investigation of (non canonical) splice sites

This study investigates the occurrence and conservation of non-canonical splice sites in 121 plant genomes using their genome annotations and RNA-Seq data from 35 species. The main findings are:

1. Splice sites are highly conserved across plant species, with canonical GT-AG splice sites being the most dominant (98.7%).

2. Non-canonical splice sites, such as GC-AG (1.2%), AT-AC (0.06%), and other minor types (0.09%), are present in most plant genomes, albeit at low frequencies.

3. The frequency of non-canonical splice sites correlates with their divergence from canonical ones, suggesting either neutral mutations or evolution towards canonical splice sites.

4. Strong conservation of non-canonical splice sites across multiple species and non-random accumulation of substitutions indicate their functional relevance.

5. RNA-Seq data validates the presence of non-canonical splice sites through gaps in sequencing read alignments and demonstrates the expression of genes containing these splice sites.

The authors conclude that bona fide non-canonical splice sites are present in most plant genomes and appear functionally relevant despite their low abundance compared to canonical splice sites.