Rogans Sarah Jane, Rey Chrissie
School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa.
PLoS One. 2016 Jan 22;11(1):e0147251. doi: 10.1371/journal.pone.0147251. eCollection 2016.
MicroRNAs (miRNAs) are an important class of endogenous non-coding single-stranded small RNAs (21-24 nt in length), which serve as post-transcriptional negative regulators of gene expression in plants. Despite the economic importance of Manihot esculenta Crantz (cassava) only 153 putative cassava miRNAs (from multiple germplasm) are available to date in miRBase (Version 21), and identification of a number of miRNAs from the cassava EST database have been limited to comparisons with Arabidopsis. In this study, mature sequences of all known plant miRNAs were used as a query for homologous searches against cassava EST and GSS databases, and additional identification of novel and conserved miRNAs were gleaned from next generation sequencing (NGS) of two cassava landraces (T200 from southern Africa and TME3 from West Africa) at three different stages post explant transplantation and acclimatization. EST and GSS derived data revealed 259 and 32 miRNAs in cassava, and one of the miRNA families (miR2118) from previous studies has not been reported in cassava. NGS data collectively displayed expression of 289 conserved miRNAs in leaf tissue, of which 230 had not been reported previously. Of the 289 conserved miRNAs identified in T200 and TME3, 208 were isomiRs. Thirty-nine novel cassava-specific miRNAs of low abundance, belonging to 29 families, were identified. Thirty-eight (98.6%) of the putative new miRNAs identified by NGS have not been previously reported in cassava. Several miRNA targets were identified in T200 and TME3, highlighting differential temporal miRNA expression between the two cassava landraces. This study contributes to the expanding knowledge base of the micronome of this important crop.
微小RNA（miRNA）是一类重要的内源性非编码单链小RNA（长度为21 - 24个核苷酸），在植物中作为基因表达的转录后负调控因子。尽管木薯（Manihot esculenta Crantz）具有重要的经济价值，但截至目前，miRBase（版本21）中仅提供了153个推定的木薯miRNA（来自多个种质），并且从木薯EST数据库中鉴定一些miRNA仅限于与拟南芥进行比较。在本研究中，所有已知植物miRNA的成熟序列被用作查询序列，针对木薯EST和GSS数据库进行同源搜索，并从两个木薯地方品种（来自南部非洲的T200和来自西非的TME3）在离体移植和驯化后的三个不同阶段的下一代测序（NGS）中收集新的和保守的miRNA的额外鉴定信息。EST和GSS衍生的数据分别揭示了木薯中的259个和32个miRNA，并且先前研究中的一个miRNA家族（miR2118）在木薯中尚未见报道。NGS数据共同显示了叶组织中289个保守miRNA的表达，其中230个以前未被报道。在T200和TME3中鉴定出的289个保守miRNA中，有208个是异源miRNA。鉴定出39个低丰度的新的木薯特异性miRNA，属于29个家族。通过NGS鉴定出的推定新miRNA中有38个（98.6%）以前在木薯中未被报道。在T200和TME3中鉴定出了几个miRNA靶标，突出了两个木薯地方品种之间miRNA表达的时间差异。本研究有助于扩大这种重要作物的微小基因组知识库。
