Revisit on the evolutionary relationship between alternative splicing and gene duplication

Area of Science:

• Evolutionary genetics
• Molecular biology
• Genomics

Background:

• Gene duplications and alternative splicing (AS) are key mechanisms for protein function diversification.
• The 'functional-sharing' hypothesis suggests duplicate genes acquire distinct AS isoforms.
• The 'duplicability-age' hypothesis proposes less-spliced genes duplicate more frequently.

Purpose of the Study:

• To re-evaluate genome-wide evidence regarding gene duplication and alternative splicing.
• To challenge the 'duplicability-age' hypothesis and its underlying assumptions.
• To propose a new experimental approach for testing the 'functional-sharing' hypothesis.

Main Methods:

• Re-analysis of genome-wide data on alternative splicing, gene duplicability, and copy number variation (CNV).
• Critical assessment of existing studies supporting the 'duplicability-age' hypothesis.
• Proposal of correspondence analysis of indels (insertions and deletions) between duplicate genes.

Main Results:

• Existing genome-wide analyses do not provide conclusive evidence against the 'functional-sharing' hypothesis.
• The foundation of the 'duplicability-age' hypothesis requires careful re-examination.
• Indel analysis offers a potential method to experimentally test the 'functional-sharing' hypothesis.

Conclusions:

• The 'functional-sharing' hypothesis remains a viable explanation for the evolution of duplicate genes and AS isoforms.
• The 'duplicability-age' hypothesis may be based on insufficient evidence.
• Correspondence analysis of indels provides a promising avenue for future research in this field.