Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato

Area of Science:

• Plant genetics
• Evolutionary biology
• Genomics

Background:

• Artificial selection dramatically alters plant traits over short timescales.
• Understanding genetic and expression changes in cultivated plants is crucial.

Purpose of the Study:

• To define gene sequence and expression divergence between cultivated tomato and wild relatives.
• To identify genes under positive selection and shifts in gene expression.

Main Methods:

• RNA sequencing (RNAseq) was used to analyze gene sequences and expression levels.
• Comparative analysis between cultivated tomato and five wild species.

Main Results:

• Over 50 genes showed footprints of positive selection based on sequence differences.
• Thousands of gene expression level shifts were documented, many linked to selection pressure.
• Genes rapidly evolving are associated with environmental response and stress tolerance.
• Significant alterations in the light response coexpression network were observed.

Conclusions:

• Human manipulation has profoundly impacted the tomato transcriptome.
• Both artificial and natural selection have pervasive effects on plant transcriptomes, influencing adaptation and traits.