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, 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 TanakaKyeung 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, Yasubumi Sakakibara

Research output: Contribution to journalArticle

46 Citations (Scopus)

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.

Original languageEnglish
Article number13295
JournalNature Communications
Volume7
DOIs
Publication statusPublished - 2016 Nov 8

Fingerprint

Ipomoea nil
morning
genome
Sequence Analysis
Convolvulaceae
Genes
Genome
draft
coverings
Scaffolds
mutagens
Ipomoea
Cataloging
Solanaceae
Chromosomes, Human, Pair 15
sequencing
chromosomes
Mutagens
Genomics
genes

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

Hoshino, A., Jayakumar, V., Nitasaka, E., Toyoda, A., Noguchi, H., Itoh, T., ... Sakakibara, Y. (2016). Genome sequence and analysis of the Japanese morning glory Ipomoea nil. Nature Communications, 7, [13295]. https://doi.org/10.1038/ncomms13295

Genome sequence and analysis of the Japanese morning glory Ipomoea nil. / Hoshino, Atsushi; Jayakumar, Vasanthan; Nitasaka, Eiji; Toyoda, Atsushi; Noguchi, Hideki; Itoh, Takehiko; Shin, Tadasu; Minakuchi, Yohei; Koda, Yuki; Nagano, Atsushi J.; Yasugi, Masaki; Honjo, Mie N.; Kudoh, Hiroshi; Seki, Motoaki; Kamiya, Asako; Shiraki, Toshiyuki; Carninci, Piero; Asamizu, Erika; Nishide, Hiroyo; Tanaka, Sachiko; Park, Kyeung Il; Morita, Yasumasa; Yokoyama, Kohei; Uchiyama, Ikuo; Tanaka, Yoshikazu; Tabata, Satoshi; Shinozaki, Kazuo; Hayashizaki, Yoshihide; Kohara, Yuji; Suzuki, Yutaka; Sugano, Sumio; Fujiyama, Asao; Iida, Shigeru; Sakakibara, Yasubumi.

In: Nature Communications, Vol. 7, 13295, 08.11.2016.

Research output: Contribution to journalArticle

Hoshino, A, Jayakumar, V, Nitasaka, E, Toyoda, A, Noguchi, H, Itoh, T, Shin, T, Minakuchi, Y, Koda, Y, Nagano, AJ, Yasugi, M, Honjo, MN, Kudoh, H, Seki, M, Kamiya, A, Shiraki, T, Carninci, P, Asamizu, E, Nishide, H, Tanaka, S, Park, KI, Morita, Y, Yokoyama, K, Uchiyama, I, Tanaka, Y, Tabata, S, Shinozaki, K, Hayashizaki, Y, Kohara, Y, Suzuki, Y, Sugano, S, Fujiyama, A, Iida, S & Sakakibara, Y 2016, 'Genome sequence and analysis of the Japanese morning glory Ipomoea nil', Nature Communications, vol. 7, 13295. https://doi.org/10.1038/ncomms13295
Hoshino A, Jayakumar V, Nitasaka E, Toyoda A, Noguchi H, Itoh T et al. Genome sequence and analysis of the Japanese morning glory Ipomoea nil. Nature Communications. 2016 Nov 8;7. 13295. https://doi.org/10.1038/ncomms13295
Hoshino, Atsushi ; Jayakumar, Vasanthan ; Nitasaka, Eiji ; Toyoda, Atsushi ; Noguchi, Hideki ; Itoh, Takehiko ; Shin, Tadasu ; Minakuchi, Yohei ; Koda, Yuki ; Nagano, Atsushi J. ; Yasugi, Masaki ; Honjo, Mie N. ; Kudoh, Hiroshi ; Seki, Motoaki ; Kamiya, Asako ; Shiraki, Toshiyuki ; Carninci, Piero ; Asamizu, Erika ; Nishide, Hiroyo ; Tanaka, Sachiko ; Park, Kyeung Il ; Morita, Yasumasa ; Yokoyama, Kohei ; Uchiyama, Ikuo ; Tanaka, Yoshikazu ; Tabata, Satoshi ; Shinozaki, Kazuo ; Hayashizaki, Yoshihide ; Kohara, Yuji ; Suzuki, Yutaka ; Sugano, Sumio ; Fujiyama, Asao ; Iida, Shigeru ; Sakakibara, Yasubumi. / Genome sequence and analysis of the Japanese morning glory Ipomoea nil. In: Nature Communications. 2016 ; Vol. 7.
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