Table 1.
Chelonian species with whole genome sequences.
Table 2.
Sequences used for the assembly of the Agassiz’s desert tortoise (Gopherus agassizii) genome.
Fig 1.
Assembly statistics for the genome of Gopherus agassizii and comparison with Python bivittatus and Alligator mississippiensis.
(A) Two k-mer frequency peaks exist for G. agassizii: a peak at 35X coverage, representing heterozygous regions and a peak at 71X coverage, representing homozygous regions. (B) Gene-based scaffolding greatly increased scaffold N50 from 169.2 kbp to 251.6 kbp, which places it within the range of recently published genomes of reptiles including the Burmese python [71] and the American alligator [72].
Table 3.
Assembly statistics for the genome of Gopherus agassizii.
Fig 2.
Frequency distribution (proportion) of GC content calculated in 5 kbp non-overlapping windows for Gopherus agassizii and other reptilian genomes.
GC content of G. agassizii closely matches that of the turtles Chrysemys picta bellii and Pelodiscus sinensis [17,18], and overlaps the American alligator (Alligator mississippiensis) [72], the green anole (Anolis carolinensis) [73], and the chicken (Gallus gallus) [70].
Fig 3.
Gene structure of Gopherus agassizii compared to other reptiles.
Frequency distribution of genes or exons relative to (A) coding DNA sequence (CDS) lengths, (B) exon length and (C) intron length of Agassiz’s desert tortoise, chicken [74], western painted turtle [18], and Chinese softshell turtle [17]. CDS is for genes less than 10 kb.
Table 4.
Repetitive content of the Agassiz’s desert tortoise (Gopherus agassizii) and the western painted turtle (Chrysemys picta bellii) genomes, estimated with libraries of known repeats (RepBase) and de novo repeat identification (RepeatModeler).
Fig 4.
Phylogeny of 10 sauropsids including Gopherus agassizii.
Phylogeny shows the relationships of sauropsids, including four chelonians, with complete genome sequences. Branch lengths are given in terms of DNA substitutions per site derived from fourfold degenerate sites.
Fig 5.
Comparative genomics of chelonians.
Representation of Gene Ontology terms for biological processes shared by genes with pairwise Ka/Ks > 1 in comparisons of Gopherus agassizii to (A) Chrysemys picta bellii and (B) Chelonia mydas. Treemap boxes are both sized and colored by uniqueness. Abbreviations in (A): RB, receptor biosynthesis, LCFACB, long chain fatty acyl-CoA biosynthesis, MTMD, membrane to membrane docking.
Table 5.
Gene Ontology categories most enriched for fixed unique SNPs in G. agassizii compared with G. morafkai and G. evgoodei.
These results are for Biological Processes, for a complete listing see S6–S8 Tables.
Table 6.
Overlapping genes in the two most enriched GO categories for fixed unique SNPs in G. agassizii compared with key functional categories.
No overlap was identified with GO:0002456 T cell mediated immunity.
Table 7.
Genes under accelerated evolution across chelonians and genes with fixed differences between species in the Gopherus desert tortoise species complex according to this study.