# Genome Analysis of Alternaria alstroemeriae L6 Associated with Black Spot of Strawberry: Secondary Metabolite Biosynthesis and Virulence

## TL;DR

This study sequenced the genome of a fungus causing black spot on strawberries, revealing its ability to produce diverse harmful and beneficial compounds.

## Contribution

The paper provides a high-quality genome of Alternaria alstroemeriae L6 with insights into its secondary metabolite and virulence gene clusters.

## Key findings

- The genome contains 45 biosynthetic gene clusters, including pathways for phytotoxins and pharmacologically valuable compounds.
- The fungus has 596 carbohydrate-active enzymes and 996 secreted proteins, including five candidate effectors with virulence-related motifs.
- The study highlights the dual potential of the fungus as a pathogen and a source of bioactive metabolites.

## Abstract

A pathogenic fungus was isolated from the leaves of strawberry black spot in Zhengzhou China. Based on morphological and phylogenetic analysis, the isolate was identified as Alternaria alstroemeriae. Hybrid sequencing and assembly yielded a high-quality 38.7 Mb genome with 12,781 predicted genes and 99.6% Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness. Functional annotation revealed enrichment in carbohydrate metabolism, secondary metabolite biosynthesis, and virulence-associated genes. Strain L6 harbored 45 biosynthetic gene clusters(BGCs), including 12 clusters for terpenes, 7 for non-ribosomal peptide synthetases, and 7 for polyketide synthases. Six BGCs showed high similarity to known pathways producing alternariol (phytotoxic/mycotoxic compound), alternapyrone (phytotoxin), choline (osmoprotectant), terpestacin (anti-angiogenic agent), clavaric acid (anticancer terpenoid), and betaenone derivatives (phytotoxins). CAZyme analysis identified 596 carbohydrate-active enzymes, aligning with L6’s biotrophic lifestyle. Additionally, 996 secreted proteins were predicted, of which five candidate effectors contained the conserved RxLx [EDQ] host-targeting motif, suggesting potential roles in virulence. This genome resource highlights L6’s exceptional secondary metabolites (SMs) diversity, featuring both plant-pathogenic toxins and pharmacologically valuable compounds, indicating that this endophytic fungus is a potential producer of metabolites meriting further exploration and development.