Abstract
MicroRNAs (miRNAs) are endogenously short noncoding regulatory RNAs implicated in plant development and physiology. Nine small RNA (sRNA) libraries from three typical seed developmental stages (young, intermediate, and mature) were generated by deep sequencing to identify the miRNAs of J. curcas, a potential oilseed crop for the production of renewable oil. Strict criteria were adopted to identify 93 high confidence miRNAs including 48 conserved miRNAs and 45 novel miRNAs. Target genes of these miRNAs were involved in a broad range of physiological functions, including gene expression regulation, primary & secondary metabolism, growth & development, signal transduction, and stress response. About one third (29 out of 93) miRNAs showed significant changes in expression levels during the seed developmental process, indicating that the miRNAs might regulate its targets by their changes of transcription levels in seed development. However, most miRNAs were found differentially expressed in the late stage of seed development, suggesting that miRNAs play more important roles in the stage when seed accumulating organic matters and suffering dehydration stress. This study presents the first large scale identification of high confidence miRNAs in the developing seeds of J. curcas.
Highlights
Huge consumption of fossil fuel leading to higher and higher levels of carbon dioxide released into the atmosphere is a key concern in the world
J. curcas, nine small RNAs (sRNA) libraries from three typical developmental stages of seeds with three biological replicates were generated and sequenced by next-generation sequencing (NGS), resulting in 16.7~21.6 million raw reads for each sample and 162.7 million raw reads in total, which was a deep resource for extensive discovery of miRNAs
The clean reads were mapped to the SILVA rRNA, Rfam, tRNAdb, and Repbase databases to annotate the composition of the sRNA population
Summary
Huge consumption of fossil fuel leading to higher and higher levels of carbon dioxide released into the atmosphere is a key concern in the world. MicroRNAs (miRNAs) are endogenous small non-coding RNAs that act as post-transcriptional regulators of gene expression in animals and plants by targeting mRNAs for cleavage or translational repression[14,15,16]. Galli et al investigated miRNAs through small RNAs (sRNA) deep sequencing from mature seeds, and revealed 180 conserved miRNAs and 41 precursors as well as 16 novel pre-miRNAs, but miRNAs involved in other developmental stages are yet to be www.nature.com/scientificreports/. High confidence miRNAs from J. curcas were identified through the deep sequencing of sRNA from three typical developing stages of seeds (young, intermediate and mature). Differentially expressed miRNAs were found mainly in the late stages, providing important information on the possible function of miRNAs in seed development
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