Dynamics in Secondary Metabolite Gene Clusters in Otherwise Highly Syntenic and Stable Genomes in the Fungal GenusBotrytis

Abstract

Fungi of the genus Botrytis infect >1400 plant species and cause losses in many crops. Besides the broad host range pathogen B. cinerea, most other species are restricted to a single host. Long read technology was used to sequence genomes of eight Botrytis species, mostly pathogenic on Allium species, and the related onion white rot fungus, Sclerotium cepivorum. Most assemblies contained <100 contigs, with the B. aclada genome assembled in 16 gapless chromosomes. The core genome and pangenome of 16 Botrytis species were defined and the secretome, effector and secondary metabolite repertoires analysed. Among those genes, none are shared among all Allium pathogens and absent from non-Allium pathogens. The genome of each of the Allium pathogens contains 8-39 predicted effector genes that are unique for that single species, none stood out as potential determinant for host specificity. Chromosome configurations of common ancestors of the genus Botrytis and family Sclerotiniaceae were reconstructed. The genomes of B. cinerea and B. aclada were highly syntenic with only 19 rearrangements between them. Genomes of Allium pathogens were compared with 10 other Botrytis species (non-pathogenic on Allium) and with 25 Leotiomycetes for their repertoire of secondary metabolite gene clusters. The pattern was complex, with several clusters displaying patchy distribution. Two clusters involved in the synthesis of phytotoxic metabolites are at distinct genomic locations in different Botrytis species. We provide evidence that the clusters for botcinic acid production in B. cinerea and B. sinoallii were acquired by horizontal transfer from taxa within the same genus.

Deciphering the Monilinia fructicola Genome to Discover Effector Genes Possibly Involved in Virulence

“…From 10,458 proteins, there were 855 proteins predicted to be secreted, which corresponds to 8% of the proteome. This result is concordant with the proportion of secreted proteins in other members of the Sclerotiniaceae family [ 35 , 37 ]. Plant pathogenic fungi use secreted carbohydrate active enzymes (CAZymes) mainly to break down plant tissue to acquire nutrients and establish the infection or they secrete effector proteins to manipulate the defence responses of their host plants.…”

“…In M. fructicola , the genes BOA1 and BOA2 are together in a location on contig MFRU002, while the genes BOA3-13 are clustered in a different location on contig MFRU064. The BOA gene configuration in M. fructicola very much resembles that in Sclerotinia sclerotiorum [ 37 ], which prompted us to examine this in some more detail ( Figure 3 ). The loci that carry the BOA1 and BOA2 genes are located in syntenic regions in M. fructicola (MFRU002) and S. sclerotiorum (Chr5), as flanking genes on either side of the cluster are orthologous.…”

“…The resulting number of 10,086 genes is consistent with other Monilinia species such as M. laxa (9567 genes [ 52 ]) and M. fructigena (10,502 genes [ 53 ]), however, both latter genomes were also not manually curated. Other Sclerotiniaceae family members from the genera Botrytis , Sclerotinia and Sclerotium for which manually curated proteomes have been generated contain between 11,107 and 11,963 genes [ 35 , 37 , 54 ], at least 1000 genes more than M. fructicola strain CMPC6. The accurate structural and functional annotation of the M. fructicola genome will be a key asset in transcriptome studies of infected plant material and will enable functional comparisons of physiological processes in the pathogen during infection of different host species and tissues (flowers, fruit, leaves or twigs).…”

“…The prediction of secondary metabolite gene clusters in the genome of M. fructicola was performed as described by Valero-Jiménez et al [ 37 ]. Gene clusters predicted to be involved in the biosynthesis of secondary metabolites (BGCs) were identified using AntiSMASH, version 4.1.0 using default settings [ 38 ].…”

Visualization of Three Sclerotiniaceae Species Pathogenic on Onion Reveals Distinct Biology and Infection Strategies

“…Our research clearly shows that the infection process of onion by B. squamosa , B. aclada , and S. cepivorum involves three completely different infection strategies. Even the sister taxa B. aclada and B. squamosa showed a completely different biology, despite their close relatedness and their similar genome structure and gene content, with respect to secondary metabolites and effector genes [ 49 ]. It is clear that although B. squamosa , B. aclada , and S. cepivorum are related fungal pathogens of onion, they all have their own unique biology and infection strategy and cause distinct diseases.…”