Yang Mei, Xu Liming, Liu Yanling, Yang Pingfang
Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.
Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.
PLoS One. 2015 Apr 30;10(4):e0125702. doi: 10.1371/journal.pone.0125702. eCollection 2015.
RNA-Seq is an efficient way to comprehensively identify single nucleotide polymorphisms (SNPs) and alternative splicing (AS) events from the expressed genes. In this study, we conducted transcriptome sequencing of four Asian lotus (Nelumbo nucifera) cultivars using Illumina HiSeq2000 platform to identify SNPs and AS events in lotus. A total of 505 million pair-end RNA-Seq reads were generated from four cultivars, of which 86% were mapped to the lotus reference genome. Using the four sets of data together, a total of 357,689 putative SNPs were identified with an average density of one SNP per 2.2 kb. These SNPs were located in 1,253 scaffolds and 15,016 expressed genes. A/G and C/T were the two major types of SNPs in the Asian lotus transcriptome. In parallel, a total of 177,540 AS events were detected in the four cultivars and were distributed in 64% of the expressed genes of lotus. The predominant type of AS events was alternative 5' first exon, which accounted for 41.2% of all the observed AS events, and exon skipping only accounted for 4.3% of all AS. Gene Ontology analysis was conducted to analyze the function of the genes containing SNPs and AS events. Validation of selected SNPs and AS events revealed that 74% of SNPs and 80% of AS events were reliable, which indicates that RNA-Seq is an efficient approach to uncover gene-associated SNPs and AS events. A large number of SNPs and AS events identified in our study will facilitate further genetic and functional genomics research in lotus.
RNA测序是一种从已表达基因中全面鉴定单核苷酸多态性（SNP）和可变剪接（AS）事件的有效方法。在本研究中，我们使用Illumina HiSeq2000平台对四个亚洲莲（Nelumbo nucifera）品种进行了转录组测序，以鉴定莲中的SNP和AS事件。从四个品种中共产生了5.05亿对末端RNA测序读数，其中86%被定位到莲参考基因组上。综合使用这四组数据，共鉴定出357,689个推定的SNP，平均密度为每2.2 kb一个SNP。这些SNP位于1,253个支架和15,016个已表达基因中。A/G和C/T是亚洲莲转录组中SNP的两种主要类型。同时，在四个品种中总共检测到177,540个AS事件，分布在莲64%的已表达基因中。AS事件的主要类型是可变5'第一外显子，占所有观察到的AS事件的41.2%，而外显子跳跃仅占所有AS的4.3%。进行了基因本体分析以分析包含SNP和AS事件的基因的功能。对选定的SNP和AS事件的验证表明，74%的SNP和80%的AS事件是可靠的，这表明RNA测序是揭示与基因相关的SNP和AS事件的有效方法。我们研究中鉴定出的大量SNP和AS事件将有助于莲的进一步遗传和功能基因组学研究。
