Identification of known and novel miRNAs in the apical and basal spikelets of rice Oryza sativa cv. Mahalaxmi

The advent of next generation sequencing (NGS) has greatly enriched the database of miRNAs. For plants so far 8455 miRNAs sequences from 73 species and 15401 miRNAs sequences from 150 species have been deposited in miRBase 22.0 and Plant Non-coding RNA Database, respectively. The occurrence of miRNAs in such a huge number, which is still increasing, is because of the fact that the profile of miRNAs expression differs greatly from species to species, both quantitatively and qualitatively. Besides, even within a species it is expected that the miRNA expression profile would differ from cultivar to cultivar depending on the trait with regard to which the two cultivars differ. Beises, the expression of a miRNA in a plant organ may differ depending upon it spatial location. The same is reflected in the NGS data of the apical and basal spikelets of the panicle of the rice cultivar Mahalaxmi. Spikelets of Oryza sativa cv. Mahalaxmi were sampled on the 6th days after fertilization from the apical and basal region. sRNAs were isolated from the apical and basal spikelets. Known and novel miRnAs were identified bioinformatically, and their expression was validated by Northern.

下一代测序（Next Generation Sequencing, NGS）技术的出现极大地丰富了微小RNA（microRNA, miRNA）的数据库。截至目前，已有来自73个物种的8455条miRNA序列、以及来自150个物种的15401条miRNA序列分别提交至miRBase 22.0数据库与植物非编码RNA数据库。这类miRNA的数量庞大且仍在持续增长，究其原因在于不同物种间miRNA的表达谱在定量与定性层面均存在显著差异。此外，即便在同一物种内部，不同栽培品种间的miRNA表达谱也会因二者所具有的特异性状差异而有所不同。此外，植物器官中miRNA的表达还会因其空间位置的不同而存在差异。这一点在水稻品种Mahalaxmi穗部的顶端小穗与基部小穗的NGS数据中得到了体现。研究人员于受精后第6天，从栽培稻（Oryza sativa cv. Mahalaxmi）的顶端与基部区域采集了小穗样本。从顶端与基部小穗中分离得到了小分子RNA（small RNA, sRNA）。通过生物信息学方法鉴定出已知与新型miRNA，并利用Northern印迹杂交技术验证了其表达情况。