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GENETICS, GENOMICS, AND MOLECULAR EVOLUTION

Comparative Cross-Species Alternative Splicing in Plants^1,[W],[OA]

Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel (H.N.-G., N.L., R.F.); and Department of Microbiology and Immunology, Ben Gurion University of the Negev, Beer-Sheva 84105, Israel (E.R.)

Alternative splicing (AS) can add significantly to genome complexity. Plants are thought to exhibit less AS than animals. An algorithm, based on expressed sequence tag (EST) pairs gapped alignment, was developed that takes advantage of the relatively small intron and exon size in plants and directly compares pairs of ESTs to search for AS. EST pairs gapped alignment was first evaluated in Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and tomato (Solanum lycopersicum) 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 (Lactuca sativa) and sorghum (Sorghum bicolor) 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.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Robert Fluhr (robert.fluhr{at}weizmann.ac.il).

^[W] The online version of this article contains Web-only data.

^[OA] Open Access articles can be viewed online without a subscription.

www.plantphysiol.org/cgi/doi/10.1104/pp.107.098640

^* Corresponding author; e-mail robert.fluhr{at}weizmann.ac.il; fax 972–8–9344181.

Received February 27, 2007; accepted April 30, 2007; published May 11, 2007.

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Plant Physiol. 2007 144: 1235-1236. [Full Text]