Hybrid de novo genome assembly data and comparative genomics of Fusarium chlamydosporum isolated from infected blackberry fields

Abstract

Here, we present a dataset of ITS and β-tubulin sequences, along with a phylogenetic analysis using these molecular markers, for six putative Fusarium strains isolated from blackberry field soil. Additionally, we report the sequencing and hybrid assembly of one of these strains, identified as Fusarium chlamydosporum. Whole-genome sequencing of this strain was conducted using Illumina NovaSeq 6000 and Oxford Nanopore MinION technologies, resulting in a high-quality hybrid assembly of approximately 37 Mb across 23 contigs, with over 99 % completeness. Phylogenomic analysis, incorporating 88 Fusarium genomes, confidently placed this strain within the F. chlamydosporum clade. This assembly is now the NCBI reference genome for F. chlamydosporum, providing a valuable resource for future genomic and evolutionary studies of this species.

Keywords: Blackberry infection; Fusarium; Genomics; Pathogenic strain; Phylogenomics.

Fig. 1

IraGTOF6 most likely belongs to Fusarium chlamydosporum based on phylogenetic analysis and BLAST results. A) A phylogenetic tree was constructed using the ITS sequences (∼500 bp) from six field isolates (strain names “IraGTO”) associated with fusariosis and 17 ITS sequences extracted from the NCBI database as references. The tree was built using the Neighbor-Joining model, and 1000 bootstrap replicates were used to validate the branch support. B) Table showing the BLAST results for the ITS and β-tubulin markers of the IraGTOF6 isolate. Per. Ident: percentage of identity; Acc. Len: alignment length.

Fig. 2

The hybrid assembly of IraGTOF6 shows significant improvements in contiguity and completeness over NRRL13444. A) Overview of whole-genome shotgun sequencing project descriptions and global genome assembly statistics utilizing Illumina and Oxford Nanopore technologies compared to the previously reported F. chlamydosporum genome. The Hypocreales lineage, from which BUSCOs were used to assess genome completeness, comprises 4494 BUSCOs. As such, the percentage values represent the proportion of BUSCOs within each category, while the values in parentheses indicate the total counts for the respective categories. B) Circos plot highlighting the fragmented nature of NRRL13444, the previous reference genome for F. chlamydosporum. Contigs in IraGTOF6 are represented in blue in the exterior circle, while red lines represent gaps in the NRRL13444 genome.

Fig. 3

Phylogenomics analysis of Fusarium based on proteome core placed IraGTOF6 next to F. Chlamydosporum species. Bootstrap values are shown in colored circles, corresponding to the scale in the legend.