Evolution of gene structural complexity: an alternative-splicing-based model accounts for intron-containing...

Area of Science:

• Genomics
• Molecular Biology
• Evolutionary Biology

Background:

• Eukaryotic gene structure evolves via intron gain/loss.
• Existing models (Fink, retroposition) explain intron loss but not intron retention in retrogenes.
• Evolutionary processes behind complex exon-intron structures in retrogenes were unclear.

Purpose of the Study:

• To investigate retroduplication-derived genes with both intron loss and retention.
• To propose a new model for the generation of intron-retaining (IR) type gene pairs.
• To explain the prevalence of complex gene structures in plants.

Main Methods:

• Detection and categorization of retroduplication-derived genes in humans, flies, rice, and Arabidopsis.
• Comparison of intron content between parental genes and their retroduplicated copies.
• Development of a model integrating alternative splicing with existing evolutionary mechanisms.

Main Results:

• Hundreds of retroduplication-derived genes were identified and classified as intron-lost or intron-retaining (IR) types.
• A new model linking intron retention and alternative splicing to IR-type gene generation was proposed.
• 25 parental genes with intron retention isoforms and corresponding IR-type duplicates were presented as evidence.
• Plants exhibit a higher percentage of IR-type genes compared to animals.

Conclusions:

• The proposed alternative-splicing-based model, combined with Fink and retroposition models, explains the existence of IR-type genes.
• The abundance of intron retention in plants likely contributes to their higher proportion of IR-type genes.
• This study supports the notion of highly complex gene structures in plant genomes due to intron retention.