Xu C et al. (2016), Peltaster fructicola genome reveals evolution f...

ECB-ART-44558

Sci Rep 2016 Mar 11;6:22926. doi: 10.1038/srep22926.

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Peltaster fructicola genome reveals evolution from an invasive phytopathogen to an ectophytic parasite.

Xu C , Chen H , Gleason ML , Xu JR , Liu H , Zhang R , Sun G .

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Sooty blotch and flyspeck (SBFS) fungi are unconventional plant pathogens that cause economic losses by blemishing the surface appearance of infected fruit. Here, we introduce the 18.14-Mb genome of Peltaster fructicola, one of the most prevalent SBFS species on apple. This undersized assembly contains only 8,334 predicted protein-coding genes and a very small repertoire of repetitive elements. Phylogenomics and comparative genomics revealed that P. fructicola had undergone a reductive evolution, during which the numbers of orphan genes and genes involved in plant cell wall degradation, secondary metabolism, and secreted peptidases and effectors were drastically reduced. In contrast, the genes controlling 1,8-dihydroxynaphthalene (DHN)-melanin biosynthesis and appressorium-mediated penetration were retained substantially. Additionally, microscopic examination of the surfaces of infected apple indicated for the first time that P. fructicola can not only dissolve epicuticular waxes but also partially penetrate the cuticle proper. Our findings indicate that genome contraction, characterized mainly by the massive loss of pathogenicity-related genes, has played an important role in the evolution of P. fructicola (and by implication other SBFS species) from a plant-penetrating ancestor to a non-invasive ectophyte, displaying a novel form of trophic interaction between plants and fungi.

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Genes referenced: agl LOC105439570 LOC115919910 LOC115924219 LOC115925116 pelo sgpl1

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	Figure 1. Phylogenetic relationship and analysis of gene families.(a) Predicted pattern of gain and loss of gene families in 12 representative fungal genomes used in this study. The numbers on the branches of the phylogenetic tree correspond to acquired (left, black), lost (right, red), and inferred ancestral (oval) gene families along each lineage by comparison with the putative pan-proteome. For each species, the number of gene families, orphan genes, and the total gene number are indicated on the right. The black arrows represent the divergence time of each two lineages with Myr used to abbreviate million years. (b) Venn diagram of the predicted genes and gene families in P. fructicola and Z. tritici versus those of 10 other fungal species. RF, ZT, BC, CH, LB, MO, NC, PG, RI, RO, SC, and UM respectively represent the abbreviations of the 12 fungal names shown in Fig. 1a. The numbers of genes (without mark), gene families (Fam) and orphan genes (Orp) are indicated in separate areas for P. fructicola and Z. tritici.
	Figure 2. The numbers of genes encoding putative plant cell wall-degrading enzymes, key secondary metabolite synthetases and secreted proteins identified in the genomes of P. fructicola and 11 additional fungal species included in this study.The boxes on the left represent the life style of the selected organisms. ECT, ectophyte; HEM, hemibiotrophs; NEC, necrotroph; BIO, biotrophs; SAP, saprotrophs; SYM, symbionts. The colored bars representing the secondary metabolic enzymes are identified by the key at the top. PKS, polyketide synthases; NRPS, nonribosomal peptide synthases; TC, terpene cyclase; DMATS, dimethyl allyl tryptophan synthases; HYBRID, PKS-NRPS hybrids.
	Figure 3. Functional analysis of the genes involved in adaptation of P. fructicola to its ecological niche.(a) Expression profiling of genes encoding secreted proteins and plant cell wall degrading enzymes and genes involved in biosynthesis of secondary metabolites. For the heatmaps, two columns represent different treatments, i.e., inoculation on apple fruit (in vivo) and growth on PDA media (in vitro), and each row is marked with the name of one gene (in italics). The colored scale bar of expression levels is divided into three grades: low (0 < RPKM < 10, including 0), medium (10 < RPKM < 80), and high (80 < RPKM). (b) Schematic representation of the fungal DHN-melanin biosynthesis pathway. Enzymes catalyzing the first five steps have been detected in the P. fructicola genome with their corresponding encoding genes listed in parentheses. RPKM, reads per kilobase per million mapped reads.
	Figure 4. Schematic representation of plant cell wall polysaccharides and selected corresponding polysaccharide-degrading enzymes.(a) Cellulose; (b) Xylan and heteroxylan; (c) Galactomannan; (d) Xyloglucan; (e) Pectin. BGL, β-1,4-glucosidase; EG, β-1,4-endoglucanase; CBHI, cellobiohydrolase (reducing end); CBHII, cellobiohydrolase (nonreducing end); BXL, β-1,4-xylosidase; XLN, β-1,4-endoxylanase; ABF, α-arabinofuranosidase; AGU, α-glucuronidase; MND, β-1,4-mannosidase; AGL, α-1,4-galactosidase; MAN, β-1,4-endomannanase; AXL, α-xylosidase; XEG, xyloglucan β-1,4-endoglucanase; AFC, α-fucosidase; LAC, β-1,4-galactosidase; PGX, exopolygalacturonase; PEL, pectin lyase; PGA, endopolygalacturonase; PME, pectin methyl esterase; PLY, pectate lyase; ABF, α-arabinofuranosidase; RHG, rhamnogalacturonase; RHX, rhamnogalacturonan α-1,2-galacturonohydrolase; RGXB, rhamnogalacturonan α-L-rhamnopyranohydrolase; RHA, α-L-rhamnosidase; GAL, β-1,4-endogalactanase; RGL, rhamnogalacturonan lyase; ABN, endoarabinanase; ABX, exoarabinanase; XGH, endo-xylogalacturonan hydrolase; BXL, β-1,4-xylosidase.
	Figure 5. Photographs and scanning electron micrographs of P. fructicola on apple fruit.(a,b) SBFS signs caused by P. fructicola on apple fruit. (c) Germinating conidium and primary hypha partly submerged into the surface of epicuticular waxes. (d,e) Hyphae partly submerged into the surface of epicuticular waxes. (f) Sclerotium-like body and hyphae, both of which are partly submerged into the surface of epicuticular waxes. CO, conidium; HY, hypha; EW, epicuticular wax; SB, sclerotium-like body.
	Figure 6. Scanning electron (a–f), optical (g–i) and transmission electron (j,k) micrographs of P. fructicola on apple fruit with epicuticular waxes removed. (a) Germinating conidium and and primary hypha. (b) Immature sclerotium-like body. (c) Sclerotium-like bodies and hyphae. (d) Sclerotium-like body without surrounding hyphae. (e,f) Degradation of the cuticle proper beneath sclerotium-like bodies. (g–k) Cross sections showing degradation of the cuticle proper beneath sclerotium-like bodies. CO, conidium; HY, hypha; SB, sclerotium-like body; ISB, immature sclerotium-like body; CP, cuticle proper; ET, eroded trace; RSB, remnant of sclerotium-like body; EC, epidermal cell.
	Figure 7. Inferred colonization pattern of P. fructicola on apple fruit.(a) Overhead view of P. fructicola growing on the apple fruit surface. (b) Sectional view of P. fructicola growing on the apple fruit surface.
	Figure 8. Schematic representation of a hypothesis for the evolutionary route of SBFS fungi.PPG, plant pathogenicity-related gene; PMP, primary metabolism pathway; SMP, secondary metabolism pathway; PCWDE, plant cell wall degrading enzyme; SP, spore; AP, appressorium; HA, haustorium; BH, biotrophic hyphae; NH, necrotrophic hyphae; SB, sclerotium-like body; MN, mycelial network.

References [+] :

Batzer, Expansion of the sooty blotch and flyspeck complex on apples based on analysis of ribosomal DNA gene sequences and morphology. 2005, Pubmed, Echinobase