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  4. The Agassiz’s Desert Tortoise Genome Provides a Resource for the Conservation of a Threatened Species
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The Agassiz’s Desert Tortoise Genome Provides a Resource for the Conservation of a Threatened Species

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Description

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.

Data Availability: All genomic and transcriptomic sequence files are available from the NIH-NCBI BioProject database (accession numbers PRJNA352725, PRJNA352726, and PRJNA281763). All genome assembly, transcriptome assembly, predicted protein, transcript, genome annotation, repeatmasker, phylogenetic trees, .vcf and GO enrichment files are available on Harvard Dataverse (doi:10.7910/DVN/EH2S9K).

Date Created
2017-05-31
Contributors
  • Tollis, Marc (Author)
  • DeNardo, Dale F (Author)
  • Cornelius, John A (Author)
  • Dolby, Greer A (Author)
  • Edwards, Taylor (Author)
  • Henen, Brian T. (Author)
  • Karl, Alice E. (Author)
  • Murphy, Robert W. (Author)
  • Kusumi, Kenro (Author)
Topical Subject
  • desert
  • reptile genomic
  • tortoise
  • comparitive genomic
  • genomic library
  • genome annotation
Extent
18 pages, 12 images, 1 appendix (.zip)
Language
eng
Copyright Statement
In Copyright
Reuse Permissions
Attribution
Primary Member of
ASU Scholarship Showcase
Identifier
Digital object identifier: https://doi.org/10.1371/journal.pone.0177708
Peer-reviewed
No
Open Access
No
Series
PLOS ONE
Handle
https://hdl.handle.net/2286/R.I.44375
Preferred Citation

Tollis M, DeNardo DF, Cornelius JA, Dolby GA, Edwards T, Henen BT, et al. (2017) The Agassiz’s desert tortoise genome provides a resource for the conservation of a threatened species. PLoS ONE 12(5): e0177708. https://doi.org/10.1371/journal.pone.0177708

Level of coding
minimal
Cataloging Standards
asu1
Note
See also, Decoded genome may help tortoise win race to survive (https://asunow.asu.edu/20170531-discoveries-decoded-genome-may-help-tortoise-win-race-survive), opens in a new window
System Created
  • 2017-06-05 11:33:57
System Modified
  • 2021-10-25 11:56:12
  •     
  • 1 year 3 months ago
Additional Formats
  • OAI Dublin Core
  • MODS XML

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