Resolution of the enigmatic phylogenetic relationship of the critically endangered Western Swamp Tortoise Pseudemydura umbrina (Pleurodira

Chelidae) using a complete mitochondrial genome

Xiuwen ZHANG, Peter J. Unmack, Gerald Kuchling, Yinan Wang, Arthur Georges

    Research output: Contribution to journalArticle

    2 Citations (Scopus)

    Abstract

    Pseudemydura umbrina is one of the most endangered turtle species in the world, and the imperative for its conservation is its distinctive morphology and relict status among the Chelidae. We use Illumina sequencing to obtain the complete mitogenome for resolving its uncertain phylogenetic position. A novel nuclear paralogue confounded the assembly, and resolution of the authentic mitogenome required further Sanger sequencing. The P. umbrina mitogenome is 16,414 bp comprising 37 genes organized in a conserved pattern for other vertebrates. The nuclear paralogue is 547 bp, 97.8% identity to the corresponding mitochondrial sequence. Particular features of the mitogenome include an nd3 174+1A frameshift, loss of DHC loop in tRNASer (AGN), and a light-strand replication initiation site in Wancy region that extends into an adjacent tRNA gene. Phylogenetic analysis showed that P. umbrina is the monotypic sister lineage to the remaining Australasian Chelidae, a lineage probably dating back to the Cretaceous.

    Original languageEnglish
    Pages (from-to)58-61
    Number of pages4
    JournalMolecular Phylogenetics and Evolution
    Volume115
    DOIs
    Publication statusPublished - 1 Oct 2017

    Fingerprint

    Chelidae
    Turtles
    Mitochondrial Genome
    Wetlands
    tortoises
    swamps
    swamp
    genome
    RNA, Transfer, Ser
    phylogenetics
    Endangered Species
    gene
    phylogeny
    Transfer RNA
    turtle
    Genes
    Vertebrates
    vertebrate
    Cretaceous
    Light

    Cite this

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    title = "Resolution of the enigmatic phylogenetic relationship of the critically endangered Western Swamp Tortoise Pseudemydura umbrina (Pleurodira: Chelidae) using a complete mitochondrial genome",
    abstract = "Pseudemydura umbrina is one of the most endangered turtle species in the world, and the imperative for its conservation is its distinctive morphology and relict status among the Chelidae. We use Illumina sequencing to obtain the complete mitogenome for resolving its uncertain phylogenetic position. A novel nuclear paralogue confounded the assembly, and resolution of the authentic mitogenome required further Sanger sequencing. The P. umbrina mitogenome is 16,414 bp comprising 37 genes organized in a conserved pattern for other vertebrates. The nuclear paralogue is 547 bp, 97.8{\%} identity to the corresponding mitochondrial sequence. Particular features of the mitogenome include an nd3 174+1A frameshift, loss of DHC loop in tRNASer (AGN), and a light-strand replication initiation site in Wancy region that extends into an adjacent tRNA gene. Phylogenetic analysis showed that P. umbrina is the monotypic sister lineage to the remaining Australasian Chelidae, a lineage probably dating back to the Cretaceous.",
    keywords = "Complete mitogenome, ND3 frameshift, Numt, Phylogenetic analysis, Pleurodira",
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    AU - ZHANG, Xiuwen

    AU - Unmack, Peter J.

    AU - Kuchling, Gerald

    AU - Wang, Yinan

    AU - Georges, Arthur

    PY - 2017/10/1

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    N2 - Pseudemydura umbrina is one of the most endangered turtle species in the world, and the imperative for its conservation is its distinctive morphology and relict status among the Chelidae. We use Illumina sequencing to obtain the complete mitogenome for resolving its uncertain phylogenetic position. A novel nuclear paralogue confounded the assembly, and resolution of the authentic mitogenome required further Sanger sequencing. The P. umbrina mitogenome is 16,414 bp comprising 37 genes organized in a conserved pattern for other vertebrates. The nuclear paralogue is 547 bp, 97.8% identity to the corresponding mitochondrial sequence. Particular features of the mitogenome include an nd3 174+1A frameshift, loss of DHC loop in tRNASer (AGN), and a light-strand replication initiation site in Wancy region that extends into an adjacent tRNA gene. Phylogenetic analysis showed that P. umbrina is the monotypic sister lineage to the remaining Australasian Chelidae, a lineage probably dating back to the Cretaceous.

    AB - Pseudemydura umbrina is one of the most endangered turtle species in the world, and the imperative for its conservation is its distinctive morphology and relict status among the Chelidae. We use Illumina sequencing to obtain the complete mitogenome for resolving its uncertain phylogenetic position. A novel nuclear paralogue confounded the assembly, and resolution of the authentic mitogenome required further Sanger sequencing. The P. umbrina mitogenome is 16,414 bp comprising 37 genes organized in a conserved pattern for other vertebrates. The nuclear paralogue is 547 bp, 97.8% identity to the corresponding mitochondrial sequence. Particular features of the mitogenome include an nd3 174+1A frameshift, loss of DHC loop in tRNASer (AGN), and a light-strand replication initiation site in Wancy region that extends into an adjacent tRNA gene. Phylogenetic analysis showed that P. umbrina is the monotypic sister lineage to the remaining Australasian Chelidae, a lineage probably dating back to the Cretaceous.

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    KW - Phylogenetic analysis

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