Whole Genome Sequencing and Comparative Genomics of Five Isolates of Macrophomina phaseolina Isolated from Agronomic and Prairie Plant Species

Macrophomina phaseolina has a broad host range infecting more than 500 plant species, including soybean, corn, sorghum, cotton and sunflower. The aim of this work was to: (i) sequence and assemble the genome of five isolates of M. phaseolina isolated from agronomic (soybean, corn, and sunflower) and prairie (switchgrass and roundhead lespedeza) plant species; and (ii) dissect the genomes for comparative genomics and identification of novel proteins. The sequenced genome sizes varied from 45 Mb (soybean isolate) to 48 Mb (switchgrass isolate). The average nucleotide identity (ANI), between novel genomes and the reference genome, ranged from 91.1% to 92.6% with novel regions estimated at 4.6 to 6.4% of the whole genome. Comparative genomics between five genomes revealed some unique proteins for each isolate reflecting a diverse potential function from one genome to another. It is interesting to report that the genome size and the total number of novel proteins are higher in the switchgrass isolate compared to those isolated from agronomic crops. These results suggest that the switchgrass isolate has more genomic diversity than the other isolates. Information from the current study will lead to further understanding of the molecular interactions between M. phaseolina and different plant species and will assist in designing effective genetic control strategies for charcoal rot disease.