Alternative splicing dynamics and evolutionary divergence during embryogenesis in wheat species

Area of Science:

• Plant genomics
• Molecular evolution
• Transcriptomics

Background:

• Alternative splicing (AS) offers transcriptional and proteomic plasticity, crucial for trait diversity in polyploid species.
• The evolution of AS and its impact on grain development in grasses and wheat remain largely unexplored.
• Understanding AS in polyploids is vital for crop improvement.

Purpose of the Study:

• To develop a robust pipeline for analyzing alternatively spliced transcript isoforms in polyploid wheat, accounting for subgenome similarity.
• To investigate conserved and species-specific AS events across wheat and grass species.
• To elucidate the evolutionary dynamics of AS during grain and embryo development.

Main Methods:

• Developed a specialized bioinformatics pipeline for AS analysis in polyploid genomes.
• Utilized comparative genomics, synteny analysis, and collinearity detection.
• Analyzed AS patterns across different tissues (endosperm, pericarp, embryo) and subgenomes during development.
• Performed evolutionary age analysis of novel transcript isoforms.

Main Results:

• Identified conserved and specific AS events across five wheat and grass species.
• Revealed significant diversity in AS events within and between subgenomes during grain development.
• Demonstrated evolutionary divergence in gene-level versus transcript-level regulation of embryogenesis in polyploid wheats.
• Found that younger genes generate novel transcript isoforms at a faster rate than older genes.

Conclusions:

• The developed pipeline provides a comprehensive resource for AS analysis in wheat and grasses.
• AS regulation exhibits significant diversity and evolutionary divergence during grain and embryo development in polyploid species.
• This study advances the understanding of AS evolution and its role in shaping trait diversity in wheat.