Draft Genome Sequence of a Strain of Cosmopolitan Fungus Trichoderma atroviride.

An unknown fungus has been isolated as a contaminant of in vitro-grown fungal cultures. In an attempt to identify the contamination, we isolated the causal agent and performed whole-genome sequencing. BLAST analysis of the internal transcribed spacer (ITS) sequence against the NCBI database showed 100% identity to Trichoderma atroviride, and further alignment of the genome assembly confirmed the unknown fungus to be T. atroviride. Here, we report the draft genome sequence of a T. atroviride strain.

GENOME ANNOUNCEMENT

Fungal and bacterial contamination is a widespread problem during in vitro cultivation practices. Recently, we experienced fungal contamination that frequently overgrew our cultures of the fungal plant pathogen Verticillium dahliae during routine lab cultivation on potato dextrose agar medium. In an attempt to characterize this fungal contaminant, we isolated the strain and performed whole-genome sequencing.

Using an Illumina platform, we sequenced a mate-pair library (150-bp read length, 5-kb insert size), generating 17.5 million reads in total. We subsequently assembled the genome using the A5 pipeline (1), and the remaining sequence gaps were subsequently filled using SOAP GapCloser (2). The size of the assembled draft genome is 36.4 Mb, with a G+C content of 49.7%. The assembly comprises 59 scaffolds (≥1,000 bp) and 357 contigs (>0 bp), with a scaffold N50 value of 2.1 Mb. We subsequently assessed the completeness of the assembled gene space using the CEGMA pipeline to identify orthologs of 248 core eukaryotic gene families (3), showing that 94.0% of the 248 core genes are present in our draft genome assembly. Next, repetitive elements in the genome assembly were identified with RepeatMasker (4) (http://www.repeatmasker.org) based on known repetitive elements and on de novo repeat identification. In total, 3.4% of the genomic DNA can be classified as repeats. The protein-coding genes in the genome assembly were annotated with the Maker2 pipeline (5), utilizing 35 predicted fungal proteomes to guide gene annotations, as described previously (6), identifying 9,127 protein-coding genes.

In order to reveal the identity of the fungal contamination, we first identified the internal transcribed spacer (ITS) sequence in the assembly. Nucleotide BLAST of the ITS sequence against the NCBI database resulted in 20 hits with 100% identity to various accession numbers of the ITS sequence of Trichoderma atroviride (top hit, GenBank accession no. ANT12-063), as well as a single hit with 100% identity to the ITS sequence of Trichoderma harzianum (GenBank accession no. Z48812). These were followed by a hit with 99% identity to the ITS sequence of Trichoderma koningii (GenBank accession no. FJ478089).

To further investigate the identity of the fungal contaminant, we used MUMmer (7) to align the assembled draft genome to the genomes of a previously sequenced T. atroviride strain (IMI206040) (8) and a T. harzianum strain (CBS226.95) available at the Joint Genomics Institute (JGI) (http://genome.jgi.doe.gov/Triha1/). The alignment showed that 92% of the T. atroviride genome aligns to 83% of our genome assembly, with 99.29% identity on average, whereas only 12% of the T. harzianum genome can be aligned to 23% of our genome assembly, with 84.98% identity on average. Thus, collectively, the ITS sequence and genome assembly alignment analysis revealed that our fungal contamination concerns T. atroviride. Interestingly, T. atroviride is one of the most common soil-borne fungal species and has been described as an antagonist to soil-borne plant pathogens (9). Therefore, T. atroviride is used as a biocontrol agent in agricultural settings (10). The draft genome sequence presented here complements the previously released T. atroviride genome sequence and will facilitate further genomic studies on the molecular biology of its biocontrol activities.

Nucleotide sequence accession number.

This whole-genome shotgun project has been deposited in DDBJ/EMBL/GenBank under the accession no. JZUQ00000000. The version described in this paper is the first version.