A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii)

Chenwei Wang, Lee Webley, Ke-jun Wei, Matthew Wakefield, H Patel, Janine Deakin, Amber Alsop, Jennifer Marshall Graves, Desmond Cooper, Frank Nicholas, Kyall Zenger

    Research output: Contribution to journalArticle

    8 Citations (Scopus)

    Abstract

    Background: The tammar wallaby, Macropus eugenii, a small kangaroo used for decades for studies of reproduction and metabolism, is the model Australian marsupial for genome sequencing and genetic investigations. The production of a more comprehensive cytogenetically-anchored genetic linkage map will significantly contribute to the deciphering of the tammar wallaby genome. It has great value as a resource to identify novel genes and for comparative studies, and is vital for the ongoing genome sequence assembly and gene ordering in this species. Results: A second-generation anchored tammar wallaby genetic linkage map has been constructed based on a total of 148 loci. The linkage map contains the original 64 loci included in the first-generation map, plus an additional 84 microsatellite loci that were chosen specifically to increase coverage and assist with the anchoring and orientation of linkage groups to chromosomes. These additional loci were derived from (a) sequenced BAC clones that had been previously mapped to tammar wallaby chromosomes by fluorescence in situ hybridization (FISH), (b) End sequence from BACs subsequently FISH-mapped to tammar wallaby chromosomes, and (c) tammar wallaby genes orthologous to opossum genes predicted to fill gaps in the tammar wallaby linkage map as well as three X-linked markers from a published study. Based on these 148 loci, eight linkage groups were formed. These linkage groups were assigned (via FISH-mapped markers) to all seven autosomes and the X chromosome. The sexpooled map size is 1402.4 cM, which is estimated to provide 82.6% total coverage of the genome, with an average interval distance of 10.9 cM between adjacent markers. The overall ratio of female/male map length is 0.84, which is comparable to the ratio of 0.78 obtained for the first-generation map. Conclusions: Construction of this second-generation genetic linkage map is a significant step towards complete coverage of the tammar wallaby genome and considerably extends that of the first-eneration map. It will be a valuable resource for ongoing tammar wallaby genetic research and assembling the genome sequence. The sexpooled map is available online at http://compldb.angis.org.au/.
    Original languageEnglish
    Pages (from-to)1-16
    Number of pages16
    JournalBMC Genetics
    Volume12:72
    DOIs
    Publication statusPublished - 2011

    Fingerprint

    Macropodidae
    Genetic Linkage
    Genome
    Fluorescence In Situ Hybridization
    Chromosomes
    Genes
    Opossums
    Marsupialia
    Genetic Research
    X Chromosome
    Microsatellite Repeats
    Reproduction
    Clone Cells

    Cite this

    Wang, Chenwei ; Webley, Lee ; Wei, Ke-jun ; Wakefield, Matthew ; Patel, H ; Deakin, Janine ; Alsop, Amber ; Marshall Graves, Jennifer ; Cooper, Desmond ; Nicholas, Frank ; Zenger, Kyall. / A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii). In: BMC Genetics. 2011 ; Vol. 12:72. pp. 1-16.
    @article{7dfa5822053f4f94848014cd5d7e2ee3,
    title = "A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii)",
    abstract = "Background: The tammar wallaby, Macropus eugenii, a small kangaroo used for decades for studies of reproduction and metabolism, is the model Australian marsupial for genome sequencing and genetic investigations. The production of a more comprehensive cytogenetically-anchored genetic linkage map will significantly contribute to the deciphering of the tammar wallaby genome. It has great value as a resource to identify novel genes and for comparative studies, and is vital for the ongoing genome sequence assembly and gene ordering in this species. Results: A second-generation anchored tammar wallaby genetic linkage map has been constructed based on a total of 148 loci. The linkage map contains the original 64 loci included in the first-generation map, plus an additional 84 microsatellite loci that were chosen specifically to increase coverage and assist with the anchoring and orientation of linkage groups to chromosomes. These additional loci were derived from (a) sequenced BAC clones that had been previously mapped to tammar wallaby chromosomes by fluorescence in situ hybridization (FISH), (b) End sequence from BACs subsequently FISH-mapped to tammar wallaby chromosomes, and (c) tammar wallaby genes orthologous to opossum genes predicted to fill gaps in the tammar wallaby linkage map as well as three X-linked markers from a published study. Based on these 148 loci, eight linkage groups were formed. These linkage groups were assigned (via FISH-mapped markers) to all seven autosomes and the X chromosome. The sexpooled map size is 1402.4 cM, which is estimated to provide 82.6{\%} total coverage of the genome, with an average interval distance of 10.9 cM between adjacent markers. The overall ratio of female/male map length is 0.84, which is comparable to the ratio of 0.78 obtained for the first-generation map. Conclusions: Construction of this second-generation genetic linkage map is a significant step towards complete coverage of the tammar wallaby genome and considerably extends that of the first-eneration map. It will be a valuable resource for ongoing tammar wallaby genetic research and assembling the genome sequence. The sexpooled map is available online at http://compldb.angis.org.au/.",
    author = "Chenwei Wang and Lee Webley and Ke-jun Wei and Matthew Wakefield and H Patel and Janine Deakin and Amber Alsop and {Marshall Graves}, Jennifer and Desmond Cooper and Frank Nicholas and Kyall Zenger",
    year = "2011",
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    Wang, C, Webley, L, Wei, K, Wakefield, M, Patel, H, Deakin, J, Alsop, A, Marshall Graves, J, Cooper, D, Nicholas, F & Zenger, K 2011, 'A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii)', BMC Genetics, vol. 12:72, pp. 1-16. https://doi.org/10.1186/1471-2156-12-72

    A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii). / Wang, Chenwei; Webley, Lee; Wei, Ke-jun; Wakefield, Matthew; Patel, H; Deakin, Janine; Alsop, Amber; Marshall Graves, Jennifer; Cooper, Desmond; Nicholas, Frank; Zenger, Kyall.

    In: BMC Genetics, Vol. 12:72, 2011, p. 1-16.

    Research output: Contribution to journalArticle

    TY - JOUR

    T1 - A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii)

    AU - Wang, Chenwei

    AU - Webley, Lee

    AU - Wei, Ke-jun

    AU - Wakefield, Matthew

    AU - Patel, H

    AU - Deakin, Janine

    AU - Alsop, Amber

    AU - Marshall Graves, Jennifer

    AU - Cooper, Desmond

    AU - Nicholas, Frank

    AU - Zenger, Kyall

    PY - 2011

    Y1 - 2011

    N2 - Background: The tammar wallaby, Macropus eugenii, a small kangaroo used for decades for studies of reproduction and metabolism, is the model Australian marsupial for genome sequencing and genetic investigations. The production of a more comprehensive cytogenetically-anchored genetic linkage map will significantly contribute to the deciphering of the tammar wallaby genome. It has great value as a resource to identify novel genes and for comparative studies, and is vital for the ongoing genome sequence assembly and gene ordering in this species. Results: A second-generation anchored tammar wallaby genetic linkage map has been constructed based on a total of 148 loci. The linkage map contains the original 64 loci included in the first-generation map, plus an additional 84 microsatellite loci that were chosen specifically to increase coverage and assist with the anchoring and orientation of linkage groups to chromosomes. These additional loci were derived from (a) sequenced BAC clones that had been previously mapped to tammar wallaby chromosomes by fluorescence in situ hybridization (FISH), (b) End sequence from BACs subsequently FISH-mapped to tammar wallaby chromosomes, and (c) tammar wallaby genes orthologous to opossum genes predicted to fill gaps in the tammar wallaby linkage map as well as three X-linked markers from a published study. Based on these 148 loci, eight linkage groups were formed. These linkage groups were assigned (via FISH-mapped markers) to all seven autosomes and the X chromosome. The sexpooled map size is 1402.4 cM, which is estimated to provide 82.6% total coverage of the genome, with an average interval distance of 10.9 cM between adjacent markers. The overall ratio of female/male map length is 0.84, which is comparable to the ratio of 0.78 obtained for the first-generation map. Conclusions: Construction of this second-generation genetic linkage map is a significant step towards complete coverage of the tammar wallaby genome and considerably extends that of the first-eneration map. It will be a valuable resource for ongoing tammar wallaby genetic research and assembling the genome sequence. The sexpooled map is available online at http://compldb.angis.org.au/.

    AB - Background: The tammar wallaby, Macropus eugenii, a small kangaroo used for decades for studies of reproduction and metabolism, is the model Australian marsupial for genome sequencing and genetic investigations. The production of a more comprehensive cytogenetically-anchored genetic linkage map will significantly contribute to the deciphering of the tammar wallaby genome. It has great value as a resource to identify novel genes and for comparative studies, and is vital for the ongoing genome sequence assembly and gene ordering in this species. Results: A second-generation anchored tammar wallaby genetic linkage map has been constructed based on a total of 148 loci. The linkage map contains the original 64 loci included in the first-generation map, plus an additional 84 microsatellite loci that were chosen specifically to increase coverage and assist with the anchoring and orientation of linkage groups to chromosomes. These additional loci were derived from (a) sequenced BAC clones that had been previously mapped to tammar wallaby chromosomes by fluorescence in situ hybridization (FISH), (b) End sequence from BACs subsequently FISH-mapped to tammar wallaby chromosomes, and (c) tammar wallaby genes orthologous to opossum genes predicted to fill gaps in the tammar wallaby linkage map as well as three X-linked markers from a published study. Based on these 148 loci, eight linkage groups were formed. These linkage groups were assigned (via FISH-mapped markers) to all seven autosomes and the X chromosome. The sexpooled map size is 1402.4 cM, which is estimated to provide 82.6% total coverage of the genome, with an average interval distance of 10.9 cM between adjacent markers. The overall ratio of female/male map length is 0.84, which is comparable to the ratio of 0.78 obtained for the first-generation map. Conclusions: Construction of this second-generation genetic linkage map is a significant step towards complete coverage of the tammar wallaby genome and considerably extends that of the first-eneration map. It will be a valuable resource for ongoing tammar wallaby genetic research and assembling the genome sequence. The sexpooled map is available online at http://compldb.angis.org.au/.

    U2 - 10.1186/1471-2156-12-72

    DO - 10.1186/1471-2156-12-72

    M3 - Article

    VL - 12:72

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    EP - 16

    JO - BMC Genetics

    JF - BMC Genetics

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