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 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; Yasubumi Sakakibara

doi:10.1038/ncomms13295

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

Biology, Faculty of Science

Research output: Contribution to journal › Article › peer-review

102 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 language	English
Article number	13295
Journal	Nature communications
Volume	7
DOIs	https://doi.org/10.1038/ncomms13295
Publication status	Published - Nov 8 2016

All Science Journal Classification (ASJC) codes

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

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10.1038/ncomms13295

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Hoshino, A., Jayakumar, V., Nitasaka, E., Toyoda, A., Noguchi, H., Itoh, T., Shin, T., Minakuchi, Y., Koda, Y., Nagano, A. J., Yasugi, M., Honjo, M. N., Kudoh, H., Seki, M., Kamiya, A., Shiraki, T., Carninci, P., Asamizu, E., Nishide, H., ... Sakakibara, Y. (2016). Genome sequence and analysis of the Japanese morning glory Ipomoea nil. Nature communications, 7, Article 13295. https://doi.org/10.1038/ncomms13295

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

@article{955632a0eb4d4ebd964c08e097769e3e,

title = "Genome sequence and analysis of the Japanese morning glory Ipomoea nil",

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.",

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

note = "Funding Information: This work was supported by MEXT KAKENHI Grant Number 221S0002, JSPS KAKENHI Grant Numbers 22770047 and 24570062, the Model Plant Research Facility, NIBB BioResource Center, the Functional Genomics Facility, NIBB Core Research Facilities, and the Joint Usage/Research program of the Center for Ecological Research, Kyoto University. Publisher Copyright: {\textcopyright} 2016 The Author(s).",

year = "2016",

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doi = "10.1038/ncomms13295",

language = "English",

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T1 - Genome sequence and analysis of the Japanese morning glory Ipomoea nil

AU - Hoshino, Atsushi

AU - Jayakumar, Vasanthan

AU - Nitasaka, Eiji

AU - Toyoda, Atsushi

AU - Noguchi, Hideki

AU - Itoh, Takehiko

AU - Shin, Tadasu

AU - Minakuchi, Yohei

AU - Koda, Yuki

AU - Nagano, Atsushi J.

AU - Yasugi, Masaki

AU - Honjo, Mie N.

AU - Kudoh, Hiroshi

AU - Seki, Motoaki

AU - Kamiya, Asako

AU - Shiraki, Toshiyuki

AU - Carninci, Piero

AU - Asamizu, Erika

AU - Nishide, Hiroyo

AU - Tanaka, Sachiko

AU - Park, Kyeung Il

AU - Morita, Yasumasa

AU - Yokoyama, Kohei

AU - Uchiyama, Ikuo

AU - Tanaka, Yoshikazu

AU - Tabata, Satoshi

AU - Shinozaki, Kazuo

AU - Hayashizaki, Yoshihide

AU - Kohara, Yuji

AU - Suzuki, Yutaka

AU - Sugano, Sumio

AU - Fujiyama, Asao

AU - Iida, Shigeru

AU - Sakakibara, Yasubumi

N1 - Funding Information: This work was supported by MEXT KAKENHI Grant Number 221S0002, JSPS KAKENHI Grant Numbers 22770047 and 24570062, the Model Plant Research Facility, NIBB BioResource Center, the Functional Genomics Facility, NIBB Core Research Facilities, and the Joint Usage/Research program of the Center for Ecological Research, Kyoto University. Publisher Copyright: © 2016 The Author(s).

PY - 2016/11/8

Y1 - 2016/11/8

N2 - 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.

AB - 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.

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VL - 7

JO - Nature communications

JF - Nature communications

M1 - 13295

ER -

Genome sequence and analysis of the Japanese morning glory Ipomoea nil

Abstract

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