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Hoshino A, Jayakumar V, Nitasaka E, Toyoda A, Noguchi H, Itoh T, Shin-I 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. Genome sequence and analysis of the Japanese morning glory Ipomoea nil. Nat Commun 2016; 7:13295. [PMID: 27824041 PMCID: PMC5105172 DOI: 10.1038/ncomms13295] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 09/21/2016] [Indexed: 12/18/2022] Open
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.
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Affiliation(s)
- Atsushi Hoshino
- 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
| | - Vasanthan Jayakumar
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Eiji Nitasaka
- Graduate School of Science, Kyushu University, Fukuoka, Fukuoka 819-0395, Japan
| | - Atsushi Toyoda
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hideki Noguchi
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takehiko Itoh
- Department of Biological Information, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Tadasu Shin-I
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yohei Minakuchi
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yuki Koda
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Atsushi J Nagano
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan.,Faculty of Agriculture, Ryukoku University, Otsu, Shiga 520-2194, Japan
| | - Masaki Yasugi
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
| | - Mie N Honjo
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
| | - Motoaki Seki
- 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
| | - Asako Kamiya
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | | | - Piero Carninci
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Erika Asamizu
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Hiroyo Nishide
- National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Sachiko Tanaka
- National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Kyeung-Il Park
- National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan.,Department of Horticulture &Life Science, Yeungnam University, Gyeongbuk 712-749, Korea
| | - Yasumasa Morita
- National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Kohei Yokoyama
- Graduate School of Science, Kyushu University, Fukuoka, Fukuoka 819-0395, Japan
| | - Ikuo Uchiyama
- 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
| | - Yoshikazu Tanaka
- Suntory Global Innovation Center Ltd, Seika, Kyoto 619-0284, Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Kazuo Shinozaki
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan
| | - Yuji Kohara
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yutaka Suzuki
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0882, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 108-8639, Japan
| | - Asao Fujiyama
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.,Principles of Informatics Research Division, National Institute of Informatics, Chiyoda-ku, Tokyo 101-8430, Japan
| | - Shigeru Iida
- 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
| | - Yasubumi Sakakibara
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
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Ly T, Fukuoka H, Otaka A, Hoshino A, Iida S, Nitasaka E, Watanabe N, Kuboyama T. Development of EST-SSR markers of Ipomoea nil. BREEDING SCIENCE 2012; 62:99-104. [PMID: 23136520 PMCID: PMC3405949 DOI: 10.1270/jsbbs.62.99] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 12/22/2011] [Indexed: 05/16/2023]
Abstract
Although Japanese morning glory (Ipomoea nil (L.) Roth.) has been used intensively for genetic studies, DNA markers have not been developed in Ipomoea nil sufficient to cover all chromosomes. Therefore, we conducted microsatellite (simple sequence repeats, SSR) marker development in I. nil for future genetic studies. From 92,662 expressed sequence tag (EST) sequences, 514 unique microsatellite-containing ESTs were identified. Primer pairs were designed automatically in 326 SSRs. Of 150 SSRs examined, 75 showed polymorphisms among strains. A phenogram based on the SSR genotypes revealed the genetic relation among seven Japanese morning glories from five different regions of the world and an ivyleaf morning glory (I. hederacea Jacq.). The developed SSR markers might be applicable for genetic studies of morning glories and their relatives.
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Affiliation(s)
- Tong Ly
- College of Agriculture, Ibaraki University, 3-21-1 Chuou, Ami, Ibaraki 300-0393, Japan
| | - Hiroyuki Fukuoka
- National Institute of Vegetable and Tea Science, National Agriculture and Food Research Organization, 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Asami Otaka
- College of Agriculture, Ibaraki University, 3-21-1 Chuou, Ami, Ibaraki 300-0393, Japan
| | - Atsushi Hoshino
- National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Shigeru Iida
- National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Eiji Nitasaka
- Department of Biological Science, Graduate School of Science, Kyushu University, 6-10-1 Hakozaki, Higashi, Fukuoka 812-8581, Japan
| | - Nobuyoshi Watanabe
- College of Agriculture, Ibaraki University, 3-21-1 Chuou, Ami, Ibaraki 300-0393, Japan
| | - Tsutomu Kuboyama
- College of Agriculture, Ibaraki University, 3-21-1 Chuou, Ami, Ibaraki 300-0393, Japan
- Corresponding author (e-mail: )
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Iwasaki M, Nitasaka E. The FEATHERED gene is required for polarity establishment in lateral organs especially flowers of the Japanese morning glory (I pomoea nil ). PLANT MOLECULAR BIOLOGY 2006; 62:913-25. [PMID: 16972166 DOI: 10.1007/s11103-006-9066-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2006] [Accepted: 07/23/2006] [Indexed: 05/11/2023]
Abstract
Most strains harboring the feathered (fe) mutation in the Japanese morning glory (Ipomoea nil or Pharbitis nil) show deformed phenotypes such as upcurled leaves and separated or tubular petals. These phenotypes seem to be caused by loss of abaxial identity in lateral organs. The FE gene was isolated using the inserted transposon as a tag. An En/Spm-related transposable element, Tpn102, inserted in the fourth intron of the FE gene, was responsible for the fe mutation. FE encodes a GARP transcription factor closely related to Arabidopsis KANADI1 (KAN1), which promotes an abaxial cell fate. Genetic analyses and molecular studies, which showed that all fe mutant strains have the same fe allele despite their phenotypic differences, revealed that fe strains with strong phenotypes have additional mutations enhancing the fe phenotype. These findings and historical records of fe phenotypes suggest that these enhancer mutations were accumulated in the fe background during selection for strong phenotypes. The mutant phenotypes and molecular analysis of fe strains suggest that FE regulates the abaxial identity of lateral organs redundantly with modifier genes, as KAN1 does in Arabidopsis. FE, however, affects flower phenotype even in the single mutant unlike KAN1, moreover, modifier mutations affect flower phenotype only in the fe mutant background, suggesting that FE may play a more crucial role in promotion of abaxial cell fate in flowers of the Japanese morning glory.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Cell Polarity/genetics
- DNA Transposable Elements/genetics
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- DNA, Plant/chemistry
- DNA, Plant/genetics
- DNA, Plant/isolation & purification
- Flowers/genetics
- Flowers/growth & development
- Flowers/ultrastructure
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Plant
- In Situ Hybridization
- Ipomoea/cytology
- Ipomoea/genetics
- Ipomoea/growth & development
- Microscopy, Electron, Scanning
- Molecular Sequence Data
- Mutagenesis, Insertional
- Mutation/genetics
- Phenotype
- Phylogeny
- Plant Proteins/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Transcription Factors/genetics
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Affiliation(s)
- Mayumi Iwasaki
- Department of Biological Science, Graduate School of Science, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581, Japan
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Morita Y, Hoshino A, Kikuchi Y, Okuhara H, Ono E, Tanaka Y, Fukui Y, Saito N, Nitasaka E, Noguchi H, Iida S. Japanese morning glory dusky mutants displaying reddish-brown or purplish-gray flowers are deficient in a novel glycosylation enzyme for anthocyanin biosynthesis, UDP-glucose:anthocyanidin 3-O-glucoside-2''-O-glucosyltransferase, due to 4-bp insertions in the gene. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005; 42:353-63. [PMID: 15842621 DOI: 10.1111/j.1365-313x.2005.02383.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Bright blue or red flowers in the Japanese morning glory (Ipomoea nil) contain anthocyanidin 3-O-sophoroside derivatives, whereas the reddish-brown or purplish-gray petals in its dusky mutants accumulate anthocyanidin 3-O-glucoside derivatives. The Dusky gene was found to encode a novel glucosyltransferase, UDP-glucose:anthocyanidin 3-O-glucoside-2''-O-glucosyltransferase (3GGT), which mediates the glucosylation of anthocyanidin 3-O-glucosides to yield anthocyanidin 3-O-sophorosides. Ipomoea nil carries one copy of the 3GGT gene that contains no intron and produces 1.6-kbp transcripts mainly in the petals and tubes of flower buds at around 24 h before flower opening. The gene products of both In3GGT in I. nil and Ip3GGT in the common morning glory (Ipomoea purpurea) comprise 459 amino acids and showed a close relationship to the petunia UDP-rhamnose:anthocyanidin 3-O-glucoside-6''-O-rhamnosyltransferase (3RT), which controls the addition of a rhamnose molecule to anthocyanidin 3-O-glucosides for conversion into anthocyanidin 3-O-rutinosides. All of the 30 dusky mutants tested were found to carry the 4-bp insertion mutations GGAT or CGAT at an identical position near the 3' end of the gene, and the insertions caused frameshift mutations. The expected 3GGT enzymatic activities were found in the crude extracts of Escherichia coli, in which the 3GGT cDNA of I. nil or I. purpurea was expressed, while no such activity was detected in the extracts expressed with the dusky mutant cDNAs containing 4-bp insertions. Moreover, the introduced Ip3GGT cDNA efficiently produced 3GGT that converted cyanidin 3-O-glucoside into cyanidin 3-O-sophoroside in transgenic petunia plants.
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Affiliation(s)
- Yasumasa Morita
- National Institute for Basic Biology, Okazaki 444-8585, Japan
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