Crop Diseases, Pests and Genetics Research Unit, USDA-ARS San Joaquin Valley Agricultural Sciences Center, Parlier, CA, 93648, USA.
BMC Genomics. 2023 Aug 11;24(1):454. doi: 10.1186/s12864-023-09544-6.
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. The mitochondrial genome of a putative strain of Trichoderma harzianum called PAR3 was analyzed after isolation from the roots of Scarlet Royal grapevine scion grafted to Freedom rootstock, located in a grapevine vineyard in Parlier, CA, USA. Here, we report the sequencing, comparative assembly, and annotation of the nuclear genome of PAR3 and confirm its identification as a strain of T. harzianum. We subsequently compared the genes found in T. harzianum PAR3 to other known T. harzianum strains. Assembly of Illumina and/or Oxford Nanopore reads by the popular long-read assemblers, Flye and Canu, and the hybrid assemblers, SPAdes and MaSuRCA, was performed and the quality of the resulting assemblies were compared to ascertain which assembler generated the highest quality draft genome assembly.
MaSuRCA produced the most complete and high-fidelity assembly yielding a nuclear genome of 40.7 Mb comprised of 112 scaffolds. Subsequent annotation of this assembly produced 12,074 gene models and 210 tRNAs. This included 221 genes that did not have equivalent genes in other T. harzainum strains. Phylogenetic analysis of ITS, rpb2, and tef1a sequences from PAR3 and established Trichoderma spp. showed that all three sequences from PAR3 possessed more than 99% identity to those of Trichoderma harzianum, confirming that PAR3 is an isolate of Trichoderma harzianum. We also found that comparison of gene models between T. harzianum PAR3 and other T. harzianum strains resulted in the identification of significant differences in gene type and number, with 221 unique genes identified in the PAR3 strain.
This study gives insight into the efficacy of several popular assembly platforms for assembly of fungal nuclear genomes, and found that the hybrid assembler, MaSuRCA, was the most effective program for genome assembly. The annotated draft nuclear genome and the identification of genes not found in other T. harzainum strains could be used to investigate the potential applications of T. harzianum PAR3 for biocontrol of grapevine fungal canker pathogens and as source of anti-microbial compounds.
木霉是一个真菌的多样性属，包括几种具有生物技术和农业应用的物种，包括对致病真菌和线虫的生物防治。从美国加利福尼亚州帕利尔的 Scarlet Royal 葡萄接穗嫁接到 Freedom 砧木的根部分离出的假定 Trichoderma harzianum 菌株 PAR3 的线粒体基因组进行了分析。在这里，我们报告了 PAR3 的核基因组的测序、比较组装和注释，并确认其为 T. harzianum 菌株。随后，我们比较了 PAR3 中发现的基因与其他已知的 T. harzianum 菌株。通过流行的长读长组装器 Flye 和 Canu 以及混合组装器 SPAdes 和 MaSuRCA 对 Illumina 和/或 Oxford Nanopore reads 进行了组装，并比较了产生的组装质量，以确定哪种组装器生成了最高质量的草图基因组组装。
MaSuRCA 产生了最完整和高保真的组装，生成了一个由 112 个支架组成的 40.7 Mb 的核基因组。随后对该组装的注释产生了 12074 个基因模型和 210 个 tRNA。其中包括 221 个在其他 T. harzainum 菌株中没有对应基因的基因。PAR3 和已建立的 Trichoderma spp 的 ITS、rpb2 和 tef1a 序列的系统发育分析表明，PAR3 的所有三个序列与 Trichoderma harzianum 的序列都具有超过 99%的同一性，证实 PAR3 是 Trichoderma harzianum 的分离株。我们还发现，比较 PAR3 与其他 T. harzianum 菌株的基因模型，发现基因类型和数量存在显著差异，在 PAR3 菌株中鉴定出 221 个独特基因。
这项研究深入了解了几种流行的真菌核基因组组装平台的效果，并发现混合组装器 MaSuRCA 是基因组组装最有效的程序。注释的草图核基因组和鉴定出在其他 T. harzainum 菌株中未发现的基因可用于研究 T. harzianum PAR3 对葡萄真菌溃疡病原体的生物防治潜力和作为抗微生物化合物的来源。
