De novo assembly and comparative transcriptome analysis of Monilinia fructicola, Monilinia laxa and Monilinia fructigena, the causal agents of brown rot on stone fruits

Abstract

BackgroundBrown rots are important fungal diseases of stone and pome fruits. They are caused by several Monilinia species but M. fructicola, M. laxa and M. fructigena are the most common all over the world. Although they have been intensively studied, the availability of genomic and transcriptomic data in public databases is still scant. We sequenced, assembled and annotated the transcriptomes of the three pathogens using mRNA from germinating conidia and actively growing mycelia of two isolates of opposite mating types per each species for comparative transcriptome analyses.ResultsIllumina sequencing was used to generate about 70 million of paired-end reads per species, that were de novo assembled in 33,861 contigs for M. fructicola, 31,103 for M. laxa and 28,890 for M. fructigena. Approximately, 50% of the assembled contigs had significant hits when blasted against the NCBI non-redundant protein database and top-hits results were represented by Botrytis cinerea, Sclerotinia sclerotiorum and Sclerotinia borealis proteins. More than 90% of the obtained sequences were complete, the percentage of duplications was always less than 14% and fragmented and missing transcripts less than 5%. Orthologous transcripts were identified by tBLASTn analysis using the B. cinerea proteome as reference. Comparative transcriptome analyses revealed 65 transcripts over-expressed (FC ≥ 8 and FDR ≤ 0.05) or unique in M. fructicola, 30 in M. laxa and 31 in M. fructigena. Transcripts were involved in processes affecting fungal development, diversity and host-pathogen interactions, such as plant cell wall-degrading and detoxifying enzymes, zinc finger transcription factors, MFS transporters, cell surface proteins, key enzymes in biosynthesis and metabolism of antibiotics and toxins, and transposable elements.ConclusionsThis is the first large-scale reconstruction and annotation of the complete transcriptomes of M. fructicola, M. laxa and M. fructigena and the first comparative transcriptome analysis among the three pathogens revealing differentially expressed genes with potential important roles in metabolic and physiological processes related to fungal morphogenesis and development, diversity and pathogenesis which need further investigations. We believe that the data obtained represent a cornerstone for research aimed at improving knowledge on the population biology, physiology and plant-pathogen interactions of these important phytopathogenic fungi.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4817-4) contains supplementary material, which is available to authorized users.

Pectin methyl esterases and rhamnogalacturonan hydrolases: weapons for successful Monilinia laxa infection in stone fruit?

“…In agreement with this, a global transcriptomic study of the three most common Monilinia spp. revealed that a PME from M. laxa was included among the differentially expressed transcripts (de Miccolis Angelini et al ., ). Furthermore, this PME ( B. cinerea protein ID: BCIN_03g03830) is coincident with the putative functionally annotated MlPME2 studied in this work.…”

“…However, the pivotal role of MfPG1, which diminishes fungal virulence when overexpressed, has also been highlighted (Chou et al, 2015). Among other CWDEs, PMEs and RG-HYDs may be involved in M. laxa pathogenicity, according to recently published transcriptomic data (de Miccolis Angelini et al, 2018). Nevertheless, no other studies have tried to elucidate the putative role that these CAZymes may play in the M. laxa-stone fruit interaction, and thus little evidence is available for their role as virulence determinants in pathogenesis.…”

New High-Quality Draft Genome of the Brown Rot Fungal Pathogen Monilinia fructicola

“…The strain was characterized at both the phenotypic and molecular levels (Abate, De Miccolis Angelini, et al. 2018; Abate, Pastore, et al 2018; De Miccolis Angelini et al. 2018).…”

Genome sequence of the brown rot fungal pathogen Monilinia fructigena

“…Our data reduced the M. fructigena assembly to 131 scaffolds without gaps. In addition, the sequence completeness and high coverage were verified by mapping RNA sequencing (RNA-Seq) reads from the same M. fructigena strain [ 7 ]. The availability of a more accurate genome sequence provides improved opportunities to the scientific community for studies aimed at exploring in more detail the pathogen epidemiology, its host interactions, and the tools to optimise brown rot management.…”

“…A monoconidial strain of M. fructigena , Mfrg269, was derived from plum during monitoring of Monilinia populations present on stone fruit in southern Italy (Tursi, Basilicata) [ 8 ]. The strain was characterised both at the phenotypic and molecular levels [ 7 – 9 ]. The strain was grown in liquid medium (2% malt extract; Oxoid) for 36 h at 24 ± 1 °C, in darkness and under shaking (150 rpm).…”