The genome of the emerging barley pathogen Ramularia collo-cygni

Background Ramularia collo-cygni is a newly important, foliar fungal pathogen of barley that causes the disease Ramularia leaf spot. The fungus exhibits a prolonged endophytic growth stage before switching life habit to become an aggressive, necrotrophic pathogen that causes significant losses to green leaf area and hence grain yield and quality. Results The R. collo-cygni genome was sequenced using a combination of Illumina and Roche 454 technologies. The draft assembly of 30.3 Mb contained 11,617 predicted gene models. Our phylogenomic analysis confirmed the classification of this ascomycete fungus within the family Mycosphaerellaceae, order Capnodiales of the class Dothideomycetes. A predicted secretome comprising 1053 proteins included redox-related enzymes and carbohydrate-modifying enzymes and proteases. The relative paucity of plant cell wall degrading enzyme genes may be associated with the stealth pathogenesis characteristic of plant pathogens from the Mycosphaerellaceae. A large number of genes associated with secondary metabolite production, including homologs of toxin biosynthesis genes found in other Dothideomycete plant pathogens, were identified. Conclusions The genome sequence of R. collo-cygni provides a framework for understanding the genetic basis of pathogenesis in this important emerging pathogen. The reduced complement of carbohydrate-degrading enzyme genes is likely to reflect a strategy to avoid detection by host defences during its prolonged asymptomatic growth. Of particular interest will be the analysis of R. collo-cygni gene expression during interactions with the host barley, to understand what triggers this fungus to switch from being a benign endophyte to an aggressive necrotroph

Characterization of DMI, QoI and SDHI fungicides sensitivity of Ramularia collo‑cygni isolates in Argentina

Ramularia leaf spot (RLS) caused by the fungus Ramularia collo-cygni (Rcc) has become a threat to barley production in Argentina. All barley varieties are susceptible to RLS; thus, disease management relies on fungicides like quinone-outside inhibitors (QoIs), demethylation inhibitors (DMIs) and succinate dehydrogenase inhibitors (SDHIs). Europe reported Rcc resistance to fungicides associated with mutations in the fungicide's target genes. The aim of this work was to assess the impact of mutations on sensitivity levels in isolates of Rcc to QoIs, DMIs, SDHIs and a multi-site fungicide used for RLS control in Argentina and others countries. Twenty-one Rcc isolates were collected in the Buenos Aires province in the years 2012, 2015 and 2017 and tested against azoxystrobin (QoI), epoxiconazole and prothioconazole-desthio (DMIs), isopyrazam and fluxapyroxad (SDHIs) and chlorothalonil. For EC50 determination, a sensitivity assay was performed and cytb, cyp51 and sdh genes were sequenced for mutation analyses. All isolates showed G143A mutation that confers total resistance to QoIs (EC50 > 1 mg L−1). Three mutations in the target genes of DMIs (Y403C/S, G404D) were observed. Isolates with both amino-exchanges showed an increase in the EC50 towards DMIs. Mutations B-H266L and C-N87S in the target genes of SDHIs were detected, and both were related to a sensitivity reduction. Mutations occurrence tended to increase from 2012 to 2017 along with higher EC50 values. We found six haplotypes showing that Rcc is potentially adapting to fungicides in Argentina. Efforts must focus on new active ingredients and resistant varieties for a less fungicide-dependent agriculture based on IPM strategies.EEA ManfrediFil: Erreguerena, Ignacio Antonio. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; ArgentinaFil: Havis, Neil David. Scotland’s Rural College. Crop and Soil Research Group; Reino UnidoFil: Heick, Thies Marten. Aarhus University. Department of Agroecology; DinamarcaFil: Gorniak, Kalina. Scotland’s Rural College. Crop and Soil Research Group; Reino UnidoFil: Quiroz, Facundo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; ArgentinaFil: Carmona, Marcelo Anibal. Universidad de Buenos Aires. Facultad de Agronomía. Catedra de Fitopatología; Argentin

Additional file 4: Table S3. of The genome of the emerging barley pathogen Ramularia collo-cygni

Small secreted protein complement of Ramularia collo-cygni genome. (XLSX 43 kb

Additional file 9: Table S7. of The genome of the emerging barley pathogen Ramularia collo-cygni

RT-PCR analysis of Ramularia collo-cygni homologs of dothistromin biosynthesis genes and predicted secondary metabolism genes on Contig17. (XLSX 13 kb

Additional file 11: Figure S3. of The genome of the emerging barley pathogen Ramularia collo-cygni

Taxon annotated GC coverage plot of Ramularia collo-cygni genome assembly. (TIF 1542 kb

Additional file 10: Table S8. of The genome of the emerging barley pathogen Ramularia collo-cygni

BLASTp top hits for putative metabolic cluster genes on Contig17. (XLSX 11 kb

Lastrea gracilescens Moore

原著和名: シマヤハラシダ科名: ヒメシダ科 = Thelypteridaceae採集地: 鹿児島県 屋久島 上屋久町 白谷雲水峡 (大隅 屋久島 上屋久町 白谷雲水峡)採集日: 1989/10/11採集者: 萩庭丈壽整理番号: JH014359国立科学博物館整理番号: TNS-VS-964359備考: 科名変更(瀬戸先生