Krzysztof M Kozak, Merly Escalona, Noravit Chumchim, Colin Fairbairn, Mohan P A Marimuthu, Oanh Nguyen, Ruta Sahasrabudhe, William Seligmann, Chris Conroy, James L Patton, Rauri C K Bowie, Michael W Nachman
{"title":"一个高度连续的口袋鼠长颚鼠基因组组装。","authors":"Krzysztof M Kozak, Merly Escalona, Noravit Chumchim, Colin Fairbairn, Mohan P A Marimuthu, Oanh Nguyen, Ruta Sahasrabudhe, William Seligmann, Chris Conroy, James L Patton, Rauri C K Bowie, Michael W Nachman","doi":"10.1093/jhered/esad060","DOIUrl":null,"url":null,"abstract":"<p><p>The little pocket mouse, Perognathus longimembris, and its nine congeners are small heteromyid rodents found in arid and seasonally arid regions of Western North America. The genus is characterized by behavioral and physiological adaptations to dry and often harsh environments, including nocturnality, seasonal torpor, food caching, enhanced osmoregulation, and a well-developed sense of hearing. Here we present a genome assembly of Perognathus longimembris longimembris generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing as part of the California Conservation Genomics Project. The assembly has a length of 2.35 Gb, contig N50 of 11.6 Mb, scaffold N50 of 73.2 Mb, and includes 93.8% of the BUSCO Glires genes. Interspersed repetitive elements constitute 41.2% of the genome. A comparison with the highly endangered Pacific pocket mouse, P. l. pacificus, reveals broad synteny. These new resources will enable studies of local adaptation, genetic diversity, and conservation of threatened taxa.</p>","PeriodicalId":54811,"journal":{"name":"Journal of Heredity","volume":null,"pages":null},"PeriodicalIF":3.0000,"publicationDate":"2024-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10838119/pdf/","citationCount":"0","resultStr":"{\"title\":\"A highly contiguous genome assembly for the pocket mouse Perognathus longimembris longimembris.\",\"authors\":\"Krzysztof M Kozak, Merly Escalona, Noravit Chumchim, Colin Fairbairn, Mohan P A Marimuthu, Oanh Nguyen, Ruta Sahasrabudhe, William Seligmann, Chris Conroy, James L Patton, Rauri C K Bowie, Michael W Nachman\",\"doi\":\"10.1093/jhered/esad060\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>The little pocket mouse, Perognathus longimembris, and its nine congeners are small heteromyid rodents found in arid and seasonally arid regions of Western North America. The genus is characterized by behavioral and physiological adaptations to dry and often harsh environments, including nocturnality, seasonal torpor, food caching, enhanced osmoregulation, and a well-developed sense of hearing. Here we present a genome assembly of Perognathus longimembris longimembris generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing as part of the California Conservation Genomics Project. The assembly has a length of 2.35 Gb, contig N50 of 11.6 Mb, scaffold N50 of 73.2 Mb, and includes 93.8% of the BUSCO Glires genes. Interspersed repetitive elements constitute 41.2% of the genome. A comparison with the highly endangered Pacific pocket mouse, P. l. pacificus, reveals broad synteny. These new resources will enable studies of local adaptation, genetic diversity, and conservation of threatened taxa.</p>\",\"PeriodicalId\":54811,\"journal\":{\"name\":\"Journal of Heredity\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":3.0000,\"publicationDate\":\"2024-02-03\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10838119/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Heredity\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1093/jhered/esad060\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"EVOLUTIONARY BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Heredity","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/jhered/esad060","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"EVOLUTIONARY BIOLOGY","Score":null,"Total":0}
A highly contiguous genome assembly for the pocket mouse Perognathus longimembris longimembris.
The little pocket mouse, Perognathus longimembris, and its nine congeners are small heteromyid rodents found in arid and seasonally arid regions of Western North America. The genus is characterized by behavioral and physiological adaptations to dry and often harsh environments, including nocturnality, seasonal torpor, food caching, enhanced osmoregulation, and a well-developed sense of hearing. Here we present a genome assembly of Perognathus longimembris longimembris generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing as part of the California Conservation Genomics Project. The assembly has a length of 2.35 Gb, contig N50 of 11.6 Mb, scaffold N50 of 73.2 Mb, and includes 93.8% of the BUSCO Glires genes. Interspersed repetitive elements constitute 41.2% of the genome. A comparison with the highly endangered Pacific pocket mouse, P. l. pacificus, reveals broad synteny. These new resources will enable studies of local adaptation, genetic diversity, and conservation of threatened taxa.
期刊介绍：
Over the last 100 years, the Journal of Heredity has established and maintained a tradition of scholarly excellence in the publication of genetics research. Virtually every major figure in the field has contributed to the journal.
Established in 1903, Journal of Heredity covers organismal genetics across a wide range of disciplines and taxa. Articles include such rapidly advancing fields as conservation genetics of endangered species, population structure and phylogeography, molecular evolution and speciation, molecular genetics of disease resistance in plants and animals, genetic biodiversity and relevant computer programs.
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