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

GigaScience

Guojie Zhang⁸  Stephen D. Sarre⁹  Jennifer A. Marshall Graves²  Paul Waters¹  Kazumi Matsubara⁹  Xiuwen Zhang⁹  Yang Zhou⁴  Clare E. Holleley⁹  Hardip R. Patel³  Matthew Fujita⁵  Pei Zhang⁴  Zongji Wang⁶  Janine Deakin⁹  Denis O’Meally⁹  Jinmin Lian⁴  Qiye Li⁷  Arthur Georges⁹ 

[1] School of Biotechnology & Biomolecular Sciences, University of New South Wales, Sydney 2052, NSW, Australia;School of Life Science, La Trobe University, Melbourne 3086, VIC, Australia;John Curtin School of Medical Research, Australian National University, Canberra 2601, ACT, Australia;China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China;Department of Biology, University of Texas at Arlington, 701 S. Nedderman Drive, Arlington 76019, TX, USA;School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China;Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350, Denmark;Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen, DK-2100, Denmark;Institute for Applied Ecology, University of Canberra, Canberra 2601, ACT, Australia

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

Others  :  1228423
DOI  :  10.1186/s13742-015-0085-2

 received in 2015-06-20, accepted in 2015-09-14,  发布年份 2015

【 摘 要 】

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.

【 授权许可】

   
2015 Georges et al.

【 图 表 】

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