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

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. Exploring exon structures and domain–exon organizations in protein-coding genes is important for understanding gene function regulation. This study presents seed-plant phylogenomic results that support the conservation of exon/domain architecture for post-transcriptional regulation of gene/protein function.