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Genome sequence and analysis of the Japanese morning glory Ipomoea nil

Author

Listed:
  • Atsushi Hoshino

    (National Institute for Basic Biology
    School of Life Science, SOKENDAI (The Graduate University for Advanced Studies))

  • Vasanthan Jayakumar

    (Keio University)

  • Eiji Nitasaka

    (Graduate School of Science, Kyushu University)

  • Atsushi Toyoda

    (National Institute of Genetics)

  • Hideki Noguchi

    (National Institute of Genetics)

  • Takehiko Itoh

    (Tokyo Institute of Technology)

  • Tadasu Shin-I

    (National Institute of Genetics)

  • Yohei Minakuchi

    (National Institute of Genetics)

  • Yuki Koda

    (Keio University)

  • Atsushi J. Nagano

    (Center for Ecological Research, Kyoto University
    Faculty of Agriculture, Ryukoku University)

  • Masaki Yasugi

    (Center for Ecological Research, Kyoto University
    Present address: National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan)

  • Mie N. Honjo

    (Center for Ecological Research, Kyoto University)

  • Hiroshi Kudoh

    (Center for Ecological Research, Kyoto University)

  • Motoaki Seki

    (RIKEN Center for Sustainable Resource Science
    Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology (JST), 4-1-8 Honcho)

  • Asako Kamiya

    (RIKEN Center for Sustainable Resource Science)

  • Toshiyuki Shiraki

    (RIKEN Brain Science Institute)

  • Piero Carninci

    (RIKEN Center for Life Science Technologies)

  • Erika Asamizu

    (Kazusa DNA Research Institute
    Present address: Faculty of Agriculture, Ryukoku University, Otsu, Shiga 520-2194, Japan)

  • Hiroyo Nishide

    (National Institute for Basic Biology)

  • Sachiko Tanaka

    (National Institute for Basic Biology)

  • Kyeung-Il Park

    (National Institute for Basic Biology
    Yeungnam University)

  • Yasumasa Morita

    (National Institute for Basic Biology
    Present address: Faculty of Agriculture, Meijo University, Kasugai 486-0804, Japan)

  • Kohei Yokoyama

    (Graduate School of Science, Kyushu University)

  • Ikuo Uchiyama

    (National Institute for Basic Biology
    School of Life Science, SOKENDAI (The Graduate University for Advanced Studies))

  • Yoshikazu Tanaka

    (Suntory Global Innovation Center Ltd)

  • Satoshi Tabata

    (Kazusa DNA Research Institute)

  • Kazuo Shinozaki

    (RIKEN Center for Sustainable Resource Science)

  • Yoshihide Hayashizaki

    (RIKEN Preventive Medicine and Diagnosis Innovation Program)

  • Yuji Kohara

    (National Institute of Genetics)

  • Yutaka Suzuki

    (Graduate School of Frontier Sciences, The University of Tokyo)

  • Sumio Sugano

    (Graduate School of Frontier Sciences, The University of Tokyo)

  • Asao Fujiyama

    (National Institute of Genetics
    National Institute of Informatics)

  • Shigeru Iida

    (National Institute for Basic Biology
    School of Life Science, SOKENDAI (The Graduate University for Advanced Studies)
    Present address: Graduate School of Nutritional and Environmental Sciences and Graduate School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan)

  • Yasubumi Sakakibara

    (Keio University)

Abstract

Ipomoea is the largest genus in the family Convolvulaceae. Ipomoea nil (Japanese morning glory) has been utilized as a model plant to study the genetic basis of floricultural traits, with over 1,500 mutant lines. In the present study, we have utilized second- and third-generation-sequencing platforms, and have reported a draft genome of I. nil with a scaffold N50 of 2.88 Mb (contig N50 of 1.87 Mb), covering 98% of the 750 Mb genome. Scaffolds covering 91.42% of the assembly are anchored to 15 pseudo-chromosomes. The draft genome has enabled the identification and cataloguing of the Tpn1 family transposons, known as the major mutagen of I. nil, and analysing the dwarf gene, CONTRACTED, located on the genetic map published in 1956. Comparative genomics has suggested that a whole genome duplication in Convolvulaceae, distinct from the recent Solanaceae event, has occurred after the divergence of the two sister families.

Suggested Citation

  • Atsushi Hoshino & Vasanthan Jayakumar & Eiji Nitasaka & Atsushi Toyoda & Hideki Noguchi & Takehiko Itoh & Tadasu Shin-I & Yohei Minakuchi & Yuki Koda & Atsushi J. Nagano & Masaki Yasugi & Mie N. Honjo, 2016. "Genome sequence and analysis of the Japanese morning glory Ipomoea nil," Nature Communications, Nature, vol. 7(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms13295
    DOI: 10.1038/ncomms13295
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