A large-scale proteogenomic atlas of pear

Area of Science:

• Plant biology
• Genomics
• Proteomics

Background:

• Pear is a globally significant fruit crop.
• Previous pear genome mapping was established a decade ago.
• Understanding global protein expression is crucial for pear improvement.

Purpose of the Study:

• To generate comprehensive pear proteome data across 24 major tissues.
• To improve pear genome annotation using a proteogenomic approach.
• To explore genes regulating key agronomic traits and identify regulatory networks.

Main Methods:

• Tissue-resolved proteomic profiling of 24 pear tissues.
• Proteogenomic strategy utilizing peptide spectrum matches for genome annotation.
• Gene coexpression module analysis to identify key genes.
• Reconstruction of regulatory networks for lignin synthesis.

Main Results:

• Detailed protein expression profiles for 17,953 proteins.
• Identification of 4,294 novel coding events and improved genome annotation.
• Discovery of expressed short open reading frames affecting pollen tube growth.
• Elucidation of key genes and receptor-like kinases in lignin synthesis and stone cell formation.
• Development of the online PearEXP database for proteogenomic resources.

Conclusions:

• This study provides a comprehensive proteogenomic resource for pear.
• The findings offer insights into the genetic regulation of important agronomic traits.
• This work establishes a paradigm for proteogenomic research in woody plants.