Comparative genomics of grass EST libraries reveals previously uncharacterized splicing events in crop plants.

ABSTRACT:

Background

Crop plants such as rice, maize and sorghum play economically-important roles as main sources of food, fuel, and animal feed. However, current genome annotations of crop plants still suffer false-positive predictions; a more comprehensive registry of alternative splicing (AS) events is also in demand. Comparative genomics of crop plants is largely unexplored.

Results

We performed a large-scale comparative analysis (ExonFinder) of the expressed sequence tag (EST) library from nine grass plants against three crop genomes (rice, maize, and sorghum) and identified 2,879 previously-unannotated exons (i.e., novel exons) in the three crops. We validated 81% of the tested exons by RT-PCR-sequencing, supporting the effectiveness of our in silico strategy. Evolutionary anal

SUBMITTER: Chuang TJ 

PROVIDER: S-EPMC4323234 | biostudies-literature | 2015 Feb

REPOSITORIES: biostudies-literature