ExonFinder

ExonFinder identifies novel cassette exons and retained introns by comparative analysis of expressed sequence tags (ESTs) mapped across species using BLAT to improve genome annotations of crop plants such as rice, maize, and sorghum.

Key Features:

• Cross-species EST mapping with BLAT: Maps EST libraries from nine grass species against three crop genomes using BLAT for cross-species exon discovery.
• Detection of cassette exons and retained introns: Identifies novel cassette exons and retained introns, reporting 2,879 novel exons across rice, maize, and sorghum.
• In silico prediction validated by RT-PCR sequencing: Predicted novel exons were validated by RT-PCR sequencing with an 81% confirmation rate.
• Evolutionary pressure analysis: Compares selection at protein and RNA levels, showing weaker protein-level selection but stronger RNA-level pressure on novel exons.
• Consistent detection across cultivated and wild rice: Findings are reported to be consistent between cultivated and wild rice species.
• Genome reannotation using evolutionary rates: Uses evolutionary rates as indicators to reannotate rice, maize, and sorghum genomes for alternative splicing events.

Scientific Applications:

• Genome annotation improvement: Enhances the accuracy of genome annotations in economically important crops by identifying previously unannotated alternative splicing events.
• Evolutionary biology of splicing: Provides data to study evolutionary mechanisms and selection dynamics underlying alternative splicing at protein and RNA levels.
• Isoform discovery for crop studies: Assists identification of novel isoforms relevant to crop improvement and domestication research.

Methodology:

Cross-species mapping of ESTs to target genomes using BLAT, comparative analysis of EST libraries from nine grass species against three crop genomes, and comparison of evolutionary pressures at protein and RNA levels.