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Abstract

Alternative pre-mRNA splicing (AS) is prevalent in plants and is involved in many
interactions between plants and environmental stresses. However, the patterns and
underlying mechanisms of AS evolution in plants remain unclear. By analyzing the
transcriptomes of four eudicot species, we revealed that the divergence of AS
is largely due to the gains and losses of AS events among orthologous genes.
Furthermore, based on a subset of AS, in which AS can be directly associated with
specific transcripts, we found that AS that generates transcripts containing premature
termination codons (PTC), are likely more conserved than those that generate non-
PTC containing transcripts. This suggests that AS coupled with nonsense-mediated
decay (NMD) might play an important role in affecting mRNA levels post-transcriptionally.
To understand the mechanisms underlying the divergence of AS, we analyzed the
key determinants of AS using a machine learning approach. We found that the
presence/absence of alternative splice site (SS) within the junction, the distance
between the authentic SS and the nearest alternative SS, the size of exon–exon
junctions were the major determinants for both alternative 50 donor site and 30 acceptor
site among the studied species, suggesting a relatively conserved AS mechanism.
The comparative analysis further demonstrated that variations of the identified AS
determinants significantly contributed to the AS divergence among closely related
species in both Solanaceae and Brassicaceae taxa. Together, these results provide detailed insights into the evolution of AS in plants.