Draft Genome Sequence of a Fungus (Fusarium tricinctum) Cultured from a Monoisolate Native to the Himalayas

ABSTRACT

Here, we report the draft de novo genome sequence assembly of Fusarium tricinctum (strain T6), using IonTorrent sequencing chemistry and an Ion 530 chip ExT kit for sequencing. The genome assembly resulted in 42,732,204 bp from a total 6.62 Gb, with a median read length of 386 bp.

GENOME ANNOUNCEMENT

Fusarium tricinctum (strain T6) was isolated from the bark samples of Taxus baccata L. subsp. wallichiana (Zucc.) Pilger, also known as Himalayan yew, collected from Bhadrewah (district Doda, Jammu and Kashmir, India). We have assembled the genomic data sequenced using IonTorrent S5XL-00694 as single reads into a draft genome sequence. We report the best assembly of the genome, with an approximate size of 42,732,204 bp, comprised of 617 contigs and 13,132 genes. F. tricinctum has been isolated as an endophytic fungus capable of producing different secondary metabolites (1).

The fungus was grown on potato dextrose broth for 3 weeks, and the genomic DNA was obtained from the mycelium according to the method described in van Kan et al. (2). IonTorrent sequencing chemistry and an Ion 530 chip ExT kit were employed for sequencing, which resulted in 42,732,204 bp from a total 6.62 Gb, with a median read length of 386 bp. Raw single-end reads (19,415,463) were trimmed using Trimmomatic (3). Specifically, reads with bases having a Phred score ≤25 were trimmed. This resulted in 18,213,812 high-quality reads being employed for the assembly. We have used two different software tools for assembling the genome, viz., Mimicking Intelligent Reads Assembly (MIRA) (4) and St. Petersburg Genome Assembler (SPAdes) (5). We summarize below the core statistics of both the assemblies.

• (i)With MIRA, the assembly resulted in 617 contigs totaling 42,732,204 bp (N₅₀, 177,443 bp; largest scaffold, 1,057,131 bp; ∼100.0× coverage).
• (ii)With SPAdes, the assembly resulted in 1,892 contigs totaling 42,821,728 bp (N₅₀, 182,652 bp; largest scaffold, 803,475 bp; ∼99.9× coverage).

The size of the assembled genome sequence compares well with those of other published genome sequences of Fusarium species (e.g., F. fujikuroi, 43.83 Mb [6]; F. graminearum, 36.44 Mb [7]; F. oxysporum, 61.35 Mb [7]; F. verticillioides, 41.77 Mb [7, 8]; and F. solani, 51.21 Mb [9]). Gene prediction was carried out using AUGUSTUS (version 3.3) (10), with the gene parameters trained from F. graminearum species. The number of genes predicted in the F. tricinctum genome assemblies (MIRA, 13,132, and SPAdes, 13,109) were in good agreement with the total number of genes reported for other Fusarium species, viz., F. fujikuroi, 14,813; F. graminearum, 13,322; F. oxysporum, 20,925; F. verticillioides, 15,869; and F. solani, 15,705. The genome completeness was assessed using Benchmarking Universal Single-Copy Orthologs (BUSCO) (11), which estimated the genome assembly to be 98.9% (MIRA) and 98.7% (SPAdes) complete, based on the presence of conserved single-copy orthologous gene sets specific to Ascomycota. The DOmain-based General Measure for transcriptome and proteome quality Assessment (DOGMA) (12) was employed for assessing the predicted proteome as a percentage of the eukaryotic core set, which comprises 950 single-domain and 493 multidomain conserved domain arrangements (CDAs). MIRA and SPAdes assemblies were observed to be 95.77% complete in terms of single-domain and multidomain CDAs. The genome sequence described here is of particular interest to further understanding the molecular mechanism behind horizontal gene transfer events and why certain species tend to evolve with enzyme profiles from pathogenic/nonpathogenic relatives.

Accession number(s).

This whole-genome shotgun project is deposited in GenBank under the accession number PTXX00000000.