Comparison of assembly platforms for the assembly of the nuclear genome of Trichoderma harzianum strain PAR3

Authors: Gorman, Zachary; Chen, Jianchi; Perez De Leon, Adalberto - Beto; Wallis, Christopher

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/28/2023
Publication Date: 8/11/2023
Citation: Gorman, Z.J., Chen, J., Perez De Leon, A.A., Wallis, C.M. 2023. Comparison of assembly platforms for the assembly of the nuclear genome of Trichoderma harzianum strain PAR3. BMC Genomics. 24. Article 454. https://doi.org/10.1186/s12864-023-09544-6.
DOI: https://doi.org/10.1186/s12864-023-09544-6

Interpretive Summary: An isolate of Trichoderma, PAR3, was previously obtained from Parlier, CA and has shown the preliminary ability to protect grapevines from grapevine trunk diseases. The underlying mechanisms behind enhanced protection against these pathogens remains unknown, and detailed genetic information is required to study these processes. There are several programs that can be used to perform genome assembly, but there is little information on the relative quality of these programs for fungal nuclear genome assembly. In this study, several popular assembly programs were utilized to generate multiple assemblies of the PAR3 genome, and the relative quality of these assemblies was assessed. The best genome assembly, generated by MaSuRCA, was used to identify the PAR3 isolate as Trichoderma harzianum, and was further used to find gene models within the PAR3 genome. Fungal researchers can use these results to make decisions on which assembly platforms to consider for nuclear genome assembly. This study can also aid research into the mechanisms behind the ability of PAR3 to enhance resistance to grapevine trunk pathogen and to identify genes associated with potentially novel, natural anti-microbial compounds. Ultimately, this study could facilitate future efforts to produce new products that growers can use to combat grapevine trunk diseases.

Technical Abstract: Trichoderma is a diverse genus of fungi that includes several species that possess biotechnological and agricultural applications, including the biocontrol of pathogenic fungi and nematodes. Previously, the mitochondrial genome of PAR3, an isolate of Trichoderma obtained from a grapevine from Parlier, CA, was published and was putatively identified as Trichoderma harzianum. Different assemblies of the nuclear genome of PAR3 was performed with two long-read assemblers, Flye and Canu, two hybrid assemblers, SPAdes and MaSuRCA, and a combination of Canu-Flye and MaSuRCA-Flye, and the quality of the resulting assemblies were assessed. MaSuRCA produced the most complete and high-fidelity assembly yielding a nuclear genome of 40.7 Mb comprised of 114 scaffolds. Subsequent annotation of this assembly produced 12,074 gene models and 210 tRNAs. All the models were functionally annotated. Phylogenetic analysis of ITS, rpb2, and tef1a sequences from PAR3 and established Trichoderma spp. confirmed that PAR3 is a strain of Trichoderma harzianum. This study gives insight into the efficacy of several popular assembly platforms for assembly of fungal nuclear genomes, and suggests that SPAdes may be the most effective platform for this. The resulting annotated draft nuclear genome assembly provides a potentially valuable resource that can be used to further investigate the potential of Trichoderma harzianum PAR3 as a biocontrol of grapevine fungal canker pathogens and producer of anti-microbial compounds.