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

Authors: BURKHARDT, ALYSSA - Former ARS Employee; CHILDS, KEVIN - Michigan State University; WANG, JEI - Michigan State University; RAMON, MARINA - Former ARS Employee; Martin, Frank

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/2/2019
Publication Date: 11/4/2019
Citation: Burkhardt, A.K., Childs, K.L., Wang, J., Ramon, M.L., Martin, F.N. 2019. Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts. BMC Genomics. 20:802. https://doi.org/10.1186/s12864-019-6168-1.
DOI: https://doi.org/10.1186/s12864-019-6168-1

Interpretive Summary: This manuscript describes the high quality assembly of the nuclear genome for two isolates of Macrophomina phaseolina that differ in host range and comparative genomics between these isolates and among 30 additional isolates to identify if there were structural differences or specific genes associated with virulence on strawberry.

Technical Abstract: 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. 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.