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

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.Plant somatic embryogenesis (SE) is physiologically and morphologically similar to that of zygotic embryos. Therefore, SE is usually used as a model system for studying embryonic development in higher plants. Previously study demonstrated that transcription factors (TFs) regulated embryogenic transformation in SE 1 ; this TFs included BABY BOOM (BBM), AGAMOUS-LIKE15 (AGL15), LEC2 and SERK, which functioned in the process of cell division and differentiation in embryonic development 2 . miRNAs are a kind of small endogenous RNAs of 18-24nt in length, which mainly recognize the complementary binding sites of their target mRNAs. miRNAs were transcribed by RNA polymerase II (Pol II). miRNAs could mediate mRNA cleavage and inhibiting translation at transcriptional or post-transcriptional level in eukaryotes 3,4 . Over the past decade, miRNAs have been reported to be involved in a broad range of metabolic and physiological processes in plants, such as plant growth, development and responses to stresses. However, the regulation of miRNA of plant SE was still unclear.The miRNA regulatory pathway is particularly important in plant growth and development, hormone regulation, organ differentiation, alternative splicing and secondary metabolite accumulation 5-7 . The SE could be influenced by epigenetics in some plant 8 . For instance, expression levels of miR171, 159, 169 and 172 affected in the embryogenic potency of Larix gmelini 9 , these particular miRNAs targeted to multifunctional TFs and participated in ABA signal transduction, growth and development, and stress response. In Citrus sinensis (L.), miR156, 168 an...

Hypermethylation of Auxin-Responsive Motifs in the Promoters of the Transcription Factor Genes Accompanies the Somatic Embryogenesis Induction in Arabidopsis

“…Consequently, we hypothesised that the methylation of the AuxRE motifs in the promoters of the LEC1 , LEC2 , BBM and WUS genes might recruit the methylation-sensitive ARFs that have a regulatory function in SE induction [ 92 ]. In Arabidopsis, a high number (over 75%) of TFs was estimated as being methylation-sensitive, including the ARF5/MONOPTEROS [ 93 ], which has been reported as playing role in SE induction [ 92 , 93 , 94 , 95 , 96 , 97 , 98 , 99 ]. Whether the auxin-controlled differential methylation of the TF gene promoters affects the binding of auxin-responsive regulatory proteins, including ARF5, to the promoters of the SE-involved genes, requires experimental confirmation.…”

Genome-Wide Identification of MicroRNAs Associated With the Somatic Embryogenesis in Eucalyptus

“…Also, miR397b-3p was up-regulated in the callus of both E. camaldulensis and E. grandis x urophylla, and miR397a-3p was up-regulated only in the dedifferentiated tissue of E. camaldulensis (Additional le 3). Like MIR397, MIR159 has been studied to regulate the development of callus in multiple plants, such as Dimocarpus longan [21,22], Moringa oleifera [23] and Larix leptolepis [24]. miR159 has been shown to be induced by ABA and to regulate MYB33 during the seed germination of Arabidopsis [25].…”

MiRNA expression profiling and zeatin dynamic changes in a new model system ofin vivoindirect regeneration of tomato

“…We identified a total of 183 miRNAs (92 conserved and 91 novel miRNAs) by next-generation sequencing. Previous studies on miRNAs, including Xu et al[30] identified 289 known miRNAs and 1087 novel miRNAs in longan, while Wu et al [26] reported 50 known and 45 novel miRNAs in citrus. Taken together, these data show that distinct types of miRNAs are expressed at different levels during the process of regeneration in different species.…”

“…Recently, the large scale application of next-generation sequencing has proved to be a useful tool to identify the patterns of miRNA expression during plant regeneration. Genome-wide miRNAs and their targets have been analyzed during explant regeneration in vitro in wheat[21], rice[22, 23], cotton[24], peanut[25], sweet orange [26], coconut[27], larch[28], maritime pine[8], Norway Spruce[29], longan[30], yellow-poplar[31], radish[32], Lilium [33], and Tuxpeno maize[34]. However, all these studies were performed on in vitro specimens, which relys on the presence of exogenous hormones to regenerate plantlets.…”