Genome-wide identification of miRNAs and their targets during early somatic embryogenesis in Dimocarpus longan Lour.

Xiaoping Xu,Zhongxiong Lai,Qinglin Zhang,Liyao Su,Yukun Chen,Zihao Zhang,Xu Chen,Xiaohui Chen,Yuling Lin,Yan Chen

doi:10.1038/s41598-020-60946-y

Xiaoping Xu, Zhongxiong Lai + Show 8 more

Open Access

https://doi.org/10.1038/s41598-020-60946-y

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Journal: Scientific Reports	Publication Date: Mar 13, 2020
Citations: 28	License type: open-access

Affiliation: Fujian Agriculture and Forestry University

Abstract

miRNAs are endogenous regulatory factors that play pivotal roles in post-transcriptional regulation. However, their specific roles in early somatic embryogenesis (SE) remain unclear. Study of the SE system is fundamental for clarifying the molecular mechanisms in Dimocarpus longan. We identified 289 known miRNAs from 106 different miRNA families and 1087 novel miRNAs during early longan SE, including embryogenic callus (EC), incomplete pro-embryogenic culture (ICpEC), globular embryo (GE), and non-embryogenic callus (NEC). The abundances of known miRNAs were concentrated in GE. The differentially expression (DE) miRNAs showed five expression patterns during early SE. Largely miRNAs were expressed highly and specially in EC, ICpEC, and GE, respectively. Some miRNAs and putative target genes were enriched in lignin metabolism. Most potential targets were related to the pathways of plant hormone signal transduction, alternative splicing, tyrosine metabolism and sulfur metabolism in early longan SE. The regulatory relationships between dlo-miR166a-3p and DlHD-zip8, dlo-miR397a and DlLAC7, dlo-miR408-3p and DlLAC12 were confirmed by RNA ligase-mediated rapid amplification of cDNA ends. The expression patterns of eight DE miRNAs detected by qRT-PCR were consistent with RNA-seq. Finally, the miRNA regulatory network in early SE was constructed, which provided new insight into molecular mechanism of early SE in longan.

Highlights

Plant somatic embryogenesis (SE) is physiologically and morphologically similar to that of zygotic embryos
A previous study demonstrated that miRNAs participate throughout the development of somatic embryogenesis in longan[11], but did not includ a large-scale genomewide analysis of the expression levels of miRNAs in every stage of somatic embryogenesis in longan
Our findings generally support those reported by Lin[11], it was beneficial for the development of embryogenic callus to down-regulate dlo-miR159a and dlo-miR319

Summary

Introduction

Plant somatic embryogenesis (SE) is physiologically and morphologically similar to that of zygotic embryos. The miRNA regulatory pathway is important in plant growth and development, hormone regulation, organ differentiation, alternative splicing and secondary metabolite accumulation[5,6,7]. The miRNAs were expressed in embryos such as spruce[12], rice[13], grape[14], cotton[15], wheat[16] and lily[17] Most of these studies mainly focused on sequencing of the miRNA transcriptome at certain www.nature.com/scientificreports embryonic stages or in mixed samples, without referencing the genome of that species. The findings revealed that the miRNA regulatory network played an important role in the development of SE in longan, and early somatic embryo development was closely associated with the totipotency of differentiated embryogenic calli and the seed size. The results of this study provided insight into the specific miRNA regulatory network in early SE of longan

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