# Comparison and Analysis of the Genomes of Three Strains of Botrytis cinerea Isolated from Pomegranate

## TL;DR

This study compares three strains of the gray mold fungus Botrytis cinerea isolated from pomegranates in Mexico, analyzing their genetic and biological differences.

## Contribution

The study provides new insights into the genomic and phenotypic variability of Botrytis cinerea strains isolated from pomegranates.

## Key findings

- MIC strain showed the highest pectinolytic activity and produced sclerotia faster than the other strains.
- BcPgIs-3 produced the most conidia and infected pomegranate fruits more rapidly.
- Genomic analysis revealed distinct phylogenomic groupings and differences in gene content among the strains.

## Abstract

Gray mold disease, caused by the fungus Botrytis cinerea, affects a wide variety of plants. In this study, we conducted several in vitro tests and genomic analyses on three strains of this fungus (BcPgIs-1, BcPgIs-3, MIC) previously isolated from diseased pomegranate fruits, collected at two geographic locations in Mexico. Our goal was to identify possible differences among these strains. The development of the three strains in distinct culture media, the production of extracellular enzymes, and their effect on the progression of infection in pomegranate fruits were evaluated. The genomes were sequenced using the Illumina platform and analyzed with various bioinformatics tools. All strains possess genetic determinants for virulence and cell wall polymer degradation, but MIC exhibited the highest pectinolytic activity in vitro. This strain also produced sclerotia in a shorter time (7 days) in PDA medium. BcPgls-3 demonstrated the highest conidia production across all the culture media used. Both BcPgls-3 and MIC damaged all the pomegranate fruits 8 days after inoculation, while the BcPgls-1 required up to 9 days. Sequencing of the three strains yielded high-quality sequences, resulting in a total of 17 scaffolds and genomes that exceed 41 million bp, with a GC content of approximately 42%. Phylogenomic analysis indicated that the MIC strain is situated in a group separate from BcPgIs-1 and BcPgIs-3. BcPgIs-3 possesses more coding sequences, but MIC has more genes for CAZymes and peptidases. The three strains share 10,174 genes, while BcPgIs-3 and MIC share 851. These findings highlight the differences among the strains studied, which may reflect their adaptive capacities to their environment. Results contribute to our understanding of the biology of gray mold in pomegranates and could assist in developing more effective control strategies.