Comprehensive transcriptome profiling reveals long noncoding RNA expression and alternative splicing regulation during fruit development and ripening in kiwifruit (Actinidia chinensis)

Authors: TANG, WEI - Hefei University Of Technology; ZHENG, YI - Cornell University; DONG, JING - Sichuan University; YU, JIA - Sichuan University; YUE, JUNYANG - Hefei University Of Technology; LIU, FANGFANG - Sichuan University; GUO, XIUHONG - Sichuan University; HUANG, SHENGXIONG - Hefei University Of Technology; Wisniewski, Michael; SUN, JIAQI - Sichuan University; NIU, XIANGLI - Hefei University Of Technology; DING, JIAN - Sichuan Institute; LIU, JIA - Hefei University Of Technology; FEI, ZHANGJUN - Cornell University; LIU, YONGSHENG - Hefei University Of Technology

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/4/2016
Publication Date: 3/29/2016
Citation: Tang, W., Zheng, Y., Dong, J., Yu, J., Yue, J., Liu, F., Guo, X., Huang, S., Wisniewski, M.E., Sun, J., Niu, X., Ding, J., Liu, J., Fei, Z., Liu, Y. 2016. Comprehensive transcriptome profiling reveals long noncoding RNA expression and alternative splicing regulation during fruit development and ripening in kiwifruit (Actinidia chinensis). Frontiers in Plant Science. 7(335):1-15.

Interpretive Summary: Public databases of plant genomes represent invaluable resources for data mining by breeders, molecular biologists, and research scientists in general. Genomic databases for kiwifruit, however, are rather limited, despite the nutritional and economic importance of this fruit worldwide. The present sequencing project mined a previously constructed database of kiwifruit genes that were expressed at various stages of fruit development. The data mining identified 7,051 coding genes and 29,327 alternative transcripts, which represent alterations in which genes are transcribed leading to different proteins. Alternative splicing was identified in genes coding for many different proteins that are responsible for a variety of different metabolic processes. The project also identified genes that were differentially expressed at different stages of fruit development. This project provides a foundation for additional studies designed to identify key regulatory genes related to kiwifruit development and the identification of genes that can be used by plant breeders utilizing marker-assisted selection.

Technical Abstract: 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 cv. '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 7,051 long noncoding RNAs (lncRNAs), 29,327 alternative splicing events and 2,980 novel protein-coding genes that were not annotated in the draft genome of 'Hongyang'. Alternative splicing events were demonstrated in genes involved in the synthesis of nutritional metabolites in fruit, such as ascorbic acid, carotenoids, anthocyanins and chlorophyll, and also in genes in the ethylene signaling pathway, which plays an indispensable role in fruit ripening. Additionally, transcriptome profiles were compared between immature, mature, and postharvest ripening stages in kiwifruits. A total of 5,931 differentially expressed genes were identified, including those associated with sugar and organic acid metabolism. 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.