FoPGDB: a pangenome database of Fusarium oxysporum, a cross-kingdom fungal pathogen

Abstract

Pangenomes, capturing the genetic diversity of a species or genus, are essential to understanding the ecology, pathobiology and evolutionary mechanisms of fungi that cause infection in crops and humans. However, fungal pangenome databases remain unavailable. Here, we report the first fungal pangenome database, specifically for Fusarium oxysporum species complex (FOSC), a group of cross-kingdom pathogens causing devastating vascular wilt to over 100 plant species and life-threatening fusariosis to immunocompromised humans. The F. oxysporum Pangenome Database (FoPGDB) is a comprehensive resource integrating 35 high-quality FOSC genomes, coupled with robust analytical tools. FoPGDB allows for both gene-based and graph-based exploration of the F. oxysporum pangenome. It also curates a large repository of putative effector sequences, crucial for understanding the mechanisms of FOSC pathogenicity. With an assortment of functionalities including gene search, genomic variant exploration and tools for functional enrichment, FoPGDB provides a platform for in-depth investigations of the genetic diversity and adaptability of F. oxysporum. The modular and user-friendly interface ensures efficient data access and interpretation. FoPGDB promises to be a valuable resource for F. oxysporum research, contributing to our understanding of this pathogen's pangenomic landscape and aiding in the development of novel disease management strategies. Database URL: http://www.fopgdb.site.

Figure 1.

The framework, core system and programming language of FOPGDB.

Figure 2.

The homepage of FoPGDB.

Figure 3.

The Pangenome Analysis section under the Pangenome module. (A) Quick access links. (B) Maximum-likelihood tree using single-copy orthologous protein sequences in 35 Fusarium oxysporum genomes. Fusarium graminearum was used as an outgroup. (C) (Top left) Modeling of pangenome and core-genome sizes as additional genomes of F. oxysporum pangenome are added. (Top right) The distribution and ratios of the pangenome gene family categories in 35 accessions. The ‘core’ genes are those present in all accessions, ‘softcore’ genes are present in 34 accessions, ‘dispensable’ genes are present in more than 3 but less than 34 accessions, ‘peripheral’ genes are present in 2 to 3 accessions and ‘private’ genes are present in only 1 accession. (Center) Presence and absence of pangenome gene families in the 35 F. oxysporum genomes. (Bottom) Violin plots showing gene sizes (left), exon numbers (middle) and CDS lengths (right) of the genes in the core, soft-core, dispensable, peripheral and private categories. (D) Numbers of effectors in each genome. (E) Visualization of the chromosomes in the graph genome with Bandage.

Figure 4.

VRPG section under the Pangenome module shows a section in the graph pangenome.

Figure 5.

The Search module sections. (A, B) Search page and result page of Batch Search, (C, D) Search page and result page of effector search, (E, F) Search page and result page of Gene Search By Location, (G) Search page and result page of Orthogroup search.

Figure 6.

BLAST section under the Tools module. (A) BLAST search page. (B) BLAST result page.

Figure 7.

JBrowse section under the Tools module. (A) Page of genome browser index, (B) available tracks for different types of genomic features, (C) a window showing detailed information of the target gene model, (D) TE information, (E) SNPs and INDELs information for 35 Fusarium oxysporum accessions, (F) SVs’ information for 35 F. oxysporum accessions.

Figure 8.

(A, B) Search page and result page of KEGG enrichment, (C, D) Search page and result page of GO Enrichment, (E, F) Search page and result page of Alignment.