High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps

Abstract

Background: The lizards of the family Agamidae are one of the most prominent elements of the Australian reptile fauna. Here, we present a genomic resource built on the basis of a wild-caught male ZZ central bearded dragon Pogona vitticeps.

Findings: The genomic sequence for P. vitticeps, generated on the Illumina HiSeq 2000 platform, comprised 317 Gbp (179X raw read depth) from 13 insert libraries ranging from 250 bp to 40 kbp. After filtering for low-quality and duplicated reads, 146 Gbp of data (83X) was available for assembly. Exceptionally high levels of heterozygosity (0.85 % of single nucleotide polymorphisms plus sequence insertions or deletions) complicated assembly; nevertheless, 96.4 % of reads mapped back to the assembled scaffolds, indicating that the assembly included most of the sequenced genome. Length of the assembly was 1.8 Gbp in 545,310 scaffolds (69,852 longer than 300 bp), the longest being 14.68 Mbp. N50 was 2.29 Mbp. Genes were annotated on the basis of de novo prediction, similarity to the green anole Anolis carolinensis, Gallus gallus and Homo sapiens proteins, and P. vitticeps transcriptome sequence assemblies, to yield 19,406 protein-coding genes in the assembly, 63 % of which had intact open reading frames. Our assembly captured 99 % (246 of 248) of core CEGMA genes, with 93 % (231) being complete.

Conclusions: The quality of the P. vitticeps assembly is comparable or superior to that of other published squamate genomes, and the annotated P. vitticeps genome can be accessed through a genome browser available at https://genomics.canberra.edu.au.

Keywords: Agamidae, Squamata, Next-generation sequencing; Central bearded dragon; Dragon lizard; Pogona vitticeps.

Fig. 1

K-mer spectrum for the genome sequence of a male Pogona vitticeps (ZZ). Sequencing DNA derived from the short-insert libraries (250, 500, 800 bp) yielded 98.35 Gbases of clean data in the form of 125 bp reads, which generated 76.89x109 17-mer sequences. The solid line shows the k-mer spectrum (percentage frequency against k-mer copy number). The second mode (copy number 48.5) represents homozygous single copy sequence, whereas the first mode (24.5), half the copy number of the first, represents heterozygous single copy sequence. Heterozygosity is high, which complicated assembly

Fig. 2

Distribution of GC content in 5 Kbp windows for a range of vertebrates including Pogona vitticeps

Fig. 3

Variation in GC content among windows for various genome sequences with increasing window size (5, 10, 20, 40, 80, 160, and 320 Kb windows). The relationship for Pogona vitticeps is disaggregated to macrochromosomes, microchromosomes and the Z sex chromosome for comparison. Scale of X axis is natural logarithm. Pogona macrochromosomes share the lack of isochore structure reported for the Anolis genomeᅟ

Fig. 4

Analysis of GC content in Pogona vitticeps. a, Distribution of GC content in all chromosomes, macrochromosomes, microchromosomes and the Z chromosome, calculated with a non-overlap 5-kb sliding windows ; b, GC content of various components of the genome, in comparison with the average GC content for macrochromosomes (red line), microchromosomes (green line) and the Z chromosome (blue line) ; c, GC content of the macrochromosomes, microchromosomes and Z chromosomes broken down for various components of the genome

Fig. 5

Comparisons of gene parameters among Pogona vitticeps, Gallus gallus, Python bivittatus, Anolis carolinensis, and Pelodiscus sinensis genomes