학술논문
Reference Genome of the Northwestern Pond Turtle, Actinemys marmorata.
Document Type
Academic Journal
Author
Todd BD; Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, CA 95616, USA.; Jenkinson TS; Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, CA 95616, USA.; Escalona M; Department of Biomolecular Engineering, University of California-Santa Cruz, Santa Cruz, CA 95064, USA.; Beraut E; Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA.; Nguyen O; DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, USA.; Sahasrabudhe R; DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, USA.; Scott PA; Department of Life, Earth, and Environmental Sciences, West Texas A&M University, Canyon, TX 79016, USA.; Toffelmier E; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095-7239, USA.; La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095-7239, USA.; Wang IJ; Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA.; Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA.; Shaffer HB; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095-7239, USA.; La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095-7239, USA.
Source
Publisher: Oxford University Press For The American Genetic Association Country of Publication: United States NLM ID: 0375373 Publication Model: Print Cited Medium: Internet ISSN: 1465-7333 (Electronic) Linking ISSN: 00221503 NLM ISO Abbreviation: J Hered Subsets: MEDLINE
Subject
Language
English
Abstract
The northwestern pond turtle, Actinemys marmorata, and its recently recognized sister species, the southwestern pond turtle, A. pallida, are the sole aquatic testudines occurring over most of western North America and the only living representatives of the genus Actinemys. Although it historically ranged from Washington state through central California, USA, populations of the northwestern pond turtle have been in decline for decades and the species is afforded state-level protection across its range; it is currently being considered for protection under the US Endangered Species Act. Here, we report a new, chromosome-level assembly of A. marmorata as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises 198 scaffolds spanning 2,319,339,408 base pairs, has a contig N50 of 75 Mb, a scaffold N50 of 146Mb, and BUSCO complete score of 96.7%, making it the most complete testudine assembly of the 24 species from 13 families that are currently available. In combination with the A. pallida reference genome that is currently under construction through the CCGP, the A. marmorata genome will be a powerful tool for documenting landscape genomic diversity, the basis of adaptations to salt tolerance and thermal capacity, and hybridization dynamics between these recently diverged species.
(© The American Genetic Association. 2022.)
(© The American Genetic Association. 2022.)