The Agassiz’s desert tortoise genome provides a resource for the conservation of a threatened species
DeNardo, Dale F.
Cornelius, John A.
Dolby, Greer A.
Henen, Brian T.
Karl, Alice E.
Murphy, Robert W.
AffiliationUniv Arizona, Genet Core
MetadataShow full item record
PublisherPUBLIC LIBRARY SCIENCE
CitationThe Agassiz’s desert tortoise genome provides a resource for the conservation of a threatened species 2017, 12 (5):e0177708 PLOS ONE
RightsThis 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 InformationThis 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 firstname.lastname@example.org.
AbstractAgassiz'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.
NoteOpen access journal.
VersionFinal published version
Except where otherwise noted, this item's license is described as 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.
- Landscape limits gene flow and drives population structure in Agassiz's desert tortoise (Gopherus agassizii).
- Authors: Sánchez-Ramírez S, Rico Y, Berry KH, Edwards T, Karl AE, Henen BT, Murphy RW
- Issue date: 2018 Jul 25
- Serologic and molecular evidence for Testudinid herpesvirus 2 infection in wild Agassiz's desert tortoises, Gopherus agassizii.
- Authors: Jacobson ER, Berry KH, Wellehan JF Jr, Origgi F, Childress AL, Braun J, Schrenzel M, Yee J, Rideout B
- Issue date: 2012 Jul
- Discovery of a New TLR Gene and Gene Expansion Event through Improved Desert Tortoise Genome Assembly with Chromosome-Scale Scaffolds.
- Authors: Dolby GA, Morales M, Webster TH, DeNardo DF, Wilson MA, Kusumi K
- Issue date: 2020 Feb 1
- Mojave desert tortoise (Gopherus agassizii) thermal ecology and reproductive success along a rainfall cline.
- Authors: Sieg AE, Gambone MM, Wallace BP, Clusella-Trullas S, Spotila JR, Avery HW
- Issue date: 2015 May
- Mycoplasmal upper respiratory tract disease across the range of the threatened Mojave Desert tortoise: associations with thermal regime and natural antibodies.
- Authors: Sandmeier FC, Tracy CR, Hagerty BE, DuPré S, Mohammadpour H, Hunter K Jr
- Issue date: 2013 Mar