The Agassiz’s desert tortoise genome provides a resource for the conservation of a threatened species
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Tollis, MarcDeNardo, Dale F.
Cornelius, John A.
Dolby, Greer A.
Edwards, Taylor
Henen, Brian T.
Karl, Alice E.
Murphy, Robert W.
Kusumi, Kenro

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Univ Arizona, Genet CoreIssue Date
2017-05-31
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PUBLIC LIBRARY SCIENCECitation
The Agassiz’s desert tortoise genome provides a resource for the conservation of a threatened species 2017, 12 (5):e0177708 PLOS ONEJournal
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This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.Collection Information
This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.Abstract
Agassiz's desert tortoise (Gopherus agassizii) is a long-lived species native to the Mojave Desert and is listed as threatened under the US Endangered Species Act. To aid conservation efforts for preserving the genetic diversity of this species, we generated a whole genome reference sequence with an annotation based on deep transcriptome sequences of adult skeletal muscle, lung, brain, and blood. The draft genome assembly for G. agassizii has a scaffold N50 length of 252 kbp and a total length of 2.4 Gbp. Genome annotation reveals 20,172 protein-coding genes in the G. agassizii assembly, and that gene structure is more similar to chicken than other turtles. We provide a series of comparative analyses demonstrating (1) that turtles are among the slowest-evolving genome-enabled reptiles, (2) amino acid changes in genes controlling desert tortoise traits such as shell development, longevity and osmoregulation, and (3) fixed variants across the Gopherus species complex in genes related to desert adaptations, including circadian rhythm and innate immune response. This G. agassizii genome reference and annotation is the first such resource for any tortoise, and will serve as a foundation for future analysis of the genetic basis of adaptations to the desert environment, allow for investigation into genomic factors affecting tortoise health, disease and longevity, and serve as a valuable resource for additional studies in this species complex.Note
Open access journal.ISSN
1932-6203PubMed ID
28562605Version
Final published versionAdditional Links
http://dx.plos.org/10.1371/journal.pone.0177708ae974a485f413a2113503eed53cd6c53
10.1371/journal.pone.0177708
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