The radish genome and comprehensive gene expression profile of tuberous root formation and development

Yuki Mitsui; Michihiko Shimomura; Kenji Komatsu; Nobukazu Namiki; Mari Shibata-Hatta; Misaki Imai; Yuichi Katayose; Yoshiyuki Mukai; Hiroyuki Kanamori; Kanako Kurita; Tsutomu Kagami; Akihito Wakatsuki; Hajime Ohyanagi; Hiroshi Ikawa; Nobuhiro Minaka; Kunihiro Nakagawa; Yu Shiwa; Takuji Sasaki

doi:10.1038/srep10835

The radish genome and comprehensive gene expression profile of tuberous root formation and development

Yuki Mitsui^*, Michihiko Shimomura, Kenji Komatsu, Nobukazu Namiki, Mari Shibata-Hatta, Misaki Imai, Yuichi Katayose, Yoshiyuki Mukai, Hiroyuki Kanamori, Kanako Kurita, Tsutomu Kagami, Akihito Wakatsuki, Hajime Ohyanagi, Hiroshi Ikawa, Nobuhiro Minaka, Kunihiro Nakagawa, Yu Shiwa, Takuji Sasaki

^*Corresponding author for this work

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

138 Citations (SciVal)

Abstract

Understanding the processes that regulate plant sink formation and development at the molecular level will contribute to the areas of crop breeding, food production and plant evolutionary studies. We report the annotation and analysis of the draft genome sequence of the radish Raphanus sativus var. hortensis (long and thick root radish) and transcriptome analysis during root development. Based on the hybrid assembly approach of next-generation sequencing, a total of 383 Mb (N50 scaffold: 138.17 kb) of sequences of the radish genome was constructed containing 54,357 genes. Syntenic and phylogenetic analyses indicated that divergence between Raphanus and Brassica coincide with the time of whole genome triplication (WGT), suggesting that WGT triggered diversification of Brassiceae crop plants. Further transcriptome analysis showed that the gene functions and pathways related to carbohydrate metabolism were prominently activated in thickening roots, particularly in cell proliferating tissues. Notably, the expression levels of sucrose synthase 1 (SUS1) were correlated with root thickening rates. We also identified the genes involved in pungency synthesis and their transcription factors.

Original language	English (US)
Article number	10835
Journal	Scientific Reports
Volume	5
DOIs	https://doi.org/10.1038/srep10835
State	Published - Jun 9 2015
Externally published	Yes

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UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1038/srep10835

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Mitsui, Y., Shimomura, M., Komatsu, K., Namiki, N., Shibata-Hatta, M., Imai, M., Katayose, Y., Mukai, Y., Kanamori, H., Kurita, K., Kagami, T., Wakatsuki, A., Ohyanagi, H., Ikawa, H., Minaka, N., Nakagawa, K., Shiwa, Y., & Sasaki, T. (2015). The radish genome and comprehensive gene expression profile of tuberous root formation and development. Scientific Reports, 5, Article 10835. https://doi.org/10.1038/srep10835

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title = "The radish genome and comprehensive gene expression profile of tuberous root formation and development",

abstract = "Understanding the processes that regulate plant sink formation and development at the molecular level will contribute to the areas of crop breeding, food production and plant evolutionary studies. We report the annotation and analysis of the draft genome sequence of the radish Raphanus sativus var. hortensis (long and thick root radish) and transcriptome analysis during root development. Based on the hybrid assembly approach of next-generation sequencing, a total of 383 Mb (N50 scaffold: 138.17 kb) of sequences of the radish genome was constructed containing 54,357 genes. Syntenic and phylogenetic analyses indicated that divergence between Raphanus and Brassica coincide with the time of whole genome triplication (WGT), suggesting that WGT triggered diversification of Brassiceae crop plants. Further transcriptome analysis showed that the gene functions and pathways related to carbohydrate metabolism were prominently activated in thickening roots, particularly in cell proliferating tissues. Notably, the expression levels of sucrose synthase 1 (SUS1) were correlated with root thickening rates. We also identified the genes involved in pungency synthesis and their transcription factors.",

author = "Yuki Mitsui and Michihiko Shimomura and Kenji Komatsu and Nobukazu Namiki and Mari Shibata-Hatta and Misaki Imai and Yuichi Katayose and Yoshiyuki Mukai and Hiroyuki Kanamori and Kanako Kurita and Tsutomu Kagami and Akihito Wakatsuki and Hajime Ohyanagi and Hiroshi Ikawa and Nobuhiro Minaka and Kunihiro Nakagawa and Yu Shiwa and Takuji Sasaki",

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Mitsui, Y, Shimomura, M, Komatsu, K, Namiki, N, Shibata-Hatta, M, Imai, M, Katayose, Y, Mukai, Y, Kanamori, H, Kurita, K, Kagami, T, Wakatsuki, A, Ohyanagi, H, Ikawa, H, Minaka, N, Nakagawa, K, Shiwa, Y & Sasaki, T 2015, 'The radish genome and comprehensive gene expression profile of tuberous root formation and development', Scientific Reports, vol. 5, 10835. https://doi.org/10.1038/srep10835

TY - JOUR

T1 - The radish genome and comprehensive gene expression profile of tuberous root formation and development

AU - Mitsui, Yuki

AU - Shimomura, Michihiko

AU - Komatsu, Kenji

AU - Namiki, Nobukazu

AU - Shibata-Hatta, Mari

AU - Imai, Misaki

AU - Katayose, Yuichi

AU - Mukai, Yoshiyuki

AU - Kanamori, Hiroyuki

AU - Kurita, Kanako

AU - Kagami, Tsutomu

AU - Wakatsuki, Akihito

AU - Ohyanagi, Hajime

AU - Ikawa, Hiroshi

AU - Minaka, Nobuhiro

AU - Nakagawa, Kunihiro

AU - Shiwa, Yu

AU - Sasaki, Takuji

PY - 2015/6/9

Y1 - 2015/6/9

N2 - Understanding the processes that regulate plant sink formation and development at the molecular level will contribute to the areas of crop breeding, food production and plant evolutionary studies. We report the annotation and analysis of the draft genome sequence of the radish Raphanus sativus var. hortensis (long and thick root radish) and transcriptome analysis during root development. Based on the hybrid assembly approach of next-generation sequencing, a total of 383 Mb (N50 scaffold: 138.17 kb) of sequences of the radish genome was constructed containing 54,357 genes. Syntenic and phylogenetic analyses indicated that divergence between Raphanus and Brassica coincide with the time of whole genome triplication (WGT), suggesting that WGT triggered diversification of Brassiceae crop plants. Further transcriptome analysis showed that the gene functions and pathways related to carbohydrate metabolism were prominently activated in thickening roots, particularly in cell proliferating tissues. Notably, the expression levels of sucrose synthase 1 (SUS1) were correlated with root thickening rates. We also identified the genes involved in pungency synthesis and their transcription factors.

AB - Understanding the processes that regulate plant sink formation and development at the molecular level will contribute to the areas of crop breeding, food production and plant evolutionary studies. We report the annotation and analysis of the draft genome sequence of the radish Raphanus sativus var. hortensis (long and thick root radish) and transcriptome analysis during root development. Based on the hybrid assembly approach of next-generation sequencing, a total of 383 Mb (N50 scaffold: 138.17 kb) of sequences of the radish genome was constructed containing 54,357 genes. Syntenic and phylogenetic analyses indicated that divergence between Raphanus and Brassica coincide with the time of whole genome triplication (WGT), suggesting that WGT triggered diversification of Brassiceae crop plants. Further transcriptome analysis showed that the gene functions and pathways related to carbohydrate metabolism were prominently activated in thickening roots, particularly in cell proliferating tissues. Notably, the expression levels of sucrose synthase 1 (SUS1) were correlated with root thickening rates. We also identified the genes involved in pungency synthesis and their transcription factors.

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VL - 5

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The radish genome and comprehensive gene expression profile of tuberous root formation and development

Abstract

ASJC Scopus subject areas

UN SDGs

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