Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts

Abstract Background Macrophomina phaseolina is traditionally considered a broad host range fungal pathogen, but one genotype was recently shown to exhibit a host preference/specificity on strawberry. This fungus lacked a high-quality genome assembly and annotation, and little is known about genomic differences between isolates from different hosts. Results This study used PacBio sequencing and Hi-C scaffolding to provide nearly complete genome assemblies from M. phaseolina isolates recovered from strawberry and alfalfa with 60 or fewer scaffolds and N50 metrics at 4.3 and 5.0 Mb, respectively. The genomes were annotated with MAKER using multiple RNA-Seq libraries generated in this study, and over 13,000 protein-coding genes were predicted. Unique groups of orthologous genes for each M. phaseolina isolate were identified when compared to several closely related fungal species. Comparative genomics between the isolates reveal large-scale structural rearrangements including chromosomal inversions and translocations. An additional 30 isolates of M. phaseolina from various hosts, including several from strawberry, were sequenced with Illumina and compared to the high-quality strawberry isolate assembly. No conserved structural rearrangements were identified among the isolates from strawberry compared to those from other hosts, but some candidate genes were identified that were largely present in isolates pathogenic on strawberry and absent in isolates not pathogenic on this host. Conclusions High-quality reference genomes of M. phaseolina generated in this study have allowed for comparative genomics to be used to investigate the genomic changes that might have led to a host preference toward strawberry and will enable future comparative genomics studies. Having more complete scaffolds allows for structural rearrangements to be more fully assessed and ensures a greater representation of all the genes that are truly present in the genome. Work with the additional isolates in this study suggests that some genes are predominately only present in isolates that are pathogenic on strawberry, but additional work is needed to confirm the role of these genes in pathogenesis. Additional work is also needed to complete the scaffolding of smaller contigs representing smaller chromosomes identified in the strawberry genotype assembly and to determine how gene expression plays a role in pathogenicity.