Microsatellite loci and the complete mitochondrial DNA sequence characterised through next-generation sequencing and de novo genome assembly, and a preliminary assessment of population genetic structure for the Australian crane, Antigone rubicunda

Adam D. Miller, Inka Veltheim, Timothy Nevard, Han Ming Gan, Martin Haase

    Research output: Contribution to journalArticleResearchpeer-review

    Abstract

    The Brolga (Antigone rubicunda) is a large Australian crane species with a broad distribution spanning from the tropical north to the south-eastern regions of the continent. Brolga populations throughout New South Wales, Victoria and South Australia have been in decline since the early twentieth century, with the species being listed as vulnerable in each state. To aid future conservation of the species, its taxonomic status needs to be validated, and patterns of gene flow and population connectivity across the species distribution need to be understood. To assist future genetic studies, we developed a suite of polymorphic microsatellite markers and the complete mitochondrial genome sequence by next-generation sequencing. A total of 18 polymorphic loci were characterised using DNA extractions from 47 individuals, comprising 30 and 17 individuals from Victoria and northern Australia, respectively. We observed moderate genetic variation across loci with only a single locus deviating significantly from Hardy–Weinberg equilibrium. De novo and reference-based genome assemblies were used to assemble the A. rubicunda mitochondrial genome sequence, which consists of 16,700 base pairs, and a typical metazoan mitochondrial gene content and arrangement. We test these new markers by conducting a preliminary analysis of genetic structure between south-eastern and northern Australian Brolga populations. Mitochondrial analyses provided evidence of shared haplotypes across the species range supporting the conspecific status of extant populations, while microsatellite markers indicated weak but significant genetic differentiation suggesting gene flow is limited. We discuss the implications of these findings and the benefits that these genetic markers will provide for future population genetic research on this iconic Australian bird species.

    Original languageEnglish
    Pages (from-to)49-58
    Number of pages10
    JournalAvian Biology Research
    Volume12
    Issue number2
    Early online date11 Mar 2019
    DOIs
    Publication statusPublished - 1 May 2019

    Fingerprint

    genome assembly
    crane
    mitochondrial DNA
    genetic structure
    population genetics
    Victoria (Australia)
    genome
    microsatellite repeats
    nucleotide sequences
    loci
    gene flow
    genetic variation
    South Australia
    New South Wales
    metazoan
    genetic techniques and protocols
    genetic marker
    haplotypes
    biogeography
    genetic differentiation

    Cite this

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    title = "Microsatellite loci and the complete mitochondrial DNA sequence characterised through next-generation sequencing and de novo genome assembly, and a preliminary assessment of population genetic structure for the Australian crane, Antigone rubicunda",
    abstract = "The Brolga (Antigone rubicunda) is a large Australian crane species with a broad distribution spanning from the tropical north to the south-eastern regions of the continent. Brolga populations throughout New South Wales, Victoria and South Australia have been in decline since the early twentieth century, with the species being listed as vulnerable in each state. To aid future conservation of the species, its taxonomic status needs to be validated, and patterns of gene flow and population connectivity across the species distribution need to be understood. To assist future genetic studies, we developed a suite of polymorphic microsatellite markers and the complete mitochondrial genome sequence by next-generation sequencing. A total of 18 polymorphic loci were characterised using DNA extractions from 47 individuals, comprising 30 and 17 individuals from Victoria and northern Australia, respectively. We observed moderate genetic variation across loci with only a single locus deviating significantly from Hardy–Weinberg equilibrium. De novo and reference-based genome assemblies were used to assemble the A. rubicunda mitochondrial genome sequence, which consists of 16,700 base pairs, and a typical metazoan mitochondrial gene content and arrangement. We test these new markers by conducting a preliminary analysis of genetic structure between south-eastern and northern Australian Brolga populations. Mitochondrial analyses provided evidence of shared haplotypes across the species range supporting the conspecific status of extant populations, while microsatellite markers indicated weak but significant genetic differentiation suggesting gene flow is limited. We discuss the implications of these findings and the benefits that these genetic markers will provide for future population genetic research on this iconic Australian bird species.",
    keywords = "Antigone rubicunda, de novo genome assembly, microsatellite library development, mitogenome sequence, next-generation DNA sequencing, population genetic structure",
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    Microsatellite loci and the complete mitochondrial DNA sequence characterised through next-generation sequencing and de novo genome assembly, and a preliminary assessment of population genetic structure for the Australian crane, Antigone rubicunda. / Miller, Adam D.; Veltheim, Inka; Nevard, Timothy; Gan, Han Ming; Haase, Martin.

    In: Avian Biology Research, Vol. 12, No. 2, 01.05.2019, p. 49-58.

    Research output: Contribution to journalArticleResearchpeer-review

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    T1 - Microsatellite loci and the complete mitochondrial DNA sequence characterised through next-generation sequencing and de novo genome assembly, and a preliminary assessment of population genetic structure for the Australian crane, Antigone rubicunda

    AU - Miller, Adam D.

    AU - Veltheim, Inka

    AU - Nevard, Timothy

    AU - Gan, Han Ming

    AU - Haase, Martin

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    N2 - The Brolga (Antigone rubicunda) is a large Australian crane species with a broad distribution spanning from the tropical north to the south-eastern regions of the continent. Brolga populations throughout New South Wales, Victoria and South Australia have been in decline since the early twentieth century, with the species being listed as vulnerable in each state. To aid future conservation of the species, its taxonomic status needs to be validated, and patterns of gene flow and population connectivity across the species distribution need to be understood. To assist future genetic studies, we developed a suite of polymorphic microsatellite markers and the complete mitochondrial genome sequence by next-generation sequencing. A total of 18 polymorphic loci were characterised using DNA extractions from 47 individuals, comprising 30 and 17 individuals from Victoria and northern Australia, respectively. We observed moderate genetic variation across loci with only a single locus deviating significantly from Hardy–Weinberg equilibrium. De novo and reference-based genome assemblies were used to assemble the A. rubicunda mitochondrial genome sequence, which consists of 16,700 base pairs, and a typical metazoan mitochondrial gene content and arrangement. We test these new markers by conducting a preliminary analysis of genetic structure between south-eastern and northern Australian Brolga populations. Mitochondrial analyses provided evidence of shared haplotypes across the species range supporting the conspecific status of extant populations, while microsatellite markers indicated weak but significant genetic differentiation suggesting gene flow is limited. We discuss the implications of these findings and the benefits that these genetic markers will provide for future population genetic research on this iconic Australian bird species.

    AB - The Brolga (Antigone rubicunda) is a large Australian crane species with a broad distribution spanning from the tropical north to the south-eastern regions of the continent. Brolga populations throughout New South Wales, Victoria and South Australia have been in decline since the early twentieth century, with the species being listed as vulnerable in each state. To aid future conservation of the species, its taxonomic status needs to be validated, and patterns of gene flow and population connectivity across the species distribution need to be understood. To assist future genetic studies, we developed a suite of polymorphic microsatellite markers and the complete mitochondrial genome sequence by next-generation sequencing. A total of 18 polymorphic loci were characterised using DNA extractions from 47 individuals, comprising 30 and 17 individuals from Victoria and northern Australia, respectively. We observed moderate genetic variation across loci with only a single locus deviating significantly from Hardy–Weinberg equilibrium. De novo and reference-based genome assemblies were used to assemble the A. rubicunda mitochondrial genome sequence, which consists of 16,700 base pairs, and a typical metazoan mitochondrial gene content and arrangement. We test these new markers by conducting a preliminary analysis of genetic structure between south-eastern and northern Australian Brolga populations. Mitochondrial analyses provided evidence of shared haplotypes across the species range supporting the conspecific status of extant populations, while microsatellite markers indicated weak but significant genetic differentiation suggesting gene flow is limited. We discuss the implications of these findings and the benefits that these genetic markers will provide for future population genetic research on this iconic Australian bird species.

    KW - Antigone rubicunda

    KW - de novo genome assembly

    KW - microsatellite library development

    KW - mitogenome sequence

    KW - next-generation DNA sequencing

    KW - population genetic structure

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    M3 - Article

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