Journal of Integrative Agriculture ›› 2015, Vol. 14 ›› Issue (1): 42-49.DOI: 10.1016/S2095-3119(14)60821-2

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Identification of microRNAs in two species of tomato, Solanum lycopersicum and Solanum habrochaites, by deep sequencing

 FAN Shan-shan, LI Qian-nan, GUO Guang-jun, GAO Jian-chang, WANG Xiao-xuan, GUO Yanmei, John C. Snyder, DU Yong-chen   

  1. 1、Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
    2、Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100094, P.R.China
    3、Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
    4、Department of Agronomy, University of Kentucky, Lexington, Kentucky 40546-0091, USA
  • 收稿日期:2014-02-13 出版日期:2015-01-01 发布日期:2015-01-08
  • 通讯作者: DU Yongchen,Fax: +86-10-62174123, E-mail: duyongchen@caas.cn
  • 作者简介:FAN Shan-shan, E-mail: fanshanshan_nine@126.com;* These authors contributed equally to this study
  • 基金资助:

    This work was supported by the National Basic Research Program of China (2009CB11900) and the Special Fund for Agro-Scientific Research in the Public Interest, China (201003065).

Identification of microRNAs in two species of tomato, Solanum lycopersicum and Solanum habrochaites, by deep sequencing

 FAN Shan-shan, LI Qian-nan, GUO Guang-jun, GAO Jian-chang, WANG Xiao-xuan, GUO Yanmei, John C. Snyder, DU Yong-chen   

  1. 1、Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
    2、Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100094, P.R.China
    3、Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
    4、Department of Agronomy, University of Kentucky, Lexington, Kentucky 40546-0091, USA
  • Received:2014-02-13 Online:2015-01-01 Published:2015-01-08
  • Contact: DU Yongchen,Fax: +86-10-62174123, E-mail: duyongchen@caas.cn
  • About author:FAN Shan-shan, E-mail: fanshanshan_nine@126.com;* These authors contributed equally to this study
  • Supported by:

    This work was supported by the National Basic Research Program of China (2009CB11900) and the Special Fund for Agro-Scientific Research in the Public Interest, China (201003065).

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摘要： MicroRNAs (miRNAs) are ~21 nucleotide (nt), endogenous RNAs that regulate gene expression in plants. Increasing evidence suggests that miRNAs play an important role in species-specific development in plants. However, the detailed miRNA profile divergence has not been performed among tomato species. In this study, the small RNA (sRNA) profiles of Solanum lycopersicum cultivar 9706 and Solanum habrochaites species PI 134417 were obtained by deep sequencing. Sixty-three known miRNA families were identified from these two species, of which 39 were common. Further miRNA profile comparison showed that 24 known non-conserved miRNA families were species-specific between these two tomato species. In addition, six conserved miRNA families displayed an apparent divergent expression pattern between the two tomato species. Our results suggested that species-specific, non-conserved miRNAs and divergent expression of conserved miRNAs might contribute to developmental changes and phenotypic variation between the two tomato species. Twenty new miRNAs were also identified in S. lycopersicum. This research significantly increases the number of known miRNA families in tomato and provides the first set of small RNAs in S. habrochaites. It also suggests that miRNAs have an important role in species-specific plant developmental regulation.

关键词: microRNAs , Solanum lycopersicum , Solanum habrochaites , deep sequencing

Abstract: MicroRNAs (miRNAs) are ~21 nucleotide (nt), endogenous RNAs that regulate gene expression in plants. Increasing evidence suggests that miRNAs play an important role in species-specific development in plants. However, the detailed miRNA profile divergence has not been performed among tomato species. In this study, the small RNA (sRNA) profiles of Solanum lycopersicum cultivar 9706 and Solanum habrochaites species PI 134417 were obtained by deep sequencing. Sixty-three known miRNA families were identified from these two species, of which 39 were common. Further miRNA profile comparison showed that 24 known non-conserved miRNA families were species-specific between these two tomato species. In addition, six conserved miRNA families displayed an apparent divergent expression pattern between the two tomato species. Our results suggested that species-specific, non-conserved miRNAs and divergent expression of conserved miRNAs might contribute to developmental changes and phenotypic variation between the two tomato species. Twenty new miRNAs were also identified in S. lycopersicum. This research significantly increases the number of known miRNA families in tomato and provides the first set of small RNAs in S. habrochaites. It also suggests that miRNAs have an important role in species-specific plant developmental regulation.

Key words: microRNAs , Solanum lycopersicum , Solanum habrochaites , deep sequencing