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    The Agassiz’s desert tortoise genome provides a resource for the conservation of a threatened species

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    Author
    Tollis, Marc
    DeNardo, Dale F.
    Cornelius, John A.
    Dolby, Greer A.
    Edwards, Taylor
    Henen, Brian T.
    Karl, Alice E.
    Murphy, Robert W.
    Kusumi, Kenro cc
    Affiliation
    Univ Arizona, Genet Core
    Issue Date
    2017-05-31
    
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    Publisher
    PUBLIC LIBRARY SCIENCE
    Citation
    The Agassiz’s desert tortoise genome provides a resource for the conservation of a threatened species 2017, 12 (5):e0177708 PLOS ONE
    Journal
    PLOS ONE
    Rights
    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
    1932-6203
    PubMed ID
    28562605
    DOI
    10.1371/journal.pone.0177708
    Version
    Final published version
    Additional Links
    http://dx.plos.org/10.1371/journal.pone.0177708
    ae974a485f413a2113503eed53cd6c53
    10.1371/journal.pone.0177708
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