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Article|04 Mar 2019|OPEN
Comparative transcriptome analysis uncovers the regulatory functions of long noncoding RNAs in fruit development and color changes of Fragaria pentaphylla
Lijun Bai1,2 , Qing Chen1 , Leiyu Jiang1 , Yuanxiu Lin1 , Yuntian Ye1 , Peng Liu2 and Xiaorong Wang1 , Haoru Tang,1 ,
1College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
2Chengdu Life Baseline Technology Co., LTD, Chengdu, China
*Corresponding author. E-mail: htang@sicau.edu.cn

Horticulture Research 6,
Article number: 42 (2019)
doi: https://doi.org/10.1038/s41438-019-0128-4
Views: 1098

Received: 07 Dec 2017
Revised: 19 Jan 2019
Accepted: 22 Jan 2019
Published online: 04 Mar 2019

Abstract

To investigate the molecular mechanism underlying fruit development and color change, comparative transcriptome analysis was employed to generate transcriptome profiles of two typical wild varieties of Fragaria pentaphylla at three fruit developmental stages (green fruit stage, turning stage, and ripe fruit stage). We identified 25,699 long noncoding RNAs (lncRNAs) derived from 25,107 loci in the F. pentaphylla fruit transcriptome, which showed distinct stage- and genotype-specific expression patterns. Time course analysis detected a large number of differentially expressed protein-coding genes and lncRNAs associated with fruit development and ripening in both of the F. pentaphylla varieties. The target genes downregulated in the late stages were enriched in terms of photosynthesis and cell wall organization or biogenesis, suggesting that lncRNAs may act as negative regulators to suppress photosynthesis and cell wall organization or biogenesis during fruit development and ripening of F. pentaphylla. Pairwise comparisons of two varieties at three developmental stages identified 365 differentially expressed lncRNAs in total. Functional annotation of target genes suggested that lncRNAs in F. pentaphylla may play roles in fruit color formation by regulating the expression of structural genes or regulatory factors. Construction of the regulatory network further revealed that the low expression of Fra a and CHS may be the main cause of colorless fruit in F. pentaphylla.