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Published on May 11, 2007; 10.1104/pp.107.098640

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Received February 27, 2007
Accepted April 30, 2007

Comparative Cross-species Alternative Splicing in Plants

Hadas Ner-Gaon , Noam Leviatan , Eitan Rubin , and Robert Fluhr *

Department of Plant Sciences, Weizmann Institute of Science, P.O.Box 26, Rehovot 76100, Israel; Department of Microbiology and Immunology, Ben Gurion University of the Negev

* Corresponding author; email: robert.fluhr{at}weizmann.ac.il.

Alternative splicing (AS) can add significantly to genome complexity. Plants are thought to exhibit less alternative splicing than animals. An algorithm, based on EST pairs gapped alignment (EPGA), was developed that takes advantage of the relatively small intron and exon size in plants and directly compares pairs of ESTs to search for alternative splicing. EPGA was first evaluated in Arabidopsis, rice and tomato for which annotated genome sequence is available and was shown to accurately predict splicing events. The method was then applied to 11 plant species that include 17 cultivars for which enough ESTs are available. The results show a large, 3.7-fold, difference in AS rates between plant species with Arabidopsis and rice in the lower range and lettuce and sorghum in the upper range. Hence, compared to higher animals, plants show a much greater degree of variety in their AS rates and in some plant species the rates of animal and plant AS are comparable although the distribution of AS types may differ. In eudicots but not monocots, a correlation between genome size and AS rates was detected implying that in eudicots the mechanisms that lead to larger genomes are a driving force for the evolution of AS.






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