Phylogenomic profile of exon-intron organization across angiosperms, their relationships with protein domains, and...

Eukaryotic genes usually encode proteins and contain exons in different size, including micro and small exon categories. However, genome-wide gene exon-intron organizations and their conservation across angiosperms have not been investigated. Among exons of protein-coding genes from 46 angiosperms and four gymnosperms, ~35% are micro and small exons affecting most genes and the remaining exons are defined here as medium, large, or super exons. Exon-intron structural comparison using our new bioinformatic tool, ExonEvo, reveals that, ~69% of conserved exons in homologous genes are found in two or more major angiosperm subgroups, including ~47% as the seed plant-wide conserved exons that are present in most genes in individual species. An examination of domain-exon correspondence revealed that most conserved protein domains match two or more conserved exon families and genes encoding the same domain family members can have different domain-exon correspondence. Moreover, most flower-preferential genes contain conserved exons and most exons with exon skipping during splicing are shared by seed plants, suggesting that alternative splicing of the exons could be a conserved mechanism for regulating protein structure. Our phylogenomic landscape of exon structure and domain-exon organization supports a model for conservation of exon/domain structure in relation to post-transcriptional regulation of gene/protein function.