Roberto Márquez, Denis Jacob Machado, Reyhaneh Nouri, Kerry L Gendreau, Daniel Janies, Ralph A Saporito, Marcus R Kronforst, Taran Grant
{"title":"箭毒蛙的基因组组装草图。","authors":"Roberto Márquez, Denis Jacob Machado, Reyhaneh Nouri, Kerry L Gendreau, Daniel Janies, Ralph A Saporito, Marcus R Kronforst, Taran Grant","doi":"10.46471/gigabyte.157","DOIUrl":null,"url":null,"abstract":"<p><p>Dendrobatid poison frogs have become well established as model systems in several fields of biology. Nevertheless, the development of molecular and genetic resources for these frogs has been hindered by their large, highly repetitive genomes, which have proven difficult to assemble. Here we present a draft assembly for <i>Phyllobates terribilis</i> (12.6 Gb), generated using a combination of sequencing platforms and bioinformatic approaches. Similar to other poison frog sequencing efforts, we recovered a highly fragmented assembly, likely due to the genome's large size and very high repeat content, which we estimated to be ≍88%. Despite the assembly's low contiguity, we were able to annotate multiple members of three gene sets of interest (voltage-gated sodium channels and <i>Notch</i> and <i>Wnt</i> signaling pathways), demonstrating the usefulness of our assembly to the amphibian research community.</p>","PeriodicalId":73157,"journal":{"name":"GigaByte (Hong Kong, China)","volume":"2025 ","pages":"gigabyte157"},"PeriodicalIF":0.0000,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12208295/pdf/","citationCount":"0","resultStr":"{\"title\":\"A draft genome assembly for the dart-poison frog <i>Phyllobates terribilis</i>.\",\"authors\":\"Roberto Márquez, Denis Jacob Machado, Reyhaneh Nouri, Kerry L Gendreau, Daniel Janies, Ralph A Saporito, Marcus R Kronforst, Taran Grant\",\"doi\":\"10.46471/gigabyte.157\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Dendrobatid poison frogs have become well established as model systems in several fields of biology. Nevertheless, the development of molecular and genetic resources for these frogs has been hindered by their large, highly repetitive genomes, which have proven difficult to assemble. Here we present a draft assembly for <i>Phyllobates terribilis</i> (12.6 Gb), generated using a combination of sequencing platforms and bioinformatic approaches. Similar to other poison frog sequencing efforts, we recovered a highly fragmented assembly, likely due to the genome's large size and very high repeat content, which we estimated to be ≍88%. Despite the assembly's low contiguity, we were able to annotate multiple members of three gene sets of interest (voltage-gated sodium channels and <i>Notch</i> and <i>Wnt</i> signaling pathways), demonstrating the usefulness of our assembly to the amphibian research community.</p>\",\"PeriodicalId\":73157,\"journal\":{\"name\":\"GigaByte (Hong Kong, China)\",\"volume\":\"2025 \",\"pages\":\"gigabyte157\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2025-06-20\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12208295/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"GigaByte (Hong Kong, China)\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.46471/gigabyte.157\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2025/1/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"GigaByte (Hong Kong, China)","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.46471/gigabyte.157","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/1/1 0:00:00","PubModel":"eCollection","JCR":"","JCRName":"","Score":null,"Total":0}
A draft genome assembly for the dart-poison frog Phyllobates terribilis.
Dendrobatid poison frogs have become well established as model systems in several fields of biology. Nevertheless, the development of molecular and genetic resources for these frogs has been hindered by their large, highly repetitive genomes, which have proven difficult to assemble. Here we present a draft assembly for Phyllobates terribilis (12.6 Gb), generated using a combination of sequencing platforms and bioinformatic approaches. Similar to other poison frog sequencing efforts, we recovered a highly fragmented assembly, likely due to the genome's large size and very high repeat content, which we estimated to be ≍88%. Despite the assembly's low contiguity, we were able to annotate multiple members of three gene sets of interest (voltage-gated sodium channels and Notch and Wnt signaling pathways), demonstrating the usefulness of our assembly to the amphibian research community.