Pan-Genome and Transcriptome-Guided Analysis Reveals Duplication-Driven Evolution and Candidate MYB-bHLH Modules...

Area of Science:

• Genomics
• Molecular Evolution
• Plant Science

Background:

• Gene duplication and selection drive genome evolution and transcription factor diversification.
• The evolutionary history and diversification of the basic helix-loop-helix (bHLH) gene family in pear, especially from a pan-genome perspective, remain underexplored.

Purpose of the Study:

• To conduct a comprehensive pan-genome and transcriptome-guided analysis of the bHLH gene family in pear.
• To elucidate the evolutionary patterns, duplication events, and functional conservation/divergence of bHLH genes in pear.
• To identify candidate bHLH genes and regulatory modules involved in pear fruit development.

Main Methods:

• Performed a pan-genome analysis across 15 pear genome assemblies.
• Classified genome-wide duplicated gene pairs and calculated evolutionary parameters (Ka, Ks, Ka/Ks).
• Identified and grouped 3222 bHLH genes into evolutionary clades and orthologous groups.
• Integrated transcriptome data from 17 tissues and fruit development stages.
• Conducted co-expression analysis with PbrMYB genes to identify regulatory modules.

Main Results:

• Identified 3222 bHLH genes in pear, revealing both conserved core and variable dispensable members.
• Whole Genome Duplication (WGD)/segmental duplication significantly contributed to bHLH gene expansion.
• Most duplicated PbrbHLH gene pairs are under purifying selection, indicating functional constraint.
• Selected 39 fruit-development-associated PbrbHLHs and identified candidate MYB-bHLH co-expression modules.

Conclusions:

• The study provides an evolutionary framework for bHLH gene diversification in pear.
• Identified conserved and variable bHLH members, highlighting functional conservation and genome diversification.
• Discovered candidate regulatory modules involving MYB and bHLH transcription factors crucial for pear fruit development.