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Genome-Wide Analysis of mRNA Splicing vaRiants in Higher Plants

Ying Li, Qianhuan Guo, Chengchao Zheng, Shizhong Zhang*, Kang Yan*

Alternative splicing (AS) produces multiple mRNA splicing variants from a single precursor transcript. Recent genome sequencing analyses and increasing experimental evidence in flowering plants have revealed that AS is far more prevalent than previously thought and plays crucial roles in the diversification of gene regulation. Despite numerous studies, the extent and complexity of mRNA variants in plants remain poorly characterized from a global perspective. In present study, 589,034 mRNA variants from 442,541 annotated genes of 12 plant species were investigated. All AS genes were classified into four groups on the basis of the numbers of mRNA variants, namely, 2V (two variants), 3V (three variants), 4V (four variants), and 5V+ (five or more variants). Interestingly, our analysis indicated that more than 50% AS genes generated only two variants in higher plants. A global analysis of gene structure revealed that AS genes contained more but shorter exons and introns as the number of mRNA variants increased. The results also suggested that AS elicited different effects on the improvement of transcriptome and proteome diversity. Taken together, cross-species analysis provided the most comprehensive set of annotated splicing variants in higher plants thus far and extended the current view about mRNA variants.