Expression Divergence Is Correlated with Sequence Evolution but Not Positive Selection in Conifers

Area of Science:

• Evolutionary biology
• Genomics
• Plant science

Background:

• Conifer evolutionary and genomic determinants are poorly understood.
• Limited evidence for positive selection in conifer sequence evolution exists.

Purpose of the Study:

• Elucidate evolutionary forces shaping conifer genomes.
• Investigate plastic responses to abiotic stress.
• Compare gene expression profiles with divergence and polymorphism patterns.

Main Methods:

• Utilized RNAseq data for gene expression analysis.
• Compared gene expression with divergence and polymorphism in lodgepole pine (Pinus contorta) and interior spruce (Picea glauca × engelmannii).
• Analyzed patterns in coding and untranslated regions.

Main Results:

• Rapidly diverging genes exhibit greater expression divergence, lower expression levels, reduced synonymous site diversity, and longer proteins.
• Genes with low expression show a higher fraction of neutral sites, indicating negative selection's role.
• Limited evidence for positive selection differences between divergent and conserved expression genes; some relaxed selection observed.

Conclusions:

• Negative selection primarily influences the relationship between evolutionary rate and expression level.
• Conifers exhibit relatively high rates of adaptive divergence, with some site-specific positive selection identified.
• Genomic evolution in conifers is shaped by both selection and expression divergence.