Comparative Analysis Reveals Dynamic Changes in miRNAs and Their Targets and Expression during Somatic Embryogenesis in Longan (<i>Dimocarpus longan</i> Lour.)

<div><p>Somatic embryogenesis (SE), which resembles zygotic embryogenesis, is an essential component of the process of plant cell differentiation and embryo development. Although microRNAs (miRNAs) are important regulators of many plant develop- mental processes, their roles in SE have not been thoroughly investigated. In this study, we used deep-sequencing, computational, and qPCR methods to identify, profile, and describe conserved and novel miRNAs involved in longan (<i>Dimocarpus longan</i>) SE. A total of 643 conserved and 29 novel miRNAs (including star strands) from more than 169 miRNA families were identified in longan embryogenic tissue using Solexa sequencing. By combining computational and degradome sequencing approaches, we were able to predict 2063 targets of 272 miRNAs and verify 862 targets of 181 miRNAs. Target annotation revealed that the putative targets were involved in a broad variety of biological processes, including plant metabolism, signal transduction, and stimulus response. Analysis of stage- and tissue-specific expressions of 20 conserved and 4 novel miRNAs indicated their possible roles in longan SE. These miRNAs were <i>dlo-miR156</i> family members and <i>dlo-miR166c*</i> associated with early embryonic culture developmental stages; <i>dlo-miR26</i>, <i>dlo-miR160a</i>, and families <i>dlo-miR159</i>, <i>dlo-miR390,</i> and <i>dlo-miR398b</i> related to heart-shaped and torpedo- shaped embryo formation; <i>dlo-miR4a, dlo-miR24, dlo-miR167a</i>, <i>dlo-miR168a*</i>, <i>dlo-miR397a</i>, <i>dlo-miR398b.1</i>, <i>dlo-miR398b.2</i>, <i>dlo-miR808</i> and <i>dlo-miR5077</i> involved in cotyledonary embryonic development; and <i>dlo-miR17</i> and <i>dlo-miR2089*-1</i> that have regulatory roles during longan SE. In addition, <i>dlo-miR167a</i>, <i>dlo-miR808</i>, and <i>dlo-miR5077</i> may be required for mature embryo formation. This study is the first reported investigation of longan SE involving large-scale cloning, characterization, and expression profiling of miRNAs and their targets. The reported results contribute to our knowledge of somatic embryo miRNAs and provide insights into miRNA biogenesis and expression in plant somatic embryo development.</p>