Regulatory divergence between parental alleles determines gene expression patterns in hybrids

Area of Science:

• Genomics
• Molecular Biology
• Evolutionary Biology

Background:

• Hybridization and allopolyploidization create new phenotypes by merging distinct genomes and regulatory networks.
• Understanding gene expression changes in hybrids is crucial for comprehending evolutionary novelty.

Purpose of the Study:

• To investigate the rewiring of gene expression in interspecific hybrids of Coffea species.
• To quantify total and allele-specific gene expression in hybrids and their parental species.

Main Methods:

• RNA-sequencing (RNA-seq) technology was employed to quantify gene expression.
• Analysis included 21,025 genes for total expression and over 11,000 for allele-specific expression.
• Comparative analysis of gene expression between Coffea canephora, Coffea eugenioides, and their hybrids.

Main Results:

• Significant cis- and trans-regulatory divergences were observed between parental species, affecting approximately 32% and 35% of genes, respectively.
• In hybrids, 77% of divergently expressed genes showed expression like one parent (expression level dominance), with 65% resembling C. eugenioides.
• C. eugenioides trans-regulatory factors strongly influenced the upregulation of C. canephora alleles, indicating asymmetric regulatory effects.

Conclusions:

• Gene expression patterns in hybrids result from complex interactions between cis- and trans-regulatory divergences and parental trans-regulatory factors.
• Biased expression level dominance is attributed to asymmetric effects of parental trans-regulatory factors.
• The transcriptional response to hybridization depends on the compatibility of gene regulatory networks, influenced by parental genetic divergence and evolutionary history.