Occurrence of a new subclade of Leptosphaeria biglobosa in Western Australia

Location and timing govern tripartite interactions of fungal phytopathogens and host in the stem canker species complex

BACKGROUND

Leptosphaeria maculans "brassicae" (Lmb) and Leptosphaeria biglobosa "brassicae" (Lbb) make up a species complex involved in the stem canker (blackleg) disease of rapeseed (Brassica napus). They coinfect rapeseed together, from the early stage of infection on leaves to the final necrotic stage at the stem base, and both perform sexual crossings on plant residues. L. biglobosa is suggested to be a potential biocontrol agent against Lmb, but there has been no mechanistic investigation of the different types of interactions that may occur between the plant and the two fungal species.

RESULTS

We investigated the bi- or tripartite interaction mechanisms by (i) confronting Lmb and Lbb in culture conditions or during cotyledon infection, with different timing and/or spore concentration regimes, (ii) performing RNA-Seq experiments in vitro or on the kinetics of infection of cotyledons infected by Lmb and/or Lbb to evaluate the transcriptomic activity and the plant response when both fungal species are inoculated together. Lbb infection of B. napus cotyledons was typical of a necrotrophic behavior, with a very early setup of one pathogenicity program and very limited colonization of tissues. This contrasted with the complex succession of pathogenicity programs of the hemibiotroph Lmb. During simultaneous co-infection by both species, Lmb was strongly impacted in its growth and transcriptomic dynamics both in vitro and in planta, while Lbb was unaffected by the presence of Lmb. However, the drastic inhibition of Lmb growth by Lbb was ineffective in the case of delayed inoculation with Lbb or a lower amount of spores of Lbb compared to Lmb.

CONCLUSIONS

Our data suggest that Lmb growth inhibition by Lbb is the result of a combination of factors that may include competition for trophic resources, the generation by Lbb of an environment unsuitable for the lifecycle of Lmb or/and the effect on Lmb of plant defense responses induced by Lbb. It indicates that growth inhibition occurs in very specific conditions (i.e., co-inoculation at the same place of an equal amount of inoculum) that are unlikely to occur in the field where their coexistence does not prevent any species from completing their life cycle.

Development of a Duplex qPCR System for Detection and Quantification of the Two Canola Blackleg Pathogens Leptosphaeria biglobosa and L. maculans

Two probe-based qPCR systems, namely P-Lb and P-Lm, specific to the canola blackleg pathogens Leptosphaeria biglobosa and L. maculans, respectively, were developed, and their efficiencies were tested. Each of the two systems targets a single-copy gene exclusively present in the corresponding species. The specificities of the two systems on the species level and their ubiquities on the subspecies level were confirmed by in silico sequence analyses and testing on L. biglobosa (17 strains), L. maculans (10 strains), and other plant pathogens (31 species). For sensitivities, the two systems were tested on synthesized DNA fragments (gBlock) of the targeted regions, from which a standard curve was generated for each system. In addition, standard curves were also generated on gBlocks for duplex qPCR in which the two systems were used in the same reaction. The two systems were further tested in both singleplex and duplex qPCR on DNA samples extracted from fungal spores, inoculated canola cotyledons, and naturally infected canola stubble samples collected from commercial fields. Our data indicated that the two systems are specific to L. biglobosa and L. maculans, respectively, and one reaction could detect as few as 200 spores of either species. When used in duplex qPCR on DNA samples with various origins, the two systems generated similar results as in singleplex qPCR. The duplex qPCR system, along with the sample preparation and DNA extraction specified in this study, constituted a first-reported duplex qPCR protocol for detection and quantification of the two blackleg pathogens from field samples.

Indirect Evidence Based on Mating-Type Ratios for the Role of Sexual Reproduction in European and Chinese Populations of Plenodomus biglobosus (Blackleg of Oilseed Rape)

Blackleg (Phoma) disease, caused by the ascomycete fungi Plenodomus biglobosus and P. lingam, threatens oilseed rape (OSR; Brassica napus) crops internationally. In many parts of the world, both species co-occur, but in China only P. biglobosus has so far been reported. Plenodomus biglobosus reproduces asexually (pycnidiospores), but also sexually (pseudothecia-yielding ascospores), via a heterothallic mating system requiring MAT1-1 and MAT1-2 genotypes. However, the roles of airborne ascospore inoculum in driving blackleg disease outbreaks in China are less well understood compared to elsewhere in the world. This is despite the very different agronomic cropping practices in parts of China, in which paddy rice and OSR are often grown in rotation; OSR stubble is often submerged under water for long periods potentially affecting pseudothecial development. Here, we indirectly investigate the potential role of sexual reproduction by developing new polymerase chain reaction (PCR) -based mating-type diagnostics for P. biglobosus and subsequently screening an international collection of 59 European and 157 Chinese isolates. Overall, in both Europe and China, P. biglobosus mating types did not deviate from a 1:1 ratio, such as is generally thought to occur under frequency-dependent selection in sexually reproducing pathogen populations. Both mating types were balanced in all the individual European countries tested (Austria, France, Poland, UK). Conversely, in China, mating types were only balanced in the eastern region; in the northern and southwestern regions there were skewed ratios, more typical of predominantly asexual reproduction, towards MAT1-1 and MAT1-2, respectively. The implications of these findings and future research directions for improved understanding of P. biglobosus epidemiology on OSR, particularly in China, are considered.

A CRISPR/Cas12a-based portable platform for rapid detection of Leptosphaeria maculans in Brassica crops

Establishing a portable diagnostic method for identifying plant pathogens is essential to prevent the spread of plant disease, especially in field and customs inspections. Leptosphaeria maculans (L. maculans) is an aggressive fungus, which causes severe phoma stem canker of Brassica napus, responsible for major yield losses of oilseed rape worldwide. In this study, CRISPR/Cas12a-based detection system and recombinase polymerase amplification (RPA) technique were employed to develop a rapid and sensitive detection method for identifying L. maculans. The involved RPA pre-amplification and CRISPR/Cas12a cleavage confer considerable sensitivity and selectivity, which can be finished within 45 min with a LOD of 4.7 genomic DNA copies. This detection system was further developed to two portable platforms, i.e., one-pot lateral flow detection and all-in-one chip lateral flow assay (AOCLFA), which integrates the lyophilized recombinase polymerase amplification (RPA) reagents and lyophilized Cas12a cleavage reagents in one tube or chip. The developed portable platforms have flexible portability and simple operation for the detection of L. maculans from plant tissues in the field. The proposed portable suitcase containing the minimum equipment, regents, and AOCLFA meets the practical needs of rapid on-site disease screening of plant fungi, port quarantine, or pathogen spreading control.

Less Virulent Leptosphaeria biglobosa Immunizes the Canola Plant to Resist Highly Virulent L. maculans, the Blackleg Pathogen

Leptosphaeria biglobosa is a less virulent Leptosphaeria spp. that causes blackleg disease in canola. Previous studies from our lab have shown that inoculation with the less virulent L. biglobosa can boost the resistance of canola plants against the highly virulent L. maculans. The objective of this study was to confirm the effectiveness of L. biglobosa as a biocontrol agent against L. maculans utilizing morphology, fluorescence microscopy, gene quantification, and transcriptomic analysis. The in planta development of two Leptosphaeria species inoculated at different time points was assessed using fluorescent protein-tagged isolates which are GFP-tagged L. maculans and DsRed-tagged L. biglobosa. The growth inhibition of L. maculans by pre-and co-inoculated L. biglobosa was supported by no lesion development on cotyledons and no or weak fluorescence protein-tagged mycelia under the confocal microscope. The host defense-related genes, WRKY33, PR1, APX6, and CHI, were upregulated in L. biglobosa inoculated Westar cotyledons compared to L. maculans inoculated cotyledons. The quantification of each pathogen through qPCR assay and gene expressions analysis on host defense-related genes by RT-qPCR confirmed the potential of L. biglobosa “brassicae’ in the management of the blackleg disease pathogen, L. maculans ‘brassicae’, in canola.

Metabolic Capacity Differentiates Plenodomus lingam from P. biglobosus Subclade 'brassicae', the Causal Agents of Phoma Leaf Spotting and Stem Canker of Oilseed Rape (Brassica napus) in Agricultural Ecosystems

In contrast to the long-lasting taxonomic classification of Plenodomus lingam and P. biglobosus as one species, formerly termed Leptosphaeria maculans, both species form separate monophyletic groups, comprising sub-classes, differing considerably with epidemiology towards Brassicaceae plants. Considering the great differences between P. lingam and P. biglobosus, we hypothesized their metabolic capacities vary to a great extent. The experiment was done using the FF microplates (Biolog Inc., Hayward, CA, USA) containing 95 carbon sources and tetrazolium dye. The fungi P. lingam and P. biglobosus subclade 'brassicae' (3 isolates per group) were cultured on PDA medium for 6 weeks at 20 °C and then fungal spores were used as inoculum of microplates. The test was carried out in triplicate. We have demonstrated that substrate richness, calculated as the number of utilized substrates (measured at λ490 nm), and the number of substrates allowing effective growth of the isolates (λ750 nm), showed significant differences among tested species. The most efficient isolate of P. lingam utilized 36 carbon sources, whereas P. biglobosus utilized 60 substrates. Among them, 25-29 carbon sources for P. lingam and 34-48 substrates for P. biglobosus were efficiently used, allowing their growth. Cluster analysis based on Senath criteria divided P. biglobosus into two groups and P. lingam isolates formed one group (33% similarity). We deduce the similarities between the tested species help them coexist on the same host plant and the differences greatly contribute to their different lifestyles, with P. biglobosus being less specialized and P. lingam coevolving more strictly with the host plant.

Black Leg and Chlorotic Leaf Spot Occurrence on Brassicaceae Crop and Weed Hosts

Black leg (caused by Plenodomus lingam and P. biglobosus) and chlorotic leaf spot (caused by Pyrenopeziza brassicae) are economically important fungal diseases of Brassicaceae crops. Surveys of seed fields and weed hosts were conducted to understand the distribution and prevalence of these diseases in Oregon after black leg and chlorotic leaf spot outbreaks occurred in Brassicaceae crops in 2014. Postharvest black leg ratings were conducted in seed fields of canola, forage rape, and turnip in 2015 and 2016. The incidence of black leg was greater for turnip (51%) than for canola (29%) and forage rape (25%). The overall average disease incidence was greater for seed crops harvested in 2015 (46%) than for crops harvested in 2016 (28%). A disease survey of wild Brassicaceae plants was conducted along Interstate 5 in Oregon. Brassicaceae weed population sites were identified and 40 sites were sampled for these diseases. Black leg and chlorotic leaf spot were present in 60 and 45%, respectively, of the sampled sites. Both species of Plenodomus were detected in weed populations, with P. lingam being the predominant species recovered (95%). The northernmost sample site with black leg was <32 km from the Oregon-Washington border, and the southernmost site with black leg was within 32 km of the Oregon-California border. Chlorotic leaf spot was detected <32 km from the Oregon-Washington border, whereas the southernmost site where it was detected was approximately 164 km from the Oregon-California border. Based on this study, infected crop residues and weed hosts may facilitate the persistence and spread of these pathogens.

LAMP Detection and Identification of the Blackleg Pathogen Leptosphaeria biglobosa 'brassicae'

Blackleg of oilseed rape is a damaging invasive disease caused by the species complex Leptosphaeria maculans (Lm)/L. biglobosa (Lb), which is composed of at least two and seven phylogenetic subclades, respectively. Generally, Lm is more virulent than Lb, but under certain conditions, Lb can cause a significant yield loss in oilseed rape. Lb 'brassicae' (Lbb) has been found to be the causal agent for blackleg of oilseed rape in China, whereas Lm and Lb 'canadensis' (Lbc) were frequently detected in imported seeds of oilseed rape, posing a risk of spread into China. To monitor the blackleg-pathogen populations, a diagnostic tool based on loop-mediated isothermal amplification (LAMP) was developed using a 615-bp-long DNA sequence from Lbb that was derived from a randomly amplified polymorphic DNA assay. The LAMP was optimized for temperature and time, and tested for specificity and sensitivity using the DNA extracted from Lbb, Lbc, Lm, and 10 other fungi. The results showed that the optimal temperature and time were 65°C and 40 min, respectively. The LAMP primer set was specific to Lbb and highly sensitive as it detected the Lbb DNA as low as 132 fg per reaction. The LAMP assay was validated using the DNA extracted from mycelia and conidia of a well-characterized Lbb isolate, and its utility was evaluated using the DNA extracted from leaves, stems, pods, and seeds of oilseed rape. The LAMP assay developed herein will help for monitoring populations of the blackleg pathogens in China and in developing strategies for management of the blackleg disease.

First Report of Leptosphaeria biglobosa 'brassicae' Causing Blackleg on Brassica juncea var. multisecta in China

Brassica juncea var. multisecta, a leafy mustard, is widely grown in China as a vegetable (Fahey 2016). In May 2018, blackleg symptoms, grayish lesions with black pycnidia, were found on stems and leaves of B. juncea var. multisecta during disease surveys in Wuhan, Hubei Province. Disease incidence was approximately 82% of plants in the surveyed fields (~1 ha in total). To determine the causal agent of the disease, twelve diseased petioles were surface-sterilized and then cultured on potato dextrose agar (PDA) at 20˚C for 5 days. Six fungal isolates (50%) were obtained. All showed fluffy white aerial mycelia on the colony surface and produced a yellow pigment in PDA. In addition, pink conidial ooze formed on top of pycnidia after 20 days of cultivation on a V8 juice agar. Pycnidia were black-brown and globose with average size of 145 × 138 μm and ranged between 78 to 240 × 71 to 220 μm, n = 50. The conidia were cylindrical, hyaline, and 5.0 × 2.1 μm (4 to 7.1 × 1.4 to 2.9 μm, n=100). These results indicated that the fungus was Leptosphaeria biglobosa rather than L. maculans, as only the former produces yellow pigment (Williams and Fitt 1999). For molecular confirmation of identify, genomic DNAs were extracted and tested through polymerase chain reaction (PCR) assay using the species-specific primers LbigF, LmacF, and LmacR (Liu et al. 2006), of which DNA samples of L. maculans isolate UK-1 (kindly provided by Dr. Yongju Huang of University of Hertfordshire) and L. biglobosa 'brassicae' isolate B2003 (Cai et al. 2014) served as controls. Moreover, the sequences coding for actin, β-tubulin, and the internal transcribed spacer (ITS) region of ribosomal DNA (Vincenot et al. 2008) of isolates HYJ-1, HYJ-2 and HYJ-3 were also cloned and sequenced. All six isolates only produced a 444-bp DNA fragment, the same as isolate B2003, indicating they belonged to L. biglobosa 'brassicae', as L. maculans generates a 331-bp DNA fragment. In addition, sequences of ITS (GenBank accession no. MN814012, MN814013, MN814014), actin (MN814292, MN814293, MN814294), and β-tubulin (MN814295, MN814296, MN814297) of isolates HYJ-1, HYJ-2 and HYJ-3 were 100% identical to the ITS (KC880981), actin (AY748949), and β-tubulin (AY748995) of L. biglobosa 'brassicae' strains in GenBank, respectively. To determine their pathogenicity, needle-wounded cotyledons (14 days) of B. juncea var. multisecta 'K618' were inoculated with a conidial suspension (1 × 107 conidia/ml, 10 μl per site) of two isolates HYJ-1 and HYJ-3, twelve seedlings per isolate (24 cotyledons), while the control group was only treated with sterile water. All seedlings were incubated in a growth chamber (20°C, 100% relative humidity under 12 h of light/12 h of dark) for 10 days. Seedlings inoculated with conidia showed necrotic lesions, whereas control group remained asymptomatic. Two fungal isolates showing the same culture morphology to the original isolates were re-isolated from the necrotic lesions. Therefore, L. biglobosa 'brassicae' was confirmed to be the causal agent of blackleg on B. juncea var. multisecta in China. L. biglobosa 'brassicae' has been reported on many Brassica crops in China, such as B. napus (Fitt et al. 2006), B. oleracea (Zhou et al. 2019), B. juncea var. multiceps (Zhou et al. 2019), B. juncea var. tumida (Deng et al. 2020). To our knowledge this is the first report of L. biglobosa 'brassicae' causing blackleg on B. juncea var. multisecta in China, and its occurrence might be a new threat to leafy mustard production of China.

First report of Leptosphaeria biglobosa 'canadensis' causing blackleg on oilseed rape (Brassica napus) in China

Oilseed rape (Brassica napus L.) is one of the most important oilseed crops in China. It is widely cultivated in China, with winter oilseed rape in Yangtze River basin and in southern China, and spring oilseed rape in northern China. In August 2017, a survey for Leptosphaeria spp. on spring oilseed rape was conducted in Minle county, Zhangye city, Gansu Province, China. The symptoms typical of blackleg on basal stems of oilseed rape were observed in the field. A large number of black fruiting bodies (pycnidia) were present on the lesions (Fig. 1A). The disease incidence of basal stem infection in the surveyed field was 19%. A total of 19 diseased stems were collected to isolate the pathogen. After surface sterilizing (75% ethanol for 30 s, 5% NaOCl for 60 s, followed by rinsing in sterilized water three times), diseased tissues were cultured on acidified potato dextrose agar (PDA) plates at 20°C for 7 days. Twelve fungal isolates were obtained. All fungal isolates produced typical tan pigment on PDA medium, and produced pycnidia after two weeks (Fig. 1B). Colony morphological characteristics indicated that these isolates might belong to Leptosphaeria biglobosa. To confirm identification, multiple PCR was conducted using the species-specific primers LmacF, LbigF, LmacR (Liu et al. 2006). Genomic DNA of each isolate was extracted using the cetyltrimethylammonium bromide (CTAB) method. DNA samples of L. maculans isolate UK-1 and L. biglobosa isolate W10 (Cai et al. 2015) were used as references. Only a 444-bp DNA band was detected in all 12 isolates and W10, whereas a 333-bp DNA band was detected only in the UK-1 isolate (Fig. 1C). PCR results suggested that these 12 isolates all belong to L. biglobosa. In addition, the internal transcribed spacer (ITS) region of these 12 isolates was analyzed for subspecies identification (Vincenot et al. 2008). Phylogenetic analysis based on ITS sequence showed that five isolates (Lb1134, Lb1136, Lb1138, Lb1139 and Lb1143) belonged to L. biglobosa 'brassicae' (Lbb) with 78% bootstrap support, and the other seven isolates (Lb1135, Lb1137, Lb1140, Lb1141, Lb1142, Lb1144 and Lb1145) belonged to L. biglobosa 'canadensis' (Lbc) with 95% bootstrap support (Fig. 1D). Two Lbb isolates (Lb1134 and Lb1136) and two Lbc isolates (Lb1142 and Lb1144) were randomly selected for pathogenicity testing on B. napus cultivar Zhongshuang No. 9 (Wang et al. 2002). Conidial suspensions (10 μL, 1 × 107 conidia mL-1) of these four isolates were inoculated on needle-wounded cotyledons (14-day-old seedling), with 10 cotyledons (20 wounded sites) per isolate. A further 10 wounded cotyledons were inoculated with water and served as controls. Seedlings were maintained in a growth chamber at 20°C with 100% relative humidity and a 12-h photoperiod. After 7 days, cotyledons inoculated with the four isolates showed necrotic lesions in the inoculated wounds. Control cotyledons had no symptoms (Fig. 2). Fungi re-isolated from the infected cotyledons showed similar colony morphology as the original isolates. Therefore, L. biglobosa 'brassicae' and L. biglobosa 'canadensis' appear to be the pathogens causing the observed blackleg symptoms on spring oilseed rape in Gansu, China. In previous studies, L. biglobosa 'brassicae' has been found in many crops in China, including oilseed rape (Liu et al. 2014; Cai et al. 2015), Chinese radish (Raphanus sativus) (Cai et al. 2014a), B. campestris ssp. chinensis var. purpurea (Cai et al. 2014b), broccoli (B. oleracea var. italica) (Luo et al. 2018), ornamental kale (B. oleracea var. acephala) (Zhou et al. 2019a), B. juncea var. multiceps (Zhou et al. 2019b), B. juncea var. tumida (Deng et al. 2020) and Chinese cabbage (B. rapa subsp. pekinensis) (Yu et al. 2021 accepted). To the best of our knowledge, this is the first report of L. biglobosa 'canadensis' causing blackleg on B. napus in China.

First report of Leptosphaeria biglobosa 'brassicae' causing Black Leg on Brassica rapa subsp. pekinensis in China

Chinese cabbage [Brassica rapa L. subsp. pekinensis (Lour.) Hanelt] is a major leafy vegetable crop grown in China and eastern Asia (Fordham and Hadley 2003). In December 2018, black leg symptoms were observed on of "Qingza No.3" of Chinese cabbage during harvest, Chibi (29°46'37.38''N, 114°05'6.88''E), Hubei, China. Symptoms were first noted in late Nov. as black spots on leaf petioles and basal stems. Then, black spots enlarged as oval or irregular-shaped grayish lesions. Finally, lesions enlarged and coalesced with black pycnidia were observed, and some diseased leaves became blighted. The disease incidence was about 80% in three fields surveyed (~2 ha in total). Diseased plant tissues were surface-sterilized, and incubated on potato dextrose agar (PDA) plates at 20°C for 4 days. Three fungal isolates, namely EP9-19, EP9-22 and EP9-26, were obtained from five of the diseased samples; all produced fluffy, white aerial mycelia and a yellow pigment on PDA. After 14 days, black-brown and globose pycnidia were produced, approximately 150 μm in diameter (n = 50). In addition, pink pycnidiospore ooze was observed on the top of pycnidium after 20-day culturing on a V8-juice (20%) agar. Conidia were cylindrical and hyaline, with the mean size of 4.6 × 2.7 μm (n = 50). Two fungal species have been reported to cause blackleg on Brassica crops (Williams and Fitt 1999), i.e. Leptosphaeria maculans and L. biglobosa. The former is much more destructive, but is not present in China. These isolates had morphological characteristics matching those of L. biglobosa (Williams and Fitt 1999). The genomic DNA of isolate EP9-22 was extracted and sequenced for its actin, β-tubulin and the internal transcribed spacer (ITS) region of ribosomal DNA as described by Vincenot et al. (2008). Sequences of ITS (GenBank accession no. MN238766), actin (MN242213) and β-tubulin (MN242214) for isolate EP9-22 showed 100%, 99.67%, and 97.93% identity to the corresponding regions of L. biglobosa 'brassicae' strain IBCN89 (Vincenot et al. 2008). In addition, the phylogenetic analysis also indicated that isolate EP9-22 belonged to L. biglobosa 'brassicae'. The pathogenicity test was performed according to established protocols (Balesdent et al., 2005). Cotyledons of the 15-day-old Chinese cabbage seedlings (cultivars Xiaoza No.55 and Hualiangzao No.5) were wound inoculated with 10 μl pycnidiospore suspension (1 × 107 conidia/ml) of the three isolates, with 20 cotyledons per isolate, respectively, and 20 cotyledons wound inoculated with sterile water served as a control group. The treated seedlings were maintained at 20°C and 100% relative humidity with a 12-h photoperiod. The experiment was repeated twice. At 7 days after inoculation, necrotic lesions became visible surrounding inoculation sites for the three isolates, while the control group remained healthy. Fungal isolates showing a similar colony morphology to the originals were re-isolated from ten diseased cotyledons but not from the control cotyledons. Based on these results, L. biglobosa 'brassicae' was shown to be the causal agent of blackleg on Chinese cabbage in China. We believe that this disease has historically often been misidentified as 'anthracnose' by local famers. The threat from L. biglobosa to the production of Chinese cabbage has been assessed. This accurate identification of the causal pathogen is a critical first step towards the development of disease management strategies.

Current Status of the Disease-Resistant Gene(s)/QTLs, and Strategies for Improvement in Brassica juncea

Brassica juncea is a major oilseed crop in tropical and subtropical countries, especially in south-east Asia like India, China, Bangladesh, and Pakistan. The widespread cultivation of genetically similar varieties tends to attract fungal pathogens which cause heavy yield losses in the absence of resistant sources. The conventional disease management techniques are often expensive, have limited efficacy, and cause additional harm to the environment. A substantial approach is to identify and use of resistance sources within the Brassica hosts and other non-hosts to ensure sustainable oilseed crop production. In the present review, we discuss six major fungal pathogens of B. juncea: Sclerotinia stem rot (Sclerotinia sclerotiorum), Alternaria blight (Alternaria brassicae), White rust (Albugo candida), Downy mildew (Hyaloperonospora parasitica), Powdery mildew (Erysiphe cruciferarum), and Blackleg (Leptoshaeria maculans). From discussing studies on pathogen prevalence in B. juncea, the review then focuses on highlighting the resistance sources and quantitative trait loci/gene identified so far from Brassicaceae and non-filial sources against these fungal pathogens. The problems in the identification of resistance sources for B. juncea concerning genome complexity in host subpopulation and pathotypes were addressed. Emphasis has been laid on more elaborate and coordinated research to identify and deploy R genes, robust techniques, and research materials. Examples of fully characterized genes conferring resistance have been discussed that can be transformed into B. juncea using advanced genomics tools. Lastly, effective strategies for B. juncea improvement through introgression of novel R genes, development of pre-breeding resistant lines, characterization of pathotypes, and defense-related secondary metabolites have been provided suggesting the plan for the development of resistant B. juncea.

Characterization of the Race Structure of Leptosphaeria maculans Causing Blackleg of Winter Canola in Oklahoma and Kansas

Blackleg, caused by the fungus Leptosphaeria maculans, is a widespread disease of winter canola (Brassica napus) in Oklahoma and Kansas. Deployment of genetic resistance is the primary strategy for managing blackleg. Resistance genes (Rlm) in canola interact with avirulence genes in the fungus (AvrLm) in a gene-for-gene manner. Little is known about the diversity and frequency of avirulence genes and the race structure in the region. Isolates of Leptosphaeria spp. were collected from diseased leaves in nine counties in Oklahoma and one county in Kansas from 2009 to 2013. Based on pathogenicity and PCR amplification of mating type and species-specific internal transcribed spacer loci, most isolates (n = 90) were L. maculans. The presence of avirulence genes was evaluated using phenotypic interactions on cotyledons of differential cultivars with Rlm1, Rlm2, Rlm3, and Rlm4 and amplification of AvrLm1, AvrLm4-7, and AvrLm6 by PCR. The avirulence alleles AvrLm6 and AvrLm7 were present in the entire L. maculans population. AvrLm1 was found in 34% of the population, AvrLm2 in 4%, and AvrLm4 in only 1%. A total of five races, defined as combinations of avirulence alleles, were identified that included AvrLm1-2-6-7, AvrLm2-6-7, AvrLm4-6-7, AvrLm1-6-7, and AvrLm6-7. Races virulent on the most Rlm genes, AvrLm1-6-7 at 32% and AvrLm6-7 at 62%, were predominant. Defining the avirulence allele frequency and race structure of L. maculans should be useful for the identification and development of resistant cultivars and hybrids for blackleg management in the region. The results suggest that Rlm6 and Rlm7 would be effective, although their deployment should be integrated with quantitative resistance and cultural practices, such as crop rotation, that limit selection pressure on Rlm genes.

A New Subclade of Leptosphaeria biglobosa Identified from Brassica rapa

Blackleg (Phoma stem canker) of crucifers is a globally important disease caused by the ascomycete species complex comprising of Leptosphaeria maculans and Leptosphaeria biglobosa. Six blackleg isolates recovered from Brassica rapa cv. Mizspoona in the Willamette Valley of Oregon were characterized as L. biglobosa based on standard pathogenicity tests and molecular phylogenetic analysis. These isolates were compared to 88 characterized L. biglobosa isolates from western Canada, 22 isolates from Australia, and 6 L. maculans isolates from Idaho, USA using maximum parsimony and distance analysis of phylogenetic trees generated from the ITS rDNA (internal transcribed spacer rDNA) sequence, and the actin and β-tubulin gene sequences. The L. biglobosa isolates derived from B. rapa collected in Oregon formed a separate subclade based on concatenated gene sequences or a single gene sequence, regardless of the analyses. Pathogenicity tests showed that these isolates failed to infect either resistant or susceptible B. napus cultivars, but caused severe symptoms on three B. rapa cultivars (Accession number: UM1113, UM1112, and UM1161), a B. oleracea var. capitata (cabbage) cultivar (Copenhagen Market), and two B. juncea cultivars (CBM, a common brown Mustard, and Forge). These findings demonstrated that the L. biglobosa isolates derived from a B. rapa crop in Oregon were genetically distinct from existing species of L. biglobosa, and constitute a new subclade, herein proposed as L. biglobosa ‘americensis’.

Effect of Water Flooding on Survival of Leptosphaeria biglobosa 'brassicae' in Stubble of Oilseed Rape (Brassica napus) in Central China

Blackleg (Phoma stem canker) caused by Leptosphaeria maculans and L. biglobosa is an economically important disease on oilseed rape and many cruciferous vegetables. Oilseed rape-rice rotation is a routine cultivation practice in central China. This study was conducted to assess the effect of flooding on survival of L. biglobosa 'brassicae' in the stubble of winter oilseed rape (Brassica napus). Basal stems with typical blackleg symptoms were collected and cut into small pieces (2 cm) that were either submerged in water at 16 and 20, 20 and 28, 28 and 33, and 33 and 40°C (12 and 12 h) or kept dry at room temperature (control). Moreover, in a field experiment, the stem pieces were placed on the soil surface in a rice field or in a cotton field and either flooded in water or not flooded, respectively. After 1, 2, 4, 6, and 8 weeks, the stem pieces were sampled for retrieval of L. biglobosa 'brassicae' on V8-juice agar and for determination of dry weight. Selected L. biglobosa 'brassicae' isolates from the stem pieces were identified by polymerase chain reaction (PCR). Results from the two experiments showed that, compared with the controls, flooding for 1 to 2 weeks substantially reduced recovery of L. biglobosa 'brassicae' and flooding for 4 weeks resulted in negligible recovery of L. biglobosa 'brassicae'. All of the 99 selected isolates produced a 444-bp DNA fragment in the PCR, confirming that they belong to L. biglobosa 'brassicae'. Results also indicated that flooding caused rapid decomposition of the stem pieces. After flooding for 8 weeks, the dry weight of the stem pieces was reduced by 28 to 42% in the laboratory experiment and by 26 to 36% in the field experiment. These results suggest that oilseed rape-rice rotation is probably an efficient way to reduce longevity of L. biglobosa 'brassicae' in stubble of winter oilseed rape in central China.

Rapid identification of the Leptosphaeria maculans avirulence gene AvrLm2 using an intraspecific comparative genomics approach

Five avirulence genes from Leptosphaeria maculans, the causal agent of blackleg of canola (Brassica napus), have been identified previously through map-based cloning. In this study, a comparative genomic approach was used to clone the previously mapped AvrLm2. Given the lack of a presence-absence gene polymorphism coincident with the AvrLm2 phenotype, 36 L. maculans isolates were resequenced and analysed for single-nucleotide polymorphisms (SNPs) in predicted small secreted protein-encoding genes present within the map interval. Three SNPs coincident with the AvrLm2 phenotype were identified within LmCys1, previously identified as a putative effector-coding gene. Complementation of a virulent isolate with LmCys1, as the candidate AvrLm2 allele, restored the avirulent phenotype on Rlm2-containing B. napus lines. AvrLm2 encodes a small cysteine-rich protein with low similarity to other proteins in the public databases. Unlike other avirulence genes, AvrLm2 resides in a small GC island within an AT-rich isochore of the genome, and was never found to be deleted completely in virulent isolates.

Transposable element-assisted evolution and adaptation to host plant within the Leptosphaeria maculans-Leptosphaeria biglobosa species complex of fungal pathogens

Background

Many plant-pathogenic fungi have a tendency towards genome size expansion, mostly driven by increasing content of transposable elements (TEs). Through comparative and evolutionary genomics, five members of the Leptosphaeria maculans-Leptosphaeria biglobosa species complex (class Dothideomycetes, order Pleosporales), having different host ranges and pathogenic abilities towards cruciferous plants, were studied to infer the role of TEs on genome shaping, speciation, and on the rise of better adapted pathogens.

Results

L. maculans ‘brassicae’, the most damaging species on oilseed rape, is the only member of the species complex to have a TE-invaded genome (32.5%) compared to the other members genomes (<4%). These TEs had an impact at the structural level by creating large TE-rich regions and are suspected to have been instrumental in chromosomal rearrangements possibly leading to speciation. TEs, associated with species-specific genes involved in disease process, also possibly had an incidence on evolution of pathogenicity by promoting translocations of effector genes to highly dynamic regions and thus tuning the regulation of effector gene expression in planta.

Conclusions

Invasion of L. maculans ‘brassicae’ genome by TEs followed by bursts of TE activity allowed this species to evolve and to better adapt to its host, making this genome species a peculiarity within its own species complex as well as in the Pleosporales lineage.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-891) contains supplementary material, which is available to authorized users.

[Transposable elements reshaping genomes and favouring the evolutionary and adaptive potential of fungal phytopathogens]

Phytopathogenic fungi are a major threat for global food security and show an extreme plasticity in pathogenicity behaviours. They often have a high adaptive potential allowing them to rapidly counteract the control methods used by men in agrosystems. In this paper, we evaluate the link between genome plasticity and adaptive potential using genomics and comparative genomics approaches. Our model is the evolutionary series Leptosphaeria maculans-Leptosphaeria biglobosa, encompassing five distinct entities, whose conspecificity or heterospecificity status is unclear, and which all are pathogens of cruciferous plants. They however differ by their host range and pathogenicity. Compared to other species of the species complex, the species best adapted to oilseed rape, L. maculans "brassicae", causing important losses in the crop, has a genome that was submitted to a recent and massive burst of transposition by a few families of transposable elements (TEs). Whether the genome invasion contributed to speciation is still unclear to-date but there is a coincidence between this burst of TEs and divergence between two species. This TE burst contributed to diversification of effector proteins and thus to generation of novel pathogenic specificities. In addition, the location of effector genes within genome regions enriched in TEs has direct consequences on adaptation to plant resistance and favours a multiplicity of mutation events allowing "breakdown" of resistance. These data are substantiated by other examples in the literature showing that fungi tend to have a "two-speed" genome, in which a plastic compartment enriched in TE host genes is involved in pathogenicity and adaptation to host.

Redisposition of phoma-like anamorphs in Pleosporales

The anamorphic genus Phoma was subdivided into nine sections based on morphological characters, and included teleomorphs in Didymella, Leptosphaeria, Pleospora and Mycosphaerella, suggesting the polyphyly of the genus. Recent molecular, phylogenetic studies led to the conclusion that Phoma should be restricted to Didymellaceae. The present study focuses on the taxonomy of excluded Phoma species, currently classified in Phoma sections Plenodomus, Heterospora and Pilosa. Species of Leptosphaeria and Phoma section Plenodomus are reclassified in Plenodomus, Subplenodomus gen. nov., Leptosphaeria and Paraleptosphaeria gen. nov., based on the phylogeny determined by analysis of sequence data of the large subunit 28S nrDNA (LSU) and Internal Transcribed Spacer regions 1 & 2 and 5.8S nrDNA (ITS). Phoma heteromorphospora, type species of Phoma section Heterospora, and its allied species Phoma dimorphospora, are transferred to the genus Heterospora stat. nov. The Phoma acuta complex (teleomorph Leptosphaeria doliolum), is revised based on a multilocus sequence analysis of the LSU, ITS, small subunit 18S nrDNA (SSU), β-tubulin (TUB), and chitin synthase 1 (CHS-1) regions. Species of Phoma section Pilosa and allied Ascochyta species were determined to belong to Pleosporaceae based on analysis of actin (ACT) sequence data. Anamorphs that are similar morphologically to Phoma and described in Ascochyta, Asteromella, Coniothyrium, Plectophomella, Pleurophoma and Pyrenochaeta are included in this study. Phoma-like species, which grouped outside the Pleosporineae based on a LSU sequence analysis, are transferred to the genera Aposphaeria, Paraconiothyrium and Westerdykella. The genera Medicopsis gen. nov. and Nigrograna gen. nov. are introduced to accommodate the medically important species formerly known as Pyrenochaeta romeroi and Pyrenochaeta mackinnonii, respectively.

TAXONOMIC NOVELTIES

New genera: Medicopsis Gruyter, Verkley & Crous, Nigrograna Gruyter, Verkley & Crous, Paraleptosphaeria Gruyter, Verkley & Crous, Subplenodomus Gruyter, Verkley & Crous. New species: Aposphaeria corallinolutea Gruyter, Aveskamp & Verkley, Paraconiothyrium maculicutis Verkley & Gruyter. New combinations: Coniothyrium carteri (Gruyter & Boerema) Verkley & Gruyter, C. dolichi (Mohanty) Verkley & Gruyter, C. glycines (R.B. Stewart) Verkley & Gruyter, C. multiporum (V.H. Pawar, P.N. Mathur & Thirum.) Verkley & Gruyter, C. telephii (Allesch.) Verkley & Gruyter, Heterospora (Boerema, Gruyter & Noordel.) Gruyter, Verkley & Crous, H. chenopodii (Westend.) Gruyter, Aveskamp & Verkley, H. dimorphospora (Speg.) Gruyter, Aveskamp & Verkley, Leptosphaeria errabunda (Desm.) Gruyter, Aveskamp & Verkley, L. etheridgei (L.J. Hutchison & Y. Hirats.) Gruyter, Aveskamp & Verkley, L. macrocapsa (Trail) Gruyter, Aveskamp & Verkley, L. pedicularis (Fuckel) Gruyter, Aveskamp & Verkley, L. rubefaciens (Togliani) Gruyter, Aveskamp & Verkley, L. sclerotioides (Sacc.) Gruyter, Aveskamp & Verkley, L. sydowii (Boerema, Kesteren & Loer.) Gruyter, Aveskamp & Verkley, L. veronicae (Hollós) Gruyter, Aveskamp & Verkley, Medicopsis romeroi (Borelli) Gruyter, Verkley & Crous, Nigrograna mackinnonii (Borelli) Gruyter, Verkley & Crous, Paraconiothyrium flavescens (Gruyter, Noordel. & Boerema) Verkley & Gruyter, Paracon. fuckelii (Sacc.) Verkley & Gruyter, Paracon. fusco-maculans (Sacc.) Verkley & Gruyter, Paracon. lini (Pass.) Verkley & Gruyter, Paracon. tiliae (F. Rudolphi) Verkley & Gruyter, Paraleptosphaeria dryadis (Johanson) Gruyter, Aveskamp & Verkley, Paralept. macrospora (Thüm.) Gruyter, Aveskamp & Verkley, Paralept. nitschkei (Rehm ex G. Winter) Gruyter, Aveskamp & Verkley, Paralept. orobanches (Schweinitz: Fr.) Gruyter, Aveskamp & Verkley, Paralept. praetermissa (P. Karst.) Gruyter, Aveskamp & Verkley, Plenodomus agnitus (Desm.) Gruyter, Aveskamp & Verkley, Plen. biglobosus (Shoemaker & H. Brun) Gruyter, Aveskamp & Verkley, Plen. chrysanthemi (Zachos, Constantinou & Panag.) Gruyter, Aveskamp & Verkley, Plen. collinsoniae (Dearn. & House) Gruyter, Aveskamp & Verkley, Plen. confertus (Niessl ex Sacc.) Gruyter, Aveskamp & Verkley, Plen. congestus (M.T. Lucas) Gruyter, Aveskamp & Verkley, Plen. enteroleucus (Sacc.) Gruyter, Aveskamp & Verkley, Plen. fallaciosus (Berl.) Gruyter, Aveskamp & Verkley, Plen. hendersoniae (Fuckel) Gruyter, Aveskamp & Verkley, Plen. influorescens (Boerema & Loer.) Gruyter, Aveskamp & Verkley, Plen. libanotidis (Fuckel) Gruyter, Aveskamp & Verkley, Plen. lindquistii (Frezzi) Gruyter, Aveskamp & Verkley, Plen. lupini (Ellis & Everh.) Gruyter, Aveskamp & Verkley, Plen. pimpinellae (Lowen & Sivan.) Gruyter, Aveskamp & Verkley, Plen. tracheiphilus (Petri) Gruyter, Aveskamp & Verkley, Plen. visci (Moesz) Gruyter, Aveskamp & Verkley, Pleospora fallens (Sacc.) Gruyter & Verkley, Pleo. flavigena (Constantinou & Aa) Gruyter & Verkley, Pleo. incompta (Sacc. & Martelli) Gruyter & Verkley, Pyrenochaetopsis pratorum (P.R. Johnst. & Boerema) Gruyter, Aveskamp & Verkley, Subplenodomus apiicola (Kleb.) Gruyter, Aveskamp & Verkley, Subplen. drobnjacensis (Bubák) Gruyter, Aveskamp & Verkley, Subplen. valerianae (Henn.) Gruyter, Aveskamp & Verkley, Subplen. violicola (P. Syd.) Gruyter, Aveskamp & Verkley, Westerdykella capitulum (V.H. Pawar, P.N. Mathur & Thirum.) de Gruyter, Aveskamp & Verkley, W. minutispora (P.N. Mathur ex Gruyter & Noordel.) Gruyter, Aveskamp & Verkley. New names: Pleospora angustis Gruyter & Verkley, Pleospora halimiones Gruyter & Verkley.

Genetic and morphological evidence that Phoma sclerotioides, causal agent of brown root rot of alfalfa, is composed of a species complex

Phoma sclerotioides, causal agent of brown root rot of alfalfa, causes severe root and crown lesions on alfalfa and other perennial forage legumes in regions with harsh winters. Isolates of P. sclerotioides exhibit diverse cultural morphologies on potato dextrose agar (PDA), suggesting that they may exhibit a high degree of genetic diversity. To investigate the genetic relatedness of P. sclerotioides isolates, 154 isolates from North America were sequenced at 10 loci. Maximum parsimony and maximum likelihood analyses of the complete 10-locus data set placed isolates into multiple strongly supported clades, and analyses of gene-jackknife and single-gene partitions of the data set indicated robust support for six major clades and three subclades. Genetic differences corresponded closely to differences in conidial size and septation, pycnidial neck length, mycelial pigmentation, and growth rate in axenic culture at 18 and 25°C. Isolates exhibited morphologies broadly consistent with the species description of P. sclerotioides, and new species were not designated. On the basis of genetic and morphological differences, we propose establishing seven infraspecific varieties within P. sclerotioides: P. sclerotioides var. sclerotioides, champlainii, viridis, obscurus, steubenii, macrospora, and saskatchewanii. All varieties of P. sclerotioides caused brown root rot of alfalfa and grew well at low temperatures.