Comparative genomics of plant pathogenic Botrytis species with distinct host specificity
Valero-Jiménez, Claudio A. ; Veloso, Javier ; Staats, Martijn ; Kan, Jan A.L. van - \ 2019
BMC Genomics 20 (2019)1. - ISSN 1471-2164
Effector - Grey mould - Necrotroph - Secondary metabolite - Secretome
Background: Fungi of the genus Botrytis (presently containing ~ 35 species) are able to infect more than 1400 different plant species and cause losses in a wide range of crops of economic importance. The best studied species is B. cinerea, which has a broad host range and is one of the best studied necrotrophic plant pathogenic fungi. Most other Botrytis spp. have a narrow host range and have been studied in less detail. To characterize genomic variation among different representatives of Botrytis spp., we sequenced and annotated the draft genomes of nine Botrytis species: B. calthae, B. convoluta, B. elliptica, B. galanthina, B. hyacinthi, B. narcissicola, B. paeoniae, B. porri and B. tulipae. Results: Bioinformatics and comparative genomics tools were applied to determine a core of 7668 shared protein families in all Botrytis species, which grouped them in two distinct phylogenetic clades. The secretome of all nine Botrytis spp. was similar in number (ranging from 716 to 784 predicted proteins). A detailed analysis of the molecular functions of the secretome revealed that shared activities were highly similar. Orthologs to effectors functionally studied in B. cinerea were also present in the other Botrytis species. A complex pattern of presence/absence of secondary metabolite biosynthetic key enzymes was observed. Conclusions: Comparative genomics of Botrytis show that overall, species share the main signatures and protein families in the secreted proteins, and of known effectors. Our study provides leads to study host range determinants in the genus Botrytis and provides a stepping stone to elucidate the roles of effector candidates in the infection process of these species.
A gapless genome sequence of the fungus Botrytis cinerea
Kan, Jan A.L. Van; Stassen, Joost H.M. ; Mosbach, Andreas ; Lee, Theo A.J. Van Der; Faino, Luigi ; Farmer, Andrew D. ; Papasotiriou, Dimitrios G. ; Zhou, Shiguo ; Seidl, Michael F. ; Cottam, Eleanor ; Edel, Dominique ; Hahn, Matthias ; Schwartz, David C. ; Dietrich, Robert A. ; Widdison, Stephanie ; Scalliet, Gabriel - \ 2017
Molecular Plant Pathology 18 (2017)1. - ISSN 1464-6722 - p. 75 - 89.
Genetic map - Grey mould - Optical map - SMRT sequencing
Following earlier incomplete and fragmented versions of a genome sequence for the grey mould Botrytis cinerea, a gapless, near-finished genome sequence for B. cinerea strain B05.10 is reported. The assembly comprised 18 chromosomes and was confirmed by an optical map and a genetic map based on approximately 75 000 single nucleotide polymorphism (SNP) markers. All chromosomes contained fully assembled centromeric regions, and 10 chromosomes had telomeres on both ends. The genetic map consisted of 4153 cM and a comparison of the genetic distances with the physical distances identified 40 recombination hotspots. The linkage map also identified two mutations, located in the previously described genes Bos1 and BcsdhB, that conferred resistance to the fungicides boscalid and iprodione. The genome was predicted to encode 11 701 proteins. RNAseq data from >20 different samples were used to validate and improve gene models. Manual curation of chromosome 1 revealed interesting features, such as the occurrence of a dicistronic transcript and fully overlapping genes in opposite orientations, as well as many spliced antisense transcripts. Manual curation also revealed that the untranslated regions (UTRs) of genes can be complex and long, with many UTRs exceeding lengths of 1 kb and possessing multiple introns. Community annotation is in progress.