Sequence and gene expression evolution of paralogous genes in willows

Area of Science:

• Evolutionary Biology
• Genomics
• Plant Science

Background:

• Whole genome duplications (WGD) are key drivers of species diversification and evolutionary novelty.
• The evolutionary fate of duplicated genes post-WGD, particularly gene loss versus retention, remains incompletely understood.
• The Salicoid whole genome duplication event in willows, occurring over 45 million years ago, provides a model for studying these processes.

Purpose of the Study:

• To investigate the balance between gene loss and retention mechanisms for duplicated genes originating from the Salicoid WGD in willows.
• To explore the expression patterns and evolutionary pressures acting on Salicoid duplicates.
• To elucidate the functional divergence and conservation of these duplicated genes.

Main Methods:

• De novo assembly of RNA-seq data from willow leaves and roots.
• Identification of Salicoid duplicates using synonymous third-codon transversion rates and syntenic analysis.
• Analysis of gene expression levels (tissue-specific and differential expression) and evolutionary rates (Ka/Ks).
• Gene Ontology enrichment analysis to infer functional roles.

Main Results:

• Identified 3,778 pairs of Salicoid duplicates from 48,508 contigs.
• Most duplicates were expressed in both tissues, with 74% showing significant differential expression.
• Salicoid duplicates evolve under purifying selection (mean Ka/Ks = 0.23).
• Non-differentially expressed duplicates were enriched for DNA/nucleic acid binding functions, suggesting dosage sensitivity.
• Differentially expressed duplicates were enriched for biosynthesis and metabolism functions, indicating regulatory neofunctionalization or subfunctionalization.

Conclusions:

• Willow Salicoid duplicates are retained through a combination of dosage sensitivity and regulatory sub/neofunctionalization.
• Differential expression patterns correlate with specific functional enrichments, highlighting distinct evolutionary trajectories.
• Multiple evolutionary processes contribute to the long-term persistence of duplicated genes following whole genome duplication in willows.