Alternative splicing (AS) is a post- transcriptional regulation mechanism, in which multiple isoforms are generated from a single pre- mRNA, enriching RNA and protein diversity. Through this regulating mechanism, gene plays different roles in the development and growth of plant tissues or in different biological pathways. However, in the evolution of closely related species, how the expression patterns of isoforms from the interspecies orthologous genes evolve and contribute to the differentiation of tissue traits among species is unclear. Also, the relative contribution of gene duplication and AS to the evolution of gene function is largely unknown.

To solve the above questions, research teams from Wuhan Botanical Garden and Ghent University compared isoforms between two Nelumbo species (Nelumbo lutea and N. Nucifera), and the outgroup Arabidopsis thaliana, which has the greatest resource of transcriptomes and functional assay data among plants, to study the evolution of AS.

Results showed that most splicing events evolved rapidly between orthologs and that the origin of lineage- specific splice variants or isoforms contributed to gene functional changes during species divergence within Nelumbo. Single- copy genes underwent significantly more AS events, and displayed significantly more interspecies conserved AS event than duplicated genes.

Through comparative analysis of isoform expression networks, the study identified orthologous genes of which the expression of at least some of their isoforms displayed a conserved tissue bias across species, indicating a strong selection for maintaining a stable expression pattern of these isoforms. Moreover, the expression divergence of isoform from the genes in the floral “ABCE” gene models contributeed to the differentiation of floral tissue in both two lotuses and Arabidopsis.

The research was funded by the Strategic Priority Research Program of Chinese Academy of Sciences, the National Natural Science Foundation of China, and the Youth Innovation Promotion Association of Chinese Academy of Sciences.

The results have been published in The Plant Journal entitled “Evolution of isoform-level gene expression patterns across tissues during lotus species divergence”.

The expression divergence of different types of duplicated genes in N. lutea, N. nucifera, and Arabidopsis. (Image by WBG)