RNA-Seq Uncovers SNPs and Alternative Splicing Events in Asian Lotus ( XXXX ).

@entity16666 @entity4373
RNA-Seq is an efficient way to comprehensively identify single nucleotide polymorphisms (SNPs) and @entity4373 ( @entity4373 ) events from the expressed genes. In this study, we conducted transcriptome sequencing of four Asian lotus ( @entity16666 ) cultivars using Illumina HiSeq2000 platform to identify SNPs and @entity4373 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 @entity4373 events were detected in the four cultivars and were distributed in 64% of the expressed genes of lotus. The predominant type of @entity4373 events was alternative 5' first exon, which accounted for 41.2% of all the observed @entity4373 events, and exon skipping only accounted for 4.3% of all @entity4373 . Gene Ontology analysis was conducted to analyze the function of the genes containing SNPs and @entity4373 events. Validation of selected SNPs and @entity4373 events revealed that 74% of SNPs and 80% of @entity4373 events were reliable, which indicates that RNA-Seq is an efficient approach to uncover gene-associated SNPs and @entity4373 events. A large number of SNPs and @entity4373 events identified in our study will facilitate further genetic and functional genomics research in lotus.
