High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps. Issue 1 (December 2015)

• Record Type: Journal Article
• Authors: Georges, Arthur; Li, Qiye; Lian, Jinmin; O'Meally, Denis; Deakin, Janine; Wang, Zongji; Zhang, Pei; Fujita, Matthew; Patel, Hardip; Holleley, Clare; Zhou, Yang; Zhang, Xiuwen; Matsubara, Kazumi; Waters, Paul; Graves, Jennifer; Sarre, Stephen; Zhang, Guojie
• Is Part Of: GigaScience. Volume 4:Issue 1(2015)
• Page Start: 1
• Page End: 11
• Publication Date: 2015-12
• Subjects: Pogona vitticeps -- Dragon lizard -- Central bearded dragon -- Agamidae, Squamata, Next-generation sequencing; Information storage and retrieval systems -- Research -- Periodicals; Biology -- Research -- Periodicals; Medical sciences -- Research -- Periodicals; Database management -- Periodicals; 570.285
• DOI: 10.1186/s13742-015-0085-2
• Languages: English
• ISSNs: 2047-217X

Abstract

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 dragonPogona vitticeps . Findings The genomic sequence forP. 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 ofde novo prediction, similarity to the green anoleAnolis carolinensis, Gallus gallus andHomo sapiens proteins, andP. 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 theP. vitticeps assembly is comparable or superior to that of other published squamate genomes, and the annotatedP. vitticeps genome can be accessed through a genome browser available athttps://genomics.canberra.edu.au .