Whole genome sequence and annotation of the brown rot fungal pathogen Monilinia fructigena

Monilinia fructigena, M. laxa and M. fructicola are examples of the several apothecial ascomycetes that can cause brown rot and blossom blight in pome-fruit and stone-fruit trees. Worldwide, these result in serious economic damage and losses for crops of the family Rosaceae. Here, we describe the sequencing and assembly of the M. fructigena strain Mfrg269. A hybrid assembly strategy was applied using a combination of 2× 92-bp paired-end reads (Illumina Sequencing Technology; HiScanSQ platform; SELGE Network Sequencing Service, Bari, Italy) and long 20-kb reads (Pacific Biosciences Sequencing Technology; PacBio RSII platform; Macrogen Inc., NGS Service, Geumcheon-gu, Seoul, South Korea). A final assembly of 131 scaffolds that corresponded to a total size of 43.125 Mb, and ~210× sequencing coverage. In more detail, this defined 42.05% GC content, N50 scaffold length 767.732 kb, scaffold L50 of 20, and maximum scaffold size of 1,863,841 bp. About 83% of the RNA-Seq reads mapped on the draft version of the finalgenome. Functional annotation data were obtained using the Augustus software implemented in the BLAST2GO PRO package (v.4.1.9), using Botrytis cinerea as the model species and the RNA-Seq reads as the guide. This predicted 10,511 genes, with 10,811 transcripts that coded for 9,970 predicted proteins that were functionally annotated. This genome sequencing of M. fructigena, as well as for other Monilinia spp. involved in brown rot diseases, will serve as a valuable resource for studies on populations biology and plant–pathogen interactions.