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

Arthur GEORGES, Qiye Li, Jinmin Lian, Denis O'Meally, Janine DEAKIN, Zongji Wang, Pei Zhang, Matthew Fujita, Hardip Patel, Yang Zhou, Kazumi MATSUBARA, Paul Waters, Jennifer Graves, Stephen SARRE, Guoije Zhang

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    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.

    Original languageEnglish
    Article number45
    Pages (from-to)1-10
    Number of pages10
    JournalGiga Science
    Volume4
    Issue number1
    DOIs
    Publication statusPublished - 2015

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    Lizards
    Genes
    Genome
    Reptiles
    Sequence Deletion
    Insertional Mutagenesis
    Genomics
    Transcriptome
    Scaffolds
    Open Reading Frames
    Libraries
    Single Nucleotide Polymorphism
    Chickens
    Proteins
    Nucleotides
    Polymorphism

    Cite this

    GEORGES, Arthur ; Li, Qiye ; Lian, Jinmin ; O'Meally, Denis ; DEAKIN, Janine ; Wang, Zongji ; Zhang, Pei ; Fujita, Matthew ; Patel, Hardip ; Zhou, Yang ; MATSUBARA, Kazumi ; Waters, Paul ; Graves, Jennifer ; SARRE, Stephen ; Zhang, Guoije. / High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps. In: Giga Science. 2015 ; Vol. 4, No. 1. pp. 1-10.
    @article{61d3882170c74f94aaee41ba5be15817,
    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. 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.",
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    author = "Arthur GEORGES and Qiye Li and Jinmin Lian and Denis O'Meally and Janine DEAKIN and Zongji Wang and Pei Zhang and Matthew Fujita and Hardip Patel and Yang Zhou and Kazumi MATSUBARA and Paul Waters and Jennifer Graves and Stephen SARRE and Guoije Zhang",
    year = "2015",
    doi = "10.1186/s13742-015-0085-2",
    language = "English",
    volume = "4",
    pages = "1--10",
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    GEORGES, A, Li, Q, Lian, J, O'Meally, D, DEAKIN, J, Wang, Z, Zhang, P, Fujita, M, Patel, H, Zhou, Y, MATSUBARA, K, Waters, P, Graves, J, SARRE, S & Zhang, G 2015, 'High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps', Giga Science, vol. 4, no. 1, 45, pp. 1-10. https://doi.org/10.1186/s13742-015-0085-2

    High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps. / GEORGES, Arthur; Li, Qiye; Lian, Jinmin; O'Meally, Denis; DEAKIN, Janine; Wang, Zongji; Zhang, Pei; Fujita, Matthew; Patel, Hardip; Zhou, Yang; MATSUBARA, Kazumi; Waters, Paul; Graves, Jennifer; SARRE, Stephen; Zhang, Guoije.

    In: Giga Science, Vol. 4, No. 1, 45, 2015, p. 1-10.

    Research output: Contribution to journalArticle

    TY - JOUR

    T1 - High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps

    AU - GEORGES, Arthur

    AU - Li, Qiye

    AU - Lian, Jinmin

    AU - O'Meally, Denis

    AU - DEAKIN, Janine

    AU - Wang, Zongji

    AU - Zhang, Pei

    AU - Fujita, Matthew

    AU - Patel, Hardip

    AU - Zhou, Yang

    AU - MATSUBARA, Kazumi

    AU - Waters, Paul

    AU - Graves, Jennifer

    AU - SARRE, Stephen

    AU - Zhang, Guoije

    PY - 2015

    Y1 - 2015

    N2 - 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.

    AB - 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.

    KW - Agamidae

    KW - Central bearded dragon

    KW - Dragon lizard

    KW - Next-generation sequencing

    KW - Pogona vitticeps

    KW - Squamata

    KW - Lizards/genetics

    KW - Animals

    KW - High-Throughput Nucleotide Sequencing

    KW - Genome

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    UR - http://www.mendeley.com/research/highcoverage-sequencing-annotated-assembly-genome-australian-dragon-lizard-pogona-vitticeps

    U2 - 10.1186/s13742-015-0085-2

    DO - 10.1186/s13742-015-0085-2

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    SN - 2047-217X

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    ER -