Genome sequence and analysis of the Japanese morning glory Ipomoea nil

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, Hiroshi Kudoh, Motoaki Seki, Asako Kamiya, Toshiyuki Shiraki, Piero Carninci, Erika Asamizu, Hiroyo Nishide, Sachiko Tanaka, Kyeung-Il Park, Yasumasa Morita, Kohei Yokoyama, Ikuo Uchiyama, Yoshikazu Tanaka, Satoshi Tabata, Kazuo Shinozaki, Yoshihide Hayashizaki, Yuji Kohara, Yutaka Suzuki, Sumio Sugano, Asao Fujiyama, Shigeru Iida and Yasubumi Sakakibara ()
Additional contact information
Atsushi Hoshino: National Institute for Basic Biology
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
Masaki Yasugi: Center for Ecological Research, Kyoto University
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
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
Hiroyo Nishide: National Institute for Basic Biology
Sachiko Tanaka: National Institute for Basic Biology
Kyeung-Il Park: National Institute for Basic Biology
Yasumasa Morita: National Institute for Basic Biology
Kohei Yokoyama: Graduate School of Science, Kyushu University
Ikuo Uchiyama: National Institute for Basic Biology
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
Shigeru Iida: National Institute for Basic Biology
Yasubumi Sakakibara: Keio University

Nature Communications, 2016, vol. 7, issue 1, 1-10

Abstract: 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.

Date: 2016
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DOI: 10.1038/ncomms13295

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