title: 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.
  
  
  RESULTS
  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.
authors.affiliation: Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601 Australia.
authors.forename: Arthur
authors.initials: A
authors.lastname: Georges
authors.affiliation: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, 1350 Denmark.
authors.forename: Qiye
authors.initials: Q
authors.lastname: Li
authors.affiliation: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Jinmin
authors.initials: J
authors.lastname: Lian
authors.affiliation: Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601 Australia.
authors.forename: Denis
authors.initials: D
authors.lastname: O'Meally
authors.affiliation: Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601 Australia.
authors.forename: Janine
authors.initials: J
authors.lastname: Deakin
authors.affiliation: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China ; School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006 China.
authors.forename: Zongji
authors.initials: Z
authors.lastname: Wang
authors.affiliation: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Pei
authors.initials: P
authors.lastname: Zhang
authors.affiliation: Department of Biology, University of Texas at Arlington, 701 S. Nedderman Drive, Arlington, TX 76019 USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Fujita
authors.affiliation: John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601 Australia.
authors.forename: Hardip R
authors.initials: HR
authors.lastname: Patel
authors.affiliation: Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601 Australia.
authors.forename: Clare E
authors.initials: CE
authors.lastname: Holleley
authors.affiliation: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601 Australia.
authors.forename: Xiuwen
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601 Australia.
authors.forename: Kazumi
authors.initials: K
authors.lastname: Matsubara
authors.affiliation: School of Biotechnology & Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052 Australia.
authors.forename: Paul
authors.initials: P
authors.lastname: Waters
authors.affiliation: Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601 Australia ; School of Life Science, La Trobe University, Melbourne, VIC 3086 Australia.
authors.forename: Jennifer A Marshall
authors.initials: JA
authors.lastname: Graves
authors.affiliation: Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601 Australia.
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Sarre
authors.affiliation: China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China ; Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark.
authors.forename: Guojie
authors.initials: G
authors.lastname: Zhang
mesh_terms: D000818:Animals; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D008116:Lizards / Q000235:genetics*
keywords: Agamidae, Squamata, Next-generation sequencing; Central bearded dragon; Dragon lizard; Pogona vitticeps