AsianScientist (May 25, 2015) – A study on the transcriptome of the lotus plant Nelumbo nucifera has identified unique alternative splicing patterns. The results have been published in the journal PLOS ONE.
The lotus has been cultivated for more than 7,000 years through Asia and has ornamental, edible and medicinal value, as well as religious significance. Although the lotus genome has been sequenced and assembled, a comprehensive analysis of its transcriptome—which could reveal post-transcriptional regulatory mechanisms—has not been performed to date.
In the present study, Professor Yang Pingfang and Associate Professor Yang Mei from Wuhan Botanical Garden, Chinese Academy of Sciences, conducted transcriptome sequencing of four Asian lotus cultivars by using Illumina HiSeq2000 platform to identify single nucleotide polymorphism (SNP) markers and alternative splicing events.
A total of 505.03 million high-quality reads were generated from four cultivars, 86.5 percent 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 kilobyte 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 percent of all SNPs, respectively. 177,540 alternative splicing events were identified and distributed in 18,842 genes, accounting for 64 percent 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 percent.
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.
The article can be found at: Yang et al. (2015) RNA-Seq Uncovers SNPs And Alternative Splicing Events In Asian Lotus (Nelumbo nucifera).
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Source: Chinese Academy of Sciences.
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