Reconstruction of the ancestral marsupial karyotype from comparative gene maps

Janine DEAKIN, Margaret L. Delbridge, Edda Koina, Nerida Harley, Amber E. Alsop, Chenwei Wang, Vidushi S. Patel, Jennifer A Marshall Graves

    Research output: Contribution to journalArticle

    16 Citations (Scopus)

    Abstract

    Background: The increasing number of assembled mammalian genomes makes it possible to compare genome organisation across mammalian lineages and reconstruct chromosomes of the ancestral marsupial and therian (marsupial and eutherian) mammals. However, the reconstruction of ancestral genomes requires genome assemblies to be anchored to chromosomes. The recently sequenced tammar wallaby (Macropus eugenii) genome was assembled into over 300,000 contigs. We previously devised an efficient strategy for mapping large evolutionarily conserved blocks in non-model mammals, and applied this to determine the arrangement of conserved blocks on all wallaby chromosomes, thereby permitting comparative maps to be constructed and resolve the long debated issue between a 2n = 14 and 2n = 22 ancestral marsupial karyotype. Results: We identified large blocks of genes conserved between human and opossum, and mapped genes corresponding to the ends of these blocks by fluorescence in situ hybridization (FISH). A total of 242 genes was assigned to wallaby chromosomes in the present study, bringing the total number of genes mapped to 554 and making it the most densely cytogenetically mapped marsupial genome. We used these gene assignments to construct comparative maps between wallaby and opossum, which uncovered many intrachromosomal rearrangements, particularly for genes found on wallaby chromosomes X and 3. Expanding comparisons to include chicken and human permitted the putative ancestral marsupial (2n = 14) and therian mammal (2n = 19) karyotypes to be reconstructed. Conclusions: Our physical mapping data for the tammar wallaby has uncovered the events shaping marsupial genomes and enabled us to predict the ancestral marsupial karyotype, supporting a 2n = 14 ancestor. Futhermore, our predicted therian ancestral karyotype has helped to understand the evolution of the ancestral eutherian genome.
    Original languageEnglish
    Pages (from-to)1-15
    Number of pages15
    JournalBMC Evolutionary Biology
    Volume13:258
    DOIs
    Publication statusPublished - 2013

    Fingerprint

    marsupial
    karyotype
    Metatheria
    karyotyping
    genome
    Macropodidae
    Macropus eugenii
    gene
    chromosome
    genes
    chromosomes
    opossums
    mammals
    mammal
    genome assembly
    physical chromosome mapping
    X chromosome
    fluorescence in situ hybridization
    ancestry
    fluorescence

    Cite this

    DEAKIN, J., Delbridge, M. L., Koina, E., Harley, N., Alsop, A. E., Wang, C., ... Graves, J. A. M. (2013). Reconstruction of the ancestral marsupial karyotype from comparative gene maps. BMC Evolutionary Biology, 13:258, 1-15. https://doi.org/10.1186/1471-2148-13-258
    DEAKIN, Janine ; Delbridge, Margaret L. ; Koina, Edda ; Harley, Nerida ; Alsop, Amber E. ; Wang, Chenwei ; Patel, Vidushi S. ; Graves, Jennifer A Marshall. / Reconstruction of the ancestral marsupial karyotype from comparative gene maps. In: BMC Evolutionary Biology. 2013 ; Vol. 13:258. pp. 1-15.
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    abstract = "Background: The increasing number of assembled mammalian genomes makes it possible to compare genome organisation across mammalian lineages and reconstruct chromosomes of the ancestral marsupial and therian (marsupial and eutherian) mammals. However, the reconstruction of ancestral genomes requires genome assemblies to be anchored to chromosomes. The recently sequenced tammar wallaby (Macropus eugenii) genome was assembled into over 300,000 contigs. We previously devised an efficient strategy for mapping large evolutionarily conserved blocks in non-model mammals, and applied this to determine the arrangement of conserved blocks on all wallaby chromosomes, thereby permitting comparative maps to be constructed and resolve the long debated issue between a 2n = 14 and 2n = 22 ancestral marsupial karyotype. Results: We identified large blocks of genes conserved between human and opossum, and mapped genes corresponding to the ends of these blocks by fluorescence in situ hybridization (FISH). A total of 242 genes was assigned to wallaby chromosomes in the present study, bringing the total number of genes mapped to 554 and making it the most densely cytogenetically mapped marsupial genome. We used these gene assignments to construct comparative maps between wallaby and opossum, which uncovered many intrachromosomal rearrangements, particularly for genes found on wallaby chromosomes X and 3. Expanding comparisons to include chicken and human permitted the putative ancestral marsupial (2n = 14) and therian mammal (2n = 19) karyotypes to be reconstructed. Conclusions: Our physical mapping data for the tammar wallaby has uncovered the events shaping marsupial genomes and enabled us to predict the ancestral marsupial karyotype, supporting a 2n = 14 ancestor. Futhermore, our predicted therian ancestral karyotype has helped to understand the evolution of the ancestral eutherian genome.",
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    author = "Janine DEAKIN and Delbridge, {Margaret L.} and Edda Koina and Nerida Harley and Alsop, {Amber E.} and Chenwei Wang and Patel, {Vidushi S.} and Graves, {Jennifer A Marshall}",
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    DEAKIN, J, Delbridge, ML, Koina, E, Harley, N, Alsop, AE, Wang, C, Patel, VS & Graves, JAM 2013, 'Reconstruction of the ancestral marsupial karyotype from comparative gene maps', BMC Evolutionary Biology, vol. 13:258, pp. 1-15. https://doi.org/10.1186/1471-2148-13-258

    Reconstruction of the ancestral marsupial karyotype from comparative gene maps. / DEAKIN, Janine; Delbridge, Margaret L.; Koina, Edda; Harley, Nerida; Alsop, Amber E.; Wang, Chenwei; Patel, Vidushi S.; Graves, Jennifer A Marshall.

    In: BMC Evolutionary Biology, Vol. 13:258, 2013, p. 1-15.

    Research output: Contribution to journalArticle

    TY - JOUR

    T1 - Reconstruction of the ancestral marsupial karyotype from comparative gene maps

    AU - DEAKIN, Janine

    AU - Delbridge, Margaret L.

    AU - Koina, Edda

    AU - Harley, Nerida

    AU - Alsop, Amber E.

    AU - Wang, Chenwei

    AU - Patel, Vidushi S.

    AU - Graves, Jennifer A Marshall

    PY - 2013

    Y1 - 2013

    N2 - Background: The increasing number of assembled mammalian genomes makes it possible to compare genome organisation across mammalian lineages and reconstruct chromosomes of the ancestral marsupial and therian (marsupial and eutherian) mammals. However, the reconstruction of ancestral genomes requires genome assemblies to be anchored to chromosomes. The recently sequenced tammar wallaby (Macropus eugenii) genome was assembled into over 300,000 contigs. We previously devised an efficient strategy for mapping large evolutionarily conserved blocks in non-model mammals, and applied this to determine the arrangement of conserved blocks on all wallaby chromosomes, thereby permitting comparative maps to be constructed and resolve the long debated issue between a 2n = 14 and 2n = 22 ancestral marsupial karyotype. Results: We identified large blocks of genes conserved between human and opossum, and mapped genes corresponding to the ends of these blocks by fluorescence in situ hybridization (FISH). A total of 242 genes was assigned to wallaby chromosomes in the present study, bringing the total number of genes mapped to 554 and making it the most densely cytogenetically mapped marsupial genome. We used these gene assignments to construct comparative maps between wallaby and opossum, which uncovered many intrachromosomal rearrangements, particularly for genes found on wallaby chromosomes X and 3. Expanding comparisons to include chicken and human permitted the putative ancestral marsupial (2n = 14) and therian mammal (2n = 19) karyotypes to be reconstructed. Conclusions: Our physical mapping data for the tammar wallaby has uncovered the events shaping marsupial genomes and enabled us to predict the ancestral marsupial karyotype, supporting a 2n = 14 ancestor. Futhermore, our predicted therian ancestral karyotype has helped to understand the evolution of the ancestral eutherian genome.

    AB - Background: The increasing number of assembled mammalian genomes makes it possible to compare genome organisation across mammalian lineages and reconstruct chromosomes of the ancestral marsupial and therian (marsupial and eutherian) mammals. However, the reconstruction of ancestral genomes requires genome assemblies to be anchored to chromosomes. The recently sequenced tammar wallaby (Macropus eugenii) genome was assembled into over 300,000 contigs. We previously devised an efficient strategy for mapping large evolutionarily conserved blocks in non-model mammals, and applied this to determine the arrangement of conserved blocks on all wallaby chromosomes, thereby permitting comparative maps to be constructed and resolve the long debated issue between a 2n = 14 and 2n = 22 ancestral marsupial karyotype. Results: We identified large blocks of genes conserved between human and opossum, and mapped genes corresponding to the ends of these blocks by fluorescence in situ hybridization (FISH). A total of 242 genes was assigned to wallaby chromosomes in the present study, bringing the total number of genes mapped to 554 and making it the most densely cytogenetically mapped marsupial genome. We used these gene assignments to construct comparative maps between wallaby and opossum, which uncovered many intrachromosomal rearrangements, particularly for genes found on wallaby chromosomes X and 3. Expanding comparisons to include chicken and human permitted the putative ancestral marsupial (2n = 14) and therian mammal (2n = 19) karyotypes to be reconstructed. Conclusions: Our physical mapping data for the tammar wallaby has uncovered the events shaping marsupial genomes and enabled us to predict the ancestral marsupial karyotype, supporting a 2n = 14 ancestor. Futhermore, our predicted therian ancestral karyotype has helped to understand the evolution of the ancestral eutherian genome.

    KW - Comparative genomics

    KW - Comparative mapping

    KW - Physical map

    KW - Marsupial

    KW - Ancestral karyotype.

    U2 - 10.1186/1471-2148-13-258

    DO - 10.1186/1471-2148-13-258

    M3 - Article

    VL - 13:258

    SP - 1

    EP - 15

    JO - BMC Evolutionary Biology

    JF - BMC Evolutionary Biology

    SN - 1471-2148

    ER -