Genomewide analysis of small RNAs in nonembryogenic and embryogenic tissues of citrus: microRNA- and siRNA mediated transcript cleavage involved in somatic embryogenesis

Somatic embryogenesis (SE) is a process of somatic cells becoming dedifferentiated and
generating embryos. SE has been widely used in biotechnology as a powerful way of
regeneration and a model system for studying plant embryogenesis, but the controlling
mechanisms of SE are far from clear. Here, we show the genomewide profiles of miRNAs/siRNAs
and their target genes in nonembryogenic and embryogenic tissues of ‘Valencia’ sweet orange.
By high-throughput sequencing (HTS) of small RNAs and RNA degradome tags, we identified 50
known and 45 novel miRNAs, 130 miniature inverted-repeat transposable elements (MITEs)
derived, 94 other and 235 phased small interfering RNAs (siRNAs), as well as 203 target genes.
The majority of the abundantly expressed miRNAs/siRNAs exhibit lower expression levels in
embryogenic callus (EC) or during SE process than in nonembryogenic callus (NEC), which is
supposed to derepress the target genes that are involved in development and stress response,
thus to activate the biological processes required for cell differentiation. However, the conserved
csi-miR156a/b, miR164b and 171c directed suppression of specific transcription factors (TFs) are
supposed to inactivate the postembryonic growth thus to maintain normal SE. In this study,
miRNA- and siRNA-mediated silencing of target genes was found under sophisticated regulation
in citrus SE system; the enhancement effect of specific conserved miRNAs on SE was discussed,
providing new clues for future investigation of mechanisms that control SE.