Prediction of pathogenicity genes involved in adaptation to a lupin host in the fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum via comparative genomics

Abstract

Background Narrow-leafed lupin is an emerging crop of significance in agriculture, livestock feed and human health food. However, its susceptibility to various diseases is a major obstacle towards increased adoption. Sclerotinia sclerotiorum and Botrytis cinerea – both necrotrophs with broad host-ranges - are reported among the top 10 lupin pathogens. Whole-genome sequencing and comparative genomics are useful tools to discover genes responsible for interactions between pathogens and their hosts. Results Genomes were assembled for one isolate of B. cinerea and two isolates of S. sclerotiorum , which were isolated from either narrow-leafed or pearl lupin species. Comparative genomics analysis between lupin-derived isolates and others isolated from alternate hosts was used to predict between 94 to 98 effector gene candidates from among their respective non-conserved gene contents. Conclusions Detection of minor differences between relatively recently-diverged isolates, originating from distinct regions and with hosts, may highlight novel or recent gene mutations and losses resulting from host adaptation in broad host-range fungal pathogens. Electronic supplementary material The online version of this article (10.1186/s12864-019-5774-2) contains supplementary material, which is available to authorized users.

Genome Sequencing Analysis of Scleromitrula shiraiana, a Causal Agent of Mulberry Sclerotial Disease With Narrow Host Range

“…However, some Botrytis spp. with a narrow host range and some regionally diverged isolates (such as S. sclerotiorum and B. cinerea ) have specific effectors or abnormal numbers of CWDEs, which may have potentially undergone some level of host-specific adaptation ( Mousavi-Derazmahalleh et al, 2019 ; Valero-Jiménez et al, 2019 ). Some reports indicate that S. sclerotiorum and other suspected pathogens are present on diseased mulberry fruit, but it is unknown whether these fungi cause mulberry sclerotial disease.…”

Deciphering the Infectious Process of Colletotrichum lupini in Lupin through Transcriptomic and Proteomic Analysis

“…In addition, Necrosis and Ethylene-inducing Proteins (NEPs) were predicted using conserved domains specific to NEP-like proteins (IPR008701/PF05630) [ 54 ]. Cytochrome P450 were identified via the family conserved domain (PF00067) [ 55 ]. Nudix proteins were identified by a family conserved domain (PF00293; IPR015797) [ 56 ].…”

Understanding Host–Pathogen Interactions in Brassica napus in the Omics Era

“…The genome of P. brassicae was assembled using Illumina Hiseq 2500 technology [ 164 ], while the A. candida genome was assembled using Roche/454 [ 165 ]; both are short-read sequencing technologies. These high-quality genome assemblies of the Brassica pathogens revealed that the fungal pathogens contain high genomic variation, including mutations largely induced by transposable elements (TE), large-scale chromosomal re-arrangements [ 166 , 167 ], presence–absence variation [ 168 ] and the gain or loss of accessory chromosomes [ 169 , 170 , 171 ]. These genetic events are continuously and actively evolving in the adaptive response to the selection pressure by the host plant resistance mechanism, thus generating high-genome-plasticity regions, which are often found distributed in compartments where most of the virulence genes are housed [ 172 ].…”

“…The availability of these high-quality genome assemblies has greatly facilitated the discovery of candidate genes for effectors and virulence factors and significantly advanced our understanding about the pathogen in relation to its evolutionary pattern and species diversity through comparative and population genomics studies [ 137 , 168 , 174 ]. Such deep molecular information will also allow us to uncover the complex Brassica –pathogen interactions, as these omics resources are routinely applied in plant pathology research.…”