Identification and characterization of long non-coding RNA (lncRNA) in the developing seeds of Jatropha curcas

Xihuan Yan,MingFeng Yang,Lanqing Ma

doi:10.1038/s41598-020-67410-x

Abstract

Long non-coding RNAs (lncRNAs) play critical roles in plant development. However, the information of lncRNAs in Jatropha curcas remains largely unexplored. Thus, an attempt has been made in J. curcas to identify 1,850 lncRNAs based on deep sequencing of developing seeds at three typical stages. About ten percent lncRNAs (196 lncRNAs) were differentially expressed lncRNAs during seed developing process. Together with reverse transcription quantitative real-time PCR, the lncRNA expression analyses revealed the stage-specific expression patterns of some novel lncRNAs in J. curcas. The target genes of lncRNAs were annotated for their roles in various biological processes such as gene expression, metabolism, and cell growth. Besides, 10 lncRNAs were identified as the precursors of microRNAs and 26 lncRNAs were predicted to be the targets of Jatropha miRNAs. A total of 31 key lncRNAs play critical roles in the seed developing process in the context of cell growth and development, lipid metabolism, and seed maturation. Our study provides the first systematic study of lncRNAs in the developing seeds of J. curcas and facilitates the functional research of plant lncRNAs and the regulation of seed development.

Highlights

Jatropha curcas is a perennial tree belonging to Euphorbiaceae family and its seed has a high content of oil which can be used as b iodiesel[1,2]
The third group of target genes function in cell growth and development (11%), such as intracellular trafficking, secretion, and vesicular transport (U, 11), cytoskeleton (Z, 6), cell wall biogenesis (M, 2), and cell cycle control (D, 5) (Fig. 4). These results indicated that the differentially expressed long non-coding RNAs (lncRNAs) might play an important role in the seed developing and substance accumulation by regulating many target genes involved in gene expression regulation, metabolism, and cell growth
We screened and identified 1,850 lncRNAs followed by examining their expression patterns at three different developmental stages of J. curcas seeds

Summary

Introduction

Jatropha curcas is a perennial tree belonging to Euphorbiaceae family and its seed has a high content of oil which can be used as b iodiesel[1,2]. Gene expression profiles have been analyzed by several efforts in the developing seeds of Jatropha in order to understand the molecular processes of oil metabolism and seed development[3,4,5,6]. Previous work indicates that lncRNAs impact on developmental and metabolic processes as endogenous target mimics which leads to sequestering of the miRNAs18,22 In all, these reports support the fact that lncRNAs play critical roles in regulating seed development including endosperm, embryo, and fruits. Much effort has recently been made to identify the function of protein-coding genes and miRNAs in J. curcas[25,26,27], the identification and role of lncRNAs have not been revealed in this biodiesel tree. Deep sequencing was carried out in the seeds at three typical developmental stages, and functional annotation was performed on the targets of differentially expressed lncRNAs to examine their possible roles in seed developing process

Methods

Results

Conclusion