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

• Published in: Scientific reports Vol. 10; no. 1; p. 4626
• Main Authors: Xu, Xiaoping, Chen, Xiaohui, Chen, Yan, Zhang, Qinglin, Su, Liyao, Chen, Xu, Chen, Yukun, Zhang, Zihao, Lin, Yuling, Lai, Zhongxiong
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 13.03.2020; Nature Publishing Group UK
• Subjects: Alternative splicing; Callus; Dimocarpus longan; Gene Expression Profiling; Gene Expression Regulation, Developmental; Gene Expression Regulation, Plant; Gene regulation; Gene Regulatory Networks; Genomes; High-Throughput Nucleotide Sequencing; Lignin; Metabolism; MicroRNAs - genetics; miRNA; Molecular modelling; Plant Growth Regulators - genetics; Post-transcription; RNA ligase; RNA, Plant - genetics; Sapindaceae - embryology; Sapindaceae - genetics; Sequence Analysis, RNA; Signal transduction; Somatic embryogenesis; Sulfur; Tyrosine; Whole Genome Sequencing - methods
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-020-60946-y

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.