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

PLoS One. 2017 May 31;12(5):e0177708. doi: 10.1371/journal.pone.0177708. eCollection 2017.

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.

MeSH terms

  • Adaptation, Physiological / genetics
  • Animals
  • Circadian Rhythm / genetics
  • Conservation of Natural Resources*
  • Desert Climate
  • Endangered Species*
  • Genome*
  • Immunity, Innate / genetics
  • Transcriptome
  • Turtles / genetics*

Grant support

Author AEK is employed by Alice E. Karl and Associates. This company provided support in the form of salary for author AEK but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.