- evolutionary mechanisms behind multiple outbreaks of the host-specific coffee wilt pathogen Fusarium xylarioides. - Full list of author information is available at the end of the article. - Effector genes are often found in highly mutable parts of the genome [8]. - Previous work described the pathology of the epidemics [20], clarified molecular taxonomy [29, 30], showed repro- ductive isolation between the host-specialists [28], and reported the first genomes for the robusta population [31, 32]. - xylarioides strains in the CABI-IMI culture collection. - These strains illustrate the spread west of CWD from the pre-1970s strains to the post-1970s strains, and the emergence of the host-specific arabica and robusta populations. - two strains derive from the 1950s and the pre-1970s out- break in the Central African Republic and Cote D’Ivoire. - General features of the genomes in comparison with other Fusarium species. - Represen- tative whole-genome alignments revealed the presence of the 11 syntenic core chromosomes shared by F. - 0.5% of the genomes, while LS scaffolds are 3.5% and FXU scaffolds are 12% (Table 1).. - Genome size differences in the arabica and robusta strains. - “Coverage” refers to the proportion of the genome covered by coding regions. - udum are the only known members of the FFC to infect their target hosts with a wilt disease [47, 48]. - We found no large-scale matches to any of the fully mobile chromosomes in F. - 2 and S2), ruling out the recent transfer of the whole Fol mobile pathogenic chromosome. - of the LS and FXU scaffolds nor rule out that F. - Annotation of genes and transposable elements (TEs) in the MEGAHIT assemblies reveal the whole genomes, along with F. - Coloured points indicate the location of putative effector genes: square = pre-defined in the literature, circle = CAZyme, diamond = small cysteine-rich proteins. - more than in the core chromosomes. - The proportion of the whole genome made up of transposable elements also varies among species. - 8.5% of the genomes in so-called Large RIP Affected Regions (LRARs, (Fig. - xylarioides, with over 87% of genes supporting monophyly of the clade (Fig. - Phylogenetic relationships between Fusarium species reconstructed from 13 782 orthogroups support monophyly of the F. - xylarioides strains, with the exceptions of the recently described Six10 and Six7 proteins [13] which are present in arabica and Cof- fea strains, and the transcription factor Sge1, which is. - xylarioides it shares a scaffold with the small cysteine-rich putative effector OG14165, which is also only present in the robusta and Coffea strains (see below). - While these differences confirm separation of the ara- bica population from the other strains, a few putative effectors displayed contrasting affinities. - anthophilum, a member of the American FFC clade [45], as closest relative (with nearly 80% similarity), while a diverged copy in F. - xylarioides to group with FFC lineages, as in the core phylogeny (Fig. - oxysporum in the common ancestor of F. - In the final 4 cases, F. - The remain- ing ten effectors are shared by the robusta and at least one of the Coffea strains but not arabica. - oxyspo- rum appears to have played a greater role to the emer- gence of the robusta and Coffea host-specific strains than in the arabica population. - Of the formae speciales which consistently match, F. - 98% with four of these HGT effectors only found in the robusta and Coffea strains (Figure S7).. - particular interest is one scaffold found in the robusta and Coffea genomes, which contains these 4 putative effectors matching F. - Previous work implicated mimp class II TEs in the HGT of effector genes in F. - Of the 15 cases of putative horizontal transfer discov- ered by phylogenetic analysis of effector gene sequences in the previous section, all are found on scaffolds contain- ing mimps and DNA transposons. - 8e, which is present in the robusta and Coffea genomes, has close affinity to F. - However, not all of the effectors associated with class II transposons display a signal of HGT in our phylogenetic analysis of effector genes. - 0.05 in the other genomes. - oxysporum homologs, supports the role of horizontal transfer in the origin of host-specific differ- ences. - 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