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

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. Jatropha curcas is a perennial tree belonging to Euphorbiaceae family and its seed has a high content of oil which can be used as biodiesel 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 3-6. The whole genome sequence of J. curcas have been sequenced and assembled independently by Japan, China and South Korea, and these efforts lay a solid foundation for further exploration of the non-coding RNAs of J. curcas 7-9. Non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are functional transcripts that are not translated into proteins but usually function to regulate the expression of other genes. Studies demonstrate that lncRNAs regulate gene expression in plants by DNA methylation and chromatin remodeling, and in some cases, they act as miRNA sponges to enhance the expression of mRNA targeted by miRNA 10. A great body of evidence indicates that lncRNAs function in both nuclear and cytoplasmic compartments and play essential regulatory roles in plant development processes (the development of pollen, fiber and lateral root; photomorphogenesis), plant reproduction processes (vernalization, flowering time and male sterility), and plant stress responses 11-15. The role of lncRNAs in plant seed development has been acknowleged in recent years, as much effort has been made to identify the lncRNAs from seeds in many plants, including maize 16-18 , Brassica napus 19 , tree peony 20 , castor bean 21 , pigeonpea 22 , Ginkgo biloba 23 , and rice 24. In maize, lncRNAs might play a part in the complex regulation of genetic imprinting during maize endosperm development 17 , and lncRNAs probably have function in lipid metabolism regulation of Brassica napus and tree p...

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