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RNA-Seq Uncovers SNPs and AS Events in Asian Lotus

May 21, 2015     Email"> PrintText Size

Lotus (Nelumbo nucifera), cultivated for more than 7000 years through Asia, has ornamental, edible and medicinal value, as well as religious significance. Since the genome of lotus was sequenced and assembled, the genetic and genomic studies of lotus have gone into a new era.  

Single nucleotide polymorphism (SNP) markers could meet the needs on both marker density and genome coverage, which have been applied in linkage mapping and genome wide association studies (GWAS). Alternative splicing (AS) is an important posttranscriptional regulatory mechanism for modulating gene expression and functional complexity in higher eukaryotes. RNA-Sequencing (RNA-Seq) is an efficient way to comprehensively identify SNPs and AS events from the expressed genes. However, the SNPs discovery in transcriptome data by RNA-Seq and the landscape of AS from lotus RNA-Seq transcriptome data has not been reported.  

Prof. YANG Pingfang and Associate Prof. YANG Mei from Wuhan Botanical Garden conducted transcriptome sequencing of four Asian lotus cultivars by using Illumina HiSeq2000 platform to indentify SNPs and AS events in lotus.  

A total of 505.03 million high-quality reads were generated from four cultivars, 86.5% of which have been mapped on reference genome. Using the four sets of data together, a total of 357,689 putative SNPs with an average density of one SNP per 2.2 kb were identified from all four libraries. Among them, A/G and C/T were the two most abundant and evenly present, with each accounting for 34% of all SNPs, respectively. 177540 AS events were identified, and distributed in 18842 genes, accounting for 64% of the total expressed genes. Seven types of AS events were detected, among which alternative 5’first exon was the most abundant type accounting for 41.2%.  

These SNPs and AS events identified in this study could not only complement the predicted lotus gene database, but also facilitate future functional genomics studies on lotus species. 

Results were published in PLOS ONE entitled “RNA-Seq Uncovers SNPs and Alternative Splicing Events in Asian Lotus (Nelumbo nucifera)”.  It was financially supported by National Natural Science Foundation of China and The Knowledge Innovation Project of Chinese Academy of Sciences.  


Number and type of SNPs identified from the Asian lotus transcriptome (Image by YANG Mei) 


(Editor: CHEN Na)


YANG Pingfang

Wuhan Botanical Garden

E-mail: yangpf@wbgcas.cn

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