Proteogenomic Gene Structure Validation in the Pineapple Genome.

Area of Science:

• Plant genomics
• Proteomics
• Biotechnology

Background:

• The MD2 pineapple (Ananas comosus) is a globally significant crop with high water-use efficiency due to crassulacean acid metabolism (CAM).
• Despite its importance, a high-quality annotated proteome for the MD2 pineapple was previously unavailable, hindering genetic research.

Purpose of the Study:

• To conduct a pilot proteogenomic study on MD2 pineapple leaves.
• To validate existing genome annotations and discover novel genes using mass spectrometry-based proteomics.
• To improve the annotation of the pineapple genome.

Main Methods:

• Liquid chromatography-mass spectrometry (LC-MS/MS) was employed to analyze the proteome of MD2 pineapple leaves.
• Proteomic data was used to validate proteins predicted in the F153 (V3) genome annotation.
• Peptide identifications were mapped to both the standard genome and a transcriptome-derived database to identify novel gene candidates.

Main Results:

• 1781 predicted proteins in the F153 (V3) genome were validated.
• 603 additional peptide identifications mapped exclusively to an MD2 transcriptome-derived database.
• 402 nonoverlapping peptides supported 30 high-quality gene candidates novel to pineapple genomes.

Conclusions:

• The study successfully validated a significant portion of the predicted pineapple proteome and identified novel genes.
• Proteogenomic analysis, integrating transcriptomics and proteomics, is a powerful approach for discovering novel genes and refining genome annotations in plants.
• The findings contribute valuable, experimentally validated gene information to the pineapple genome, enhancing its annotation and future research.