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  • Kiwi genome provides insights into evolution of a nocturnal lifestyle

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    HuynenPUB230.pdf (1.289Mb)
    Author(s)
    Le Duc, Diana
    Renaud, Gabriel
    Krishnan, Arunkumar
    Almen, Markus Sallman
    Huynen, Leon
    Prohaska, Sonja J
    Ongyerth, Matthias
    Bitarello, Barbara D
    Schioth, Helgi B
    Hofreiter, Michael
    Stadler, Peter F
    Pruefer, Kay
    Lambert, David
    Kelso, Janet
    Schoeneberg, Torsten
    Griffith University Author(s)
    Lambert, David M.
    Huynen, Leon
    Year published
    2015
    Metadata
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    Abstract
    Background: Kiwi, comprising five species from the genus Apteryx, are endangered, ground-dwelling bird species endemic to New Zealand. They are the smallest and only nocturnal representatives of the ratites. The timing of kiwi adaptation to a nocturnal niche and the genomic innovations, which shaped sensory systems and morphology to allow this adaptation, are not yet fully understood. Results: We sequenced and assembled the brown kiwi genome to 150-fold coverage and annotated the genome using kiwi transcript data and non-redundant protein information from multiple bird species. We identified evolutionary sequence changes ...
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    Background: Kiwi, comprising five species from the genus Apteryx, are endangered, ground-dwelling bird species endemic to New Zealand. They are the smallest and only nocturnal representatives of the ratites. The timing of kiwi adaptation to a nocturnal niche and the genomic innovations, which shaped sensory systems and morphology to allow this adaptation, are not yet fully understood. Results: We sequenced and assembled the brown kiwi genome to 150-fold coverage and annotated the genome using kiwi transcript data and non-redundant protein information from multiple bird species. We identified evolutionary sequence changes that underlie adaptation to nocturnality and estimated the onset time of these adaptations. Several opsin genes involved in color vision are inactivated in the kiwi. We date this inactivation to the Oligocene epoch, likely after the arrival of the ancestor of modern kiwi in New Zealand. Genome comparisons between kiwi and representatives of ratites, Galloanserae, and Neoaves, including nocturnal and song birds, show diversification of kiwi’s odorant receptors repertoire, which may reflect an increased reliance on olfaction rather than sight during foraging. Further, there is an enrichment of genes influencing mitochondrial function and energy expenditure among genes that are rapidly evolving specifically on the kiwi branch, which may also be linked to its nocturnal lifestyle. Conclusions: The genomic changes in kiwi vision and olfaction are consistent with changes that are hypothesized to occur during adaptation to nocturnal lifestyle in mammals. The kiwi genome provides a valuable genomic resource for future genome-wide comparative analyses to other extinct and extant diurnal ratites.
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    Journal Title
    Genome Biology
    Volume
    16
    DOI
    https://doi.org/10.1186/s13059-015-0711-4
    Copyright Statement
    © Le Duc et al. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
    Subject
    Biological Sciences not elsewhere classified
    Environmental Sciences
    Biological Sciences
    Information and Computing Sciences
    Publication URI
    http://hdl.handle.net/10072/102550
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    • Journal articles

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