Comprehensive Transcriptome Profiling Reveals Long Noncoding RNA Expression and Alternative Splicing Regulation during Fruit Development and Ripening in Kiwifruit (Actinidia chinensis).
Genomic and transcriptomic data on kiwifruit (Actinidia chinensis) in public databases are very limited despite its nutritional and economic value. Previously, we have constructed and sequenced nine fruit RNA-Seq libraries of A. chinensis "Hongyang" at immature, mature, and postharvest ripening stages of fruit development, and generated over 66.2 million paired-end and 24.4 million single-end reads. From this dataset, here we have identified 7051 long noncoding RNAs (lncRNAs), 29,327 alternative splicing (AS) events and 2980 novel protein-coding genes that were not annotated in the draft genome of "Hongyang." AS events were demonstrated in genes involved in the synthesis of nutritional metabolites in fruit, such as ascorbic acids, carotenoids, anthocyanins, and chlorophylls, and also in genes in the ethylene signaling pathway, which plays an indispensable role in fruit ripening. Additionally, transcriptome profiles and the contents of sugars, organic and main amino acids were compared between immature, mature, and postharvest ripening stages in kiwifruits. A total of 5931 differentially expressed genes were identified, including those associated with the metabolism of sugar, organic acid, and main amino acids. The data generated in this study provide a foundation for further studies of fruit development and ripening in kiwifruit, and identify candidate genes and regulatory elements that could serve as targets for improving important agronomic traits through marker assisted breeding and biotechnology.
Department of Biological Sciences, School of Biotechnology and Food Engineering, Hefei University of TechnologyHefei, China; 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 UniversityChengdu, China.
Wei
W
Tang
Section of Plant Biology, Boyce Thompson Institute for Plant Research, Cornell University Ithaca, NY, USA.
Yi
Y
Zheng
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, China.
Jing
J
Dong
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, China.
Jia
J
Yu
Department of Biological Sciences, School of Biotechnology and Food Engineering, Hefei University of Technology Hefei, China.
Junyang
J
Yue
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, China.
Fangfang
F
Liu
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, China.
Xiuhong
X
Guo
Department of Biological Sciences, School of Biotechnology and Food Engineering, Hefei University of Technology Hefei, China.
Shengxiong
S
Huang
U.S. Department of Agriculture - Agricultural Research Service Kearneysville, WV, USA.
Michael
M
Wisniewski
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, China.
Jiaqi
J
Sun
Department of Biological Sciences, School of Biotechnology and Food Engineering, Hefei University of Technology Hefei, China.
Xiangli
X
Niu
Sichuan Technical Exchange Center Chengdu, China.
Jian
J
Ding
Department of Biological Sciences, School of Biotechnology and Food Engineering, Hefei University of Technology Hefei, China.
Jia
J
Liu
Section of Plant Biology, Boyce Thompson Institute for Plant Research, Cornell University Ithaca, NY, USA.
Zhangjun
Z
Fei
Department of Biological Sciences, School of Biotechnology and Food Engineering, Hefei University of TechnologyHefei, China; 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 UniversityChengdu, China.
Yongsheng
Y
Liu
alternative splicing; fruit development and ripening; gene expression; long noncoding RNAs; novel genes; transcriptome profiling