Kyriacou, Roberto Feuda","doi":"10.1093/gbe/evaf044","DOIUrl":"10.1093/gbe/evaf044","url":null,"abstract":"<p><p>Blood feeding (hematophagy) is widespread across Diptera (true flies), yet the underlying genetic basis remains poorly understood. Using phylogenomics, we show that four gene families associated with neuromodulation, immune responses, embryonic development, and iron metabolism have undergone independent expansions within mosquitoes and sandflies. Our findings illuminate the underlying genetic basis for blood-feeding adaptations in these important disease vectors.</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/PMC11925016/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604684","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 Proteinase PAPP-A has Deep Evolutionary Roots Outside of the IGF System.","authors":"Caroline M N Kjeldsen, Claus Oxvig","doi":"10.1093/gbe/evaf042","DOIUrl":"10.1093/gbe/evaf042","url":null,"abstract":"<p><p>The animal pappalysin metalloproteinases, PAPP-A and PAPP-A2, are highly specific regulatory enzymes of the insulin-like growth factor (IGF) system. Cleavage of their only known substrates, a subset of IGF binding proteins (IGFBPs), releases bioactive IGFI and IGFII, thus promoting IGF signaling. Stanniocalcin-1 and -2 (STC1 and STC2) are potent pappalysin inhibitors, completing the STC-PAPP-A-IGFBP-IGF axis. Utilizing homology searches and phylogenetic analyses, we examined the occurrence of pappalysins in the animal kingdom and their functional conservation. This revealed the extensive presence of pappalysins across metazoans, as well as the presence of 3 pappalysins: PAPP-A, PAPP-A2, and a third group of invertebrate pappalysins, which we name invertebrate PAPP-A (invPAPP-A). We show that PAPP-A and PAPP-A2 arose by duplication during early vertebrate evolution. Despite significant evolutionary distance, the domain architecture of the metazoan pappalysins is completely conserved, and several functional domains and motifs are highly conserved across all pappalysins. However, invPAPP-A exists outside the context of IGFBPs, suggesting that the animal pappalysins may have substrates beyond the IGFBPs for PAPP-A and PAPP-A2 that remain to be discovered. Since PAPP-A is an emerging drug target, it is important to understand potential involvement in regulatory systems other than the IGF system, which might be affected upon targeting of PAPP-A.</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/PMC11925022/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143624306","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":"Multiple Domestication Centers of the Indian Pig Population.","authors":"Shailesh Desai, Prajjval Pratap Singh, Rudra Kumar Pandey, Rahul Kumar Mishra, Akhilesh Kumar Chaubey, Ajit Kumar, Sachin Kr Tiwary, Sandeep Kumar Gupta, Alessandro Achilli, Nicola Rambaldi Migliore, Gyaneshwer Chaubey","doi":"10.1093/gbe/evaf030","DOIUrl":"10.1093/gbe/evaf030","url":null,"abstract":"<p><p>The domestication of animals is a major milestone in human history and has been studied in various fields. Pig domestication, in particular, has been widely studied, and it is believed that India is one of at least six domestication centers. However, there is a lack of systematic studies using high-resolution genetic markers, including complete mitogenomes, to investigate the domestication and genetic roots of pigs in India. In the present study, we investigated the origin and evolution of Indian pigs using mitochondrial genetic data to complement archaeological data sets. The phylogenetic status of Indian pig breeds was determined by analyzing all available mitochondrial data, incorporating a global data set of 239 mitogenomes. The Bayesian and maximum likelihood tree analyses unveiled at least eight haplogroups diverging from three main branches, two of which are geographically restricted to India. We propose that the North Indian domestic haplogroup might represent an independent in situ domestication event in North India, probably dating before ∼5,000 YBP. An additional North East Indian domestic haplogroup is nested within a widespread Asian clade that also includes Indian mitogenomes from the Andaman and Nicobar Islands that diverged more recently from distinct East and Southeast Asian roots. In conclusion, we propose that North Indian farmers could have been responsible for the independent domestication of local wild boars giving rise to the current domestic lineage identified in North India. At least one additional domestic lineage arrived in India more recently and remained mainly localized in the northeast. Domestic mitogenomes from the Indian islands show a notable connection with pig populations from Vietnam, and their arrival might be related to Austroasiatic-speaking human populations. Overall, this study provides valuable insights into the complex dynamics of pig domestication in India.</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/PMC11886846/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143491577","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":"Pervasive Conservation of Intron Number and Other Genetic Elements Revealed by a Chromosome-level Genome Assembly of the Hyper-polymorphic Nematode Caenorhabditis brenneri.","authors":"Anastasia A Teterina, John H Willis, Charles F Baer, Patrick C Phillips","doi":"10.1093/gbe/evaf037","DOIUrl":"10.1093/gbe/evaf037","url":null,"abstract":"<p><p>With within-species genetic diversity estimates that span the gamut of that seen across the entirety of animals, the Caenorhabditis genus of nematodes holds unique potential to provide insights into how population size and reproductive strategies influence gene and genome organization and evolution. Our study focuses on Caenorhabditis brenneri, currently known as one of the most genetically diverse nematodes within its genus and, notably, across Metazoa. Here, we present a high-quality, gapless genome assembly and annotation for C. brenneri, revealing a common nematode chromosome arrangement characterized by gene-dense central regions and repeat-rich arms. A comparison of C. brenneri with other nematodes from the \"Elegans\" group revealed conserved macrosynteny but a lack of microsynteny, characterized by frequent rearrangements and low correlation of orthogroup size, indicative of high rates of gene turnover, consistent with previous studies. We also assessed genome organization within corresponding syntenic blocks in selfing and outcrossing species, affirming that selfing species predominantly experience loss of both genes and intergenic DNA. A comparison of gene structures revealed a strikingly small number of shared introns across species, yet consistent distributions of intron number and length, regardless of population size or reproductive mode, suggesting that their evolutionary dynamics are primarily reflective of functional constraints. Our study provides valuable insights into genome evolution and expands the nematode genome resources with the highly genetically diverse C. brenneri, facilitating research into various aspects of nematode biology and evolutionary processes.</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/PMC11925023/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143556678","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":"Reconstruction of Segmental Duplication Rates and Associated Genomic Features by Network Analysis.","authors":"Eldar T Abdullaev, Dinesh A Haridoss, Peter F Arndt","doi":"10.1093/gbe/evaf011","DOIUrl":"10.1093/gbe/evaf011","url":null,"abstract":"<p><p>Segmental duplications are long genomic duplications that are fixed in a genome. Segmental duplications play an important evolutionary role because entire genes can be duplicated along with regulatory sequences. The ancestral segmental duplications of the human lineage gave rise to genes that are involved in the development of the human brain and provided sites for further genomic rearrangements. While some duplicated loci have been extensively studied, the universal principles and biological factors underlying the spread of segmental duplications remain unclear. Here, we represent segmental duplications in a network, with edges corresponding to duplication events and nodes corresponding to affected genomic sites. This representation allowed us to estimate how many duplications had occurred at each locus, and thereby enabling the prediction of genomic features associated with increased duplication rates. Our comprehensive study of genomic features associated with duplications and those associated with increased duplication rates allowed us to identify several biological factors affecting a segmental duplication process. In our study, we describe genomic features associated with increased duplication rates, three signatures of the duplication process and associations of segmental duplications with different classes of high-copy repeats. Furthermore our method is readily implemented and can easily be applied to segmental duplications of other genomes to build a network of segmental duplications or to predict real duplication events.</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/PMC11925013/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143467779","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":"Analyses of Transposable Elements in Arbuscular Mycorrhizal Fungi Support Evolutionary Parallels With Filamentous Plant Pathogens.","authors":"Jordana I N Oliveira, Catrina Lane, Ken Mugambi, Gokalp Yildirir, Ariane M Nicol, Vasilis Kokkoris, Claudia Banchini, Kasia Dadej, Jeremy Dettman, Franck Stefani, Nicolas Corradi","doi":"10.1093/gbe/evaf038","DOIUrl":"10.1093/gbe/evaf038","url":null,"abstract":"<p><p>Transposable elements are repetitive DNA sequences that excise or create copies that are inserted elsewhere in the genome. Their expansion shapes genome variability and evolution by impacting gene expression and rearrangement rates. Arbuscular mycorrhizal fungi are beneficial plant symbionts with large, transposable element-rich genomes, and recent findings showed these elements vary significantly in abundance, evolution, and regulation among model strains. Here, we aimed to obtain a more comprehensive understanding of transposable element function and evolution in arbuscular mycorrhizal fungi by investigating assembled genomes from representatives of all known families. We uncovered multiple, family-specific bursts of insertions in different species, indicating variable past and ongoing transposable element activity contributing to the diversification of arbuscular mycorrhizal fungi lineages. We also found that transposable elements are preferentially located within and around candidate effectors/secreted proteins, as well as in proximity to promoters. Altogether, these findings support the role of transposable elements in promoting the diversity in proteins involved in molecular dialogs with hosts and, more generally, in driving gene regulation. The mechanisms of transposable element evolution we observed in these prominent plant symbionts bear striking similarities to those of many filamentous plant pathogens.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"17 3","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11952901/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729757","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":"An Extensive Survey of Vertebrate-specific, Nonvisual Opsins Identifies a Novel Subfamily, Q113-Bistable Opsin.","authors":"Fuki Gyoja, Keita Sato, Takahiro Yamashita, Takehiro G Kusakabe","doi":"10.1093/gbe/evaf032","DOIUrl":"10.1093/gbe/evaf032","url":null,"abstract":"<p><p>A group of nonvisual opsins specific to vertebrates is essential to understand evolution of lateral eyes, one of the most prominent innovations in this lineage. Nevertheless, our knowledge of their evolutionary history remains limited. To develop an integrated view of their evolution, we surveyed these non-visual opsins (VA opsin, pinopsin, parapinopsin, parietopsin, and parapinopsin-like) in 451 vertebrate genomes. Through extensive manual curation, we completed a high-quality catalog. We could not find them in 202 mammals, supporting previous reports of their loss. VA opsins are highly conserved among nonmammals. In contrast, other opsin subfamilies experienced more dynamic molecular evolution with many secondary losses. In addition, we found a previously unreported opsin subfamily that we named Q113-Bistable (QB) opsin. We found its orthologs only in several lizards and the tuatara. Nevertheless, QB opsin pseudogenes were discovered in diverse taxa, including ray-finned fishes, indicating its ancient origin. QB opsin, parapinopsin, and parietopsin are extremely prone to be lost in the course of evolution, and loss events involving these opsins seem to occur concomitantly. Furthermore, we demonstrated the spectral properties of QB opsin as a UV-sensitive, bistable photo-pigment. This study provides the first integrated view of the entire evolutionary history of this group of opsins.</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/PMC11893379/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143556625","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}