Genome-Wide Identification and Comparative Analysis of Conserved and Novel MicroRNAs in Grafted Watermelon by High-Throughput Sequencing

MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs involved in the post-transcriptional gene regulation and play a critical role in plant growth, development and stresses response. However less is known about miRNAs involvement in grafting behaviors, especially with the watermelon (Citrullus lanatus L.) crop, which is one of the most important agricultural crops worldwide. Grafting method is commonly used in watermelon production in attempts to improve its adaptation to abiotic and biotic stresses, in particular to the soil-borne fusarium wilt disease. In this study, Solexa sequencing has been used to discover small RNA populations and compare miRNAs on genome-wide scale in watermelon grafting system. A total of 11,458,476, 11,614,094 and 9,339,089 raw reads representing 2,957,751, 2,880,328 and 2,964,990 unique sequences were obtained from the scions of self-grafted watermelon and watermelon grafted on-to bottle gourd and squash at two true-leaf stage, respectively. 39 known miRNAs belonging to 30 miRNA families and 80 novel miRNAs were identified in our small RNA dataset. Compared with self-grafted watermelon, 20 (5 known miRNA families and 15 novel miRNAs) and 47 (17 known miRNA families and 30 novel miRNAs) miRNAs were expressed significantly different in watermelon grafted on to bottle gourd and squash, respectively. MiRNAs expressed differentially when watermelon was grafted onto different rootstocks, suggesting that miRNAs might play an important role in diverse biological and metabolic processes in watermelon and grafting may possibly by changing miRNAs expressions to regulate plant growth and development as well as adaptation to stresses. The small RNA transcriptomes obtained in this study provided insights into molecular aspects of miRNA-mediated regulation in grafted watermelon. Obviously, this result would provide a basis for further unravelling the mechanism on how miRNAs information is exchanged between scion and rootstock in grafted watermelon, and its relevance to diverse biological processes and environmental adaptation.

微小RNA（microRNAs，miRNAs）是一类内源性小型非编码RNA，参与转录后基因调控，在植物生长、发育及胁迫响应中发挥关键作用。然而，目前关于miRNA参与嫁接行为的研究尚少，尤以西瓜（Citrullus lanatus L.）这类全球重要农作物之一的作物为甚。嫁接栽培技术是西瓜生产中的常用手段，旨在提升其对非生物胁迫与生物胁迫的适应性，尤其是对土传镰刀菌枯萎病的抗性。本研究采用Solexa测序技术，在西瓜嫁接体系中开展全基因组范围的小RNA群体挖掘与miRNA表达比较分析。本研究分别从两真叶期的自嫁接西瓜、西瓜嫁接于葫芦及南瓜的接穗样本中，获得总计11,458,476、11,614,094和9,339,089条原始读段，对应2,957,751、2,880,328和2,964,990条独特序列。在本研究的小RNA数据集中，共鉴定得到隶属于30个miRNA家族的39个已知miRNA，以及80个新发现miRNA。与自嫁接西瓜相比，嫁接于葫芦和南瓜的西瓜样本中，分别有20个（5个已知miRNA家族和15个新miRNA）及47个（17个已知miRNA家族和30个新miRNA）miRNA呈现显著差异表达。当西瓜嫁接于不同砧木时，miRNA的表达模式存在差异，这表明miRNA可能在西瓜的多种生物学过程与代谢过程中发挥重要作用，而嫁接或可通过改变miRNA的表达水平，调控植物生长发育及胁迫适应性。本研究获得的小RNA转录组，为阐明嫁接西瓜中miRNA介导的调控机制提供了分子层面的见解。显然，该研究结果将为进一步揭示嫁接西瓜接穗与砧木间的miRNA信息交换机制，及其与多种生物学过程和环境适应性的关联奠定研究基础。