Whole transcriptome sequencing reveals genes involved in plastid/chloroplast division and development are regulated by the HP1/DDB1 at an early stage of tomato fruit development

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• 作者：Xiaofeng Tang (1)
  Zizhi Tang (1)
  Shengxiong Huang (2)
  Jikai Liu (1)
  Jia Liu (2)
  Wei Shi (2)
  Xuefen Tian (1)
  Yuxiang Li (1)
  Danfeng Zhang (2)
  Jian Yang (1)
  Yongfeng Gao (1)
  Deer Zeng (1)
  Pei Hou (1)
  Xiangli Niu (2) (3)
  Ying Cao (1) (4)
  Guangwei Li (2)
  Xiao Li (1)
  Fangming Xiao (3)
  Yongsheng Liu (1) (2)
  
• 关键词：Alternative splicing ; DDB1 ; Pigmentation ; Plastid/Chloroplast ; Tomato ; Transcriptome
• 刊名：Planta
• 出版年：2013
• 出版时间：November 2013
• 年：2013
• 卷：238
• 期：5
• 页码：923-936
• 全文大小：
• 作者单位：Xiaofeng Tang (1)
  Zizhi Tang (1)
  Shengxiong Huang (2)
  Jikai Liu (1)
  Jia Liu (2)
  Wei Shi (2)
  Xuefen Tian (1)
  Yuxiang Li (1)
  Danfeng Zhang (2)
  Jian Yang (1)
  Yongfeng Gao (1)
  Deer Zeng (1)
  Pei Hou (1)
  Xiangli Niu (2) (3)
  Ying Cao (1) (4)
  Guangwei Li (2)
  Xiao Li (1)
  Fangming Xiao (3)
  Yongsheng Liu (1) (2)
  
  1. Ministry of Education Key Laboratory for Bio-resource and Eco-environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610064, China
  2. School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei, 230009, China
  3. Department of Plant, Soil and Entomological Sciences, University of Idaho Moscow, Moscow, ID, 83844-2339, USA
  4. School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
  
• ISSN：1432-2048

文摘

The phenotype of tomato high pigment-1 (hp1) mutant is characterized by overproduction of pigments including chlorophyll and carotenoids during fruit development and ripening. Although the increased plastid compartment size has been thought to largely attribute to the enhanced pigmentation, the molecular aspects of how the HP1/DDB1 gene manipulates plastid biogenesis and development are largely unknown. In the present study, we compared transcriptome profiles of immature fruit pericarp tissue between tomato cv. Ailsa Craig (WT) and its isogenic hp1 mutant. Over 20 million sequence reads, representing?>?1.6?Gb sequence data per sample, were generated and assembled into 21,972 and 22,167 gene models in WT and hp1, respectively, accounting for over 60?% official gene models in both samples. Subsequent analyses revealed that 8,322 and 7,989 alternative splicing events, 8833 or 8510 extended 5?UTRs, 8,263 or 8,939 extended 3?UTRs, and 1,136 and 1,133 novel transcripts, exist in WT and hp1, respectively. Significant differences in expression level of 880 genes were detected between the WT and hp1, many of which are involved in signaling transduction, transcription regulation and biotic and abiotic stresses response. Distinctly, RNA-seq datasets, quantitative RT-PCR analyses demonstrate that, in hp1 mutant pericarp tissue at early developmental stage, an apparent expression alteration was found in several regulators directly involved in plastid division and development. These results provide a useful reference for a more accurate and more detailed characterization of the molecular process in the development and pigmentation of tomato fruits.