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. 2019 May 17;20(1):385.
doi: 10.1186/s12864-019-5774-2.

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

Mahsa Mousavi-Derazmahalleh  1 , Steven Chang  2 , Geoff Thomas  3 , Mark Derbyshire  2 , Phillip E Bayer  4   5 , David Edwards  4   5 , Matthew N Nelson  1   5   6   7 , William Erskine  1   5 , Francisco J Lopez-Ruiz  2 , Jon Clements  3 , James K Hane  8   9
Affiliations

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

Mahsa Mousavi-Derazmahalleh et al. BMC 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.

Keywords: Botrytis cinerea; Comparative genomics; Lupin; Sclerotinia sclerotiorum.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Genome features, mutation profiles and presence-absence variations across isolates of Botrytis cinerea and Sclerotinia sclerotiorum. Chromosomes of reference isolates Botrytis cinerea B05.10 (a) and Sclerotinia sclerotiorum 1980-UF (b) are visualised alongside (from the innermost ring outwards): genome features including G:C content, gene and repeat densities; ratios of non-synonymous to synonymous mutations (Dn/Ds) relative to alignments of lupin-infecting isolates over 100 kb intervals, and the percent of 100 kb regions that aligned to lupin-infecting isolate assemblies. Yellow boxes indicate large regions of absence in the reference isolate relative to lupin-infecting isolates (Additional file 2)
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