Global expression differences and tissue specific expression differences in rice evolution result in two contrasting...

Area of Science:

• Genomics
• Evolutionary Biology
• Molecular Biology

Background:

• Previous studies on gene expression evolution often did not distinguish between global and tissue-specific expression changes.
• Different types of gene expression alterations may be influenced by distinct evolutionary forces and exhibit varied patterns between species.

Purpose of the Study:

• To investigate differentially expressed (DE) genes between rice subspecies.
• To characterize distinct types of DE genes, including global and tissue-specific alterations.
• To identify regulatory loci for differential expression using expression quantitative loci (eQTL) analysis.

Main Methods:

• Analysis of japonica and indica rice transcriptome atlases for five homologous tissues.
• Classification of DE genes into global and changed-tissues types based on expression patterns.
• Expression quantitative loci (eQTL) analysis to identify regulatory elements.

Main Results:

• Detected DE genes between rice subspecies, classifying them as global (not expressed in one subspecies) or changed-tissues (differentially expressed across tissues).
• Global DE genes (4.6 ± 0.8%) and changed-tissues DE genes (5.9 ± 1.5%) showed distinct molecular evolution rates and Gene Ontology terms.
• Global DE genes were primarily regulated by cis-eQTLs, whereas changed-tissues DE genes involved complex trans-eQTLs, especially in tissue-specific genes.

Conclusions:

• Global and changed-tissues DE genes exhibit contrasting evolutionary characteristics.
• These findings help reconcile previous controversies regarding molecular evolution, expression evolution, and expression conservation in different species.