The Genome of Fusarium oxysporum f. sp. phaseoli Provides Insight into the Evolution of Genomes and Effectors of Fusarium oxysporum Species
Yali Hao, Yan Li, Xingxing Ping, Qihong Yang, Zhenchuan Mao, Jianlong Zhao et al. · 2023 · 10 citationsRead the paper
Fusarium oxysporum f. sp. phaseoli, the causal agent of cowpea fusarium wilt, is a serious threat to cowpea production in China. In this study, a sample of cowpea fusarium wilt was identified as Fusarium oxysporum f. sp. phaseoli using the methods of morphological characters and molecular detection. We further reported the first genome assembly for Fusarium oxysporum f. sp. phaseoli, with 53.7 Mb genome sequence comprising 14,694 genes. Comparative genomic analysis among five Fusarium oxysporum genomes showed that four accessory chromosomes in the five Fusarium oxysporum display similar characteristics, with low sequence similarity (55.35%, vs. overall average of 81.76%), low gene density (2.18 genes/10 kb vs. 3.02 genes/Mb) and highly transposable element density (TEs) (15.01/100 kb vs. 4.89/100 kb), indicating that variable accessory chromosomes are the main source of Fusarium oxysporum evolution. We identified a total of 100 Fusarium oxysporum f. sp. phaseoli-specific effectors in the genome and found 13 specific effector genes located in large insertion or deletion regions, suggesting that insertion or deletion events can cause the emergence of species-specific effectors in Fusarium oxysporum. Our genome assembly of Fusarium oxysporum f. sp. phaseoli provides a valuable resource for the study of cowpea fusarium wilt, and the comparative genomic study of Fusarium oxysporum could contribute to the knowledge of genome and effector-associated pathogenicity evolution in Fusarium oxysporum study.
What the full text shows
Shown in the lab- First genome assembly of Fusarium oxysporum f. sp. phaseoli (FOP) completed. — 53.7 Mb genome with 14,694 genes (FOP strain isolated from cowpea fusarium wilt in China)
- Accessory chromosomes (ACs) in FO species exhibit significantly lower sequence similarity and gene density compared to the overall genome. — 55.35% similarity (vs 81.76% average); 2.18 genes/10 kb (vs 3.02 genes/10 kb average) (Comparative analysis of five FO genomes)
- Accessory chromosomes have a much higher density of transposable elements (TEs). — 15.01/100 kb vs 4.89/100 kb overall average (Comparative analysis of five FO genomes)
- Identification of FOP-specific putative effectors. — 100 specific effectors (Comparative genomic analysis among five FO genomes)
- Species-specific effectors are linked to large insertion or deletion (INDEL) events. — 13 specific effectors located in INDEL regions (FOP genome compared to FOL genome)
- Identification of secondary metabolism gene clusters (SMGCs) in FOP. — 14 SMGCs (including 8 NRPS and 3 terpene clusters) (Bioinformatic analysis of FOP genome)
- Setup
- One FOP strain; comparative analysis using five FO genomes (FOCA, FOL, FOCU, FOS, FOP).
- How
- The researchers performed Nanopore and Illumina sequencing followed by hybrid assembly and polishing. They used comparative genomics, phylogenetic tree construction (ITS, EF-1a, beta-tubulin, RPB2, CYP51C), and bioinformatic tools (SignalP, OrthoMcl, MUMmer) to identify effectors and structural variations.
- Limitations
- Most SMGC products have not been experimentally determined. · The effect of AC sequence rearrangement on gene function remains limited in understanding. · Pathogenicity tests were performed on a single cowpea cultivar (Fengjiang1).
Summarized by Gemma 4 from the open-access full text · 8 Oct 2026. Read it