Identification of interleukin genes in Pogona vitticeps using a de novo transcriptome assembly from RNA-seq data

Ali LIVERNOIS, Kris HARDY, Renae DOMASCHENZ, Alexie Papanicolaou, Arthur GEORGES, Stephen SARRE, Sudha RAO, Tariq EZAZ, Janine DEAKIN

    Research output: Contribution to journalArticle

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    Abstract

    Interleukins are a group of cytokines with complex immunomodulatory functions that are important for regulating immunity in vertebrate species. Reptiles and mammals last shared a common ancestor more than 350 million years ago, so it is not surprising that low sequence identity has prevented divergent interleukin genes from being identified in the central bearded dragon lizard, Pogona vitticeps, in its genome assembly. To determine the complete nucleotide sequences of key interleukin genes, we constructed full-length transcripts, using the Trinity platform, from short paired-end read RNA sequences from stimulated spleen cells. De novo transcript reconstruction and analysis allowed us to identify interleukin genes that are missing from the published P. vitticeps assembly. Identification of key cytokines in P. vitticeps will provide insight into the essential molecular mechanisms and evolution of interleukin gene families and allow for characterization of the immune response in a lizard for comparison with mammals.
    Original languageEnglish
    Pages (from-to)719-731
    Number of pages13
    JournalImmunogenetics
    Volume68
    Issue number9
    DOIs
    Publication statusPublished - 2016

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    Interleukins
    Transcriptome
    Lizards
    RNA
    Cytokines
    Genes
    Reptiles
    Vertebrates
    Mammals
    Spleen
    Genome

    Cite this

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    title = "Identification of interleukin genes in Pogona vitticeps using a de novo transcriptome assembly from RNA-seq data",
    abstract = "Interleukins are a group of cytokines with complex immunomodulatory functions that are important for regulating immunity in vertebrate species. Reptiles and mammals last shared a common ancestor more than 350 million years ago, so it is not surprising that low sequence identity has prevented divergent interleukin genes from being identified in the central bearded dragon lizard, Pogona vitticeps, in its genome assembly. To determine the complete nucleotide sequences of key interleukin genes, we constructed full-length transcripts, using the Trinity platform, from short paired-end read RNA sequences from stimulated spleen cells. De novo transcript reconstruction and analysis allowed us to identify interleukin genes that are missing from the published P. vitticeps assembly. Identification of key cytokines in P. vitticeps will provide insight into the essential molecular mechanisms and evolution of interleukin gene families and allow for characterization of the immune response in a lizard for comparison with mammals.",
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    language = "English",
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    Identification of interleukin genes in Pogona vitticeps using a de novo transcriptome assembly from RNA-seq data. / LIVERNOIS, Ali; HARDY, Kris; DOMASCHENZ, Renae; Papanicolaou, Alexie; GEORGES, Arthur; SARRE, Stephen; RAO, Sudha; EZAZ, Tariq; DEAKIN, Janine.

    In: Immunogenetics, Vol. 68, No. 9, 2016, p. 719-731.

    Research output: Contribution to journalArticle

    TY - JOUR

    T1 - Identification of interleukin genes in Pogona vitticeps using a de novo transcriptome assembly from RNA-seq data

    AU - LIVERNOIS, Ali

    AU - HARDY, Kris

    AU - DOMASCHENZ, Renae

    AU - Papanicolaou, Alexie

    AU - GEORGES, Arthur

    AU - SARRE, Stephen

    AU - RAO, Sudha

    AU - EZAZ, Tariq

    AU - DEAKIN, Janine

    PY - 2016

    Y1 - 2016

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    AB - Interleukins are a group of cytokines with complex immunomodulatory functions that are important for regulating immunity in vertebrate species. Reptiles and mammals last shared a common ancestor more than 350 million years ago, so it is not surprising that low sequence identity has prevented divergent interleukin genes from being identified in the central bearded dragon lizard, Pogona vitticeps, in its genome assembly. To determine the complete nucleotide sequences of key interleukin genes, we constructed full-length transcripts, using the Trinity platform, from short paired-end read RNA sequences from stimulated spleen cells. De novo transcript reconstruction and analysis allowed us to identify interleukin genes that are missing from the published P. vitticeps assembly. Identification of key cytokines in P. vitticeps will provide insight into the essential molecular mechanisms and evolution of interleukin gene families and allow for characterization of the immune response in a lizard for comparison with mammals.

    KW - Pogona vitticeps . De novo assembly . Cytokine .

    KW - Interleukin

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