DOI: 10.5061/dryad.zkh18935h
title: Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts

description: Background: Macrophomina phaseolina is a fungal plant pathogen with a
 broad host range, but one genotype was shown to exhibit host
 preference/specificity on strawberry. This pathogen lacked a high-quality
 genome assembly and annotation, and little was known about genomic
 differences among isolates from different hosts. Results: We used PacBio
 sequencing and Hi-C scaffolding to provide nearly complete genome
 assemblies for M. phaseolina isolates representing the strawberry-specific
 genotype and another genotype recovered from alfalfa.  The
 strawberry isolate had 59 contigs/scaffolds with an N50 of 4.3 Mb. The
 isolate from alfalfa had an N50 of 5.0 Mb and 14 nuclear contigs with half
 including telomeres.  Both genomes were annotated with MAKER
 using transcript evidence generated in this study with over 13,000
 protein-coding genes predicted. Unique groups of genes for each isolate
 were identified when compared to closely related fungal species.
 Structural comparisons between the isolates reveal large-scale
 rearrangements including chromosomal inversions and translocations. To
 include isolates representing a range of pathogen genotypes, an additional
 30 isolates were sequenced with Illumina, assembled, and compared to the
 strawberry genotype assembly. Within the limits of comparing Illumina and
 PacBio assemblies, no conserved structural rearrangements were identified
 among the isolates from the strawberry genotype compared to those from
 other hosts, but some candidate genes were identified that were largely
 present in isolates of the strawberry genotype and absent in other
 genotypes. Conclusions: High-quality reference genomes of M. phaseolina
 have allowed for the identification of structural changes associated with
 a genotype that has a host preference toward strawberry and will enable
 future comparative genomics studies. Having more complete assemblies
 allows for structural rearrangements to be more fully assessed and ensures
 a greater representation of all the genes. Work with Illumina data from
 additional isolates suggests that some genes are predominately present in
 isolates of the strawberry genotype, 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 identified in the
 strawberry genotype assembly and to determine if unique genes in the
 strawberry genotype play a role in pathogenicity.
description: The genomes were assembled using the FALCON assembly with PacBio
 and were polished with Illumina sequencing. Genomes were annotated using
 MAKER. For a full description of the methods, please see the corresponding
 manuscript.
description: The data for two separate genomes of the
 fungus <em>Macrophomina phaseolina</em> are provided. The Al1
 data sets are from an isolate recovered from alfalfa and the 11_12 data
 sets are from an isolate recovered from strawberry.
 Provided for each isolate are the final assembly (also available
 at NCBI) as well as the corresponding gff annotation files. The fasta
 files that include all of the protein and transcript data for each
 assembly are also included.