Epigenome profiling reveals distinctive regulatory features and cis-regulatory elements in pepper

Area of Science:

• Plant genomics
• Epigenetics
• Molecular biology

Background:

• Pepper (Capsicum annuum) has a large, complex genome, hindering functional genomics research.
• Regulatory elements (REs) are crucial for evolution and domestication but difficult to identify in complex plant genomes.

Purpose of the Study:

• To comprehensively map the epigenomic landscape of pepper.
• To identify regulatory elements involved in pepper development and stress responses.
• To understand the role of REs in pepper evolution and domestication.

Main Methods:

• Epigenomic profiling including chromatin accessibility, histone modifications, and DNA methylation.
• Transcriptome analysis.
• Comparative crosslinked immunoprecipitation followed by mass spectrometry (co-IP-MS) to identify proteins associated with chromatin features.
• Population genetics analysis.

Main Results:

• Detailed epigenomic landscape of Capsicum annuum (ST-8) established.
• Promoters and enhancers linked to development, heat stress, and viral challenges identified.
• Stress-responsive gene expression networks and potential transcription activators characterized.
• Evidence of lower nucleotide diversity in some REs during pepper evolution.

Conclusions:

• Variations in regulatory elements contribute to diverse and agronomically valuable pepper phenotypes.
• Provides a foundation for studying gene regulation and for targeted genetic/epigenetic improvement of pepper.