Genome sequence and analysis of the Japanese morning glory Ipomoea nil.
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.
National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan.|Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan.
Atsushi
0000-0003-1926-5028
A
Hoshino
Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan.
Vasanthan
V
Jayakumar
Graduate School of Science, Kyushu University, Fukuoka, Fukuoka 819-0395, Japan.
Eiji
E
Nitasaka
National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
Atsushi
A
Toyoda
National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
Hideki
H
Noguchi
Department of Biological Information, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.
Takehiko
T
Itoh
National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
Tadasu
T
Shin-I
National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
Yohei
Y
Minakuchi
Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan.
Yuki
Y
Koda
Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan.|Faculty of Agriculture, Ryukoku University, Otsu, Shiga 520-2194, Japan.
Atsushi J
AJ
Nagano
Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan.
Masaki
M
Yasugi
Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan.
Mie N
MN
Honjo
Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan.
Hiroshi
H
Kudoh
RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan.|Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
Motoaki
M
Seki
RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan.
Asako
A
Kamiya
RIKEN Brain Science Institute, Wako, Saitama 351-0198, Japan.
Toshiyuki
T
Shiraki
RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.
Piero
0000-0001-7202-7243
P
Carninci
Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.
Erika
E
Asamizu
National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan.
Hiroyo
H
Nishide
National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan.
Sachiko
S
Tanaka
National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan.|Department of Horticulture &Life Science, Yeungnam University, Gyeongbuk 712-749, Korea.
Kyeung-Il
KI
Park
National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan.
Yasumasa
Y
Morita
Graduate School of Science, Kyushu University, Fukuoka, Fukuoka 819-0395, Japan.
Kohei
K
Yokoyama
National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan.|Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan.
Ikuo
I
Uchiyama
Suntory Global Innovation Center Ltd, Seika, Kyoto 619-0284, Japan.
Yoshikazu
Y
Tanaka
Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.
Satoshi
S
Tabata
RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan.
Kazuo
K
Shinozaki
RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan.
Yoshihide
Y
Hayashizaki
National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.
Yuji
Y
Kohara
Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0882, Japan.
Yutaka
Y
Suzuki
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 108-8639, Japan.
Sumio
S
Sugano
National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.|Principles of Informatics Research Division, National Institute of Informatics, Chiyoda-ku, Tokyo 101-8430, Japan.
Asao
A
Fujiyama
National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan.|Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan.
Shigeru
S
Iida
Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan.
Yasubumi
Y
Sakakibara
D001483:Base Sequence; D060406:Brassinosteroids / Q000096:biosynthesis; D004251:DNA Transposable Elements / Q000235:genetics; D019143:Evolution, Molecular; D017343:Genes, Plant; D018745:Genome, Plant; D049915:Ipomoea nil / Q000235:genetics*; D058977:Molecular Sequence Annotation; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D019895:Transposases / Q000378:metabolism
D060406:Brassinosteroids; D004251:DNA Transposable Elements; D019895:Transposases