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

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.

The Mobilome of Reptiles: Evolution, Structure, and Function

“…These first reports however have likely underestimated the TE content in turtles' genomes, possibly due to a lack of de novo annotation of element families specific to reptiles. More recent annotations suggest that the 4 genomes currently sequenced -the green sea turtle ( Chelonia mydas ), western painted turtle ( Chrysemys picta belli ), Chinese soft-shell turtle ( Pelodiscus sinensis ), and Agassiz's desert tortoise (G opherus agassizii ) -display TE contents around 30% [Tollis et al, 2017]. This latter estimate would be more consistent with the general correlation between TE content and genome size observed in reptiles ( Fig.…”

“…Among LINEs, CR1/L3 elements are the most abundant in turtles Tollis et al, 2017], which is similar to other reptiles. The high number of CR1 lineages in turtles likely reflects much of the CR1 ancestral diversity in amniotes [Suh et al, 2014].…”

“…The high number of CR1 lineages in turtles likely reflects much of the CR1 ancestral diversity in amniotes [Suh et al, 2014]. Many CR1 subfamilies display a low divergence (<5%) from their con-Cytogenet Genome Res 2019;157:21-33 DOI: 10.1159/000496416 28 sensus sequence, suggesting a recent burst of activity [Tollis et al, 2017]. Overall, turtle genomes tend to diverge slowly [Shaffer et al, 2013] and do not display strong variation in size.…”

Unraveling the diversification and systematic puzzle of the highly polymorphicPsammobates tentorius(Bell, 1828) complex (Reptilia: Testudinidae) through phylogenetic analyses and species delimitation approaches

“…When dealing with a slow‐evolving group, such as tortoises (Avise et al, ; Tollis et al, ), the rapid evolving mtDNA markers are possibly more suitable and reliable for elucidating a phylogeny (Rubinoff & Holland, ) than the slower evolving nDNA markers. Phylogenetic studies of chelonians (tortoises and turtles) often rely on mtDNA loci because nDNA markers frequently provide incongruent and poorly resolved trees with poor support (e.g., Kindler et al, ; Petzold et al, ).…”

Chromosomal Rearrangements during Turtle Evolution Altered the Synteny of Genes Involved in Vertebrate Sex Determination

“…h Pelodiscus genome assembly [Wang et al, 2013]; i Gopherus genome assembly [Tollis et al, 2017]. j BAC originally mapped in Chrysemys [Badenhorst et al, 2015] but enriched in repeats which precluded clean hybridization in some more distant turtles.…”