Recent Outbreak of Soybean Stem Canker Caused by Diaporthe phaseolorum var. caulivora in the Main Soybean-Producing Region of Argentina

The genome of a Far Eastern isolate of Diaporthe caulivora, a soybean fungal pathogen

Diaporthe caulivora is an economically important fungal pathogen and a causal agent of soybean stem canker and seed decay. Here, the genome of a Russian Far Eastern isolate of D. caulivora was sequenced, assembled, and announced. Assembly quality was enough for advanced annotation, including prediction of potential disease-related genes encoding virulence factors and molecular determinants contributing to pathogen-host selection, interactions, and adaptation. Comparative analysis of 15 Diaporthe species was conducted regarding general genome properties, collinearity, and proteomes, and included detailed investigation of interspersed repeats. A notable feature of this analysis is a high recombinant variability of Diaporthe genomes, determined by the number and distribution of interspersed repeats, which also proved to be responsible for the diversity of GC content and genome size. This variability is assumed the main determinant of the divergence of Diaporthe genomes. A Bayesian multi-gene phylogeny was inferred for the 15 Diaporthe species on the basis of twenty thousand polymorphic sites of > 100 orthologous genes using independently adjusted evolutionary models. This allowed for the most accurate determination of evolutionary relationships and species boundaries for effective reporting about these plant pathogens. The evidence, obtained by different genome analysis techniques, implies the host-independent evolution of Diaporthe species. KEY POINTS: • The genome of a Far Eastern isolate of D. caulivora was announced. • A high degree of recombinant variability determines genomic divergence in Diaporthe genus. • The multi-gene phylogeny implies host-independent evolution of Diaporthe species.

Soybean Stem Canker Caused by Diaporthe caulivora; Pathogen Diversity, Colonization Process, and Plant Defense Activation

Soybean is an important crop in South America, and its production is limited by fungal diseases caused by species from the genus Diaporthe, including seed decay, pod and stem blight, and soybean stem canker (SSC). In this study, we focused on Diaporthe species isolated from soybean plants with SSC lesions in different parts of Uruguay. Diaporthe diversity was determined by sequencing the internal transcribed spacer (ITS) regions of ribosomal RNA and a partial region of the translation elongation factor 1-alpha gene (TEF1α). Phylogenetic analysis showed that the isolates belong to five defined groups of Diaporthe species, Diaporthe caulivora and Diaporthe longicolla being the most predominant species present in stem canker lesions. Due to the importance of D. caulivora as the causal agent of SSC in the region and other parts of the world, we further characterized the interaction of this pathogen with soybean. Based on genetic diversity of D. caulivora isolates evaluated with inter-sequence single repetition (ISSR), three different isolates were selected for pathogenicity assays. Differences in virulence were observed among the selected D. caulivora isolates on susceptible soybean plants. Further inspection of the infection and colonization process showed that D. caulivora hyphae are associated with trichomes in petioles, leaves, and stems, acting probably as physical adhesion sites of the hyphae. D. caulivora colonized the stem rapidly reaching the phloem and the xylem at 72 h post-inoculation (hpi), and after 96 hpi, the stem was heavily colonized. Infected soybean plants induce reinforcement of the cell walls, evidenced by incorporation of phenolic compounds. In addition, several defense genes were induced in D. caulivora-inoculated stems, including those encoding a pathogenesis-related protein-1 (PR-1), a PR-10, a β-1,3-glucanase, two chitinases, two lipoxygenases, a basic peroxidase, a defensin, a phenylalanine-ammonia lyase, and a chalcone synthase. This study provides new insights into the interaction of soybean with D. caulivora, an important pathogen causing SSC, and provides information on the activation of plant defense responses.

Morphologic, Molecular, and Pathogenic Characterization of Diaporthe phaseolorum Variability in the Core Soybean-Producing Area of Argentina

ABSTRACT Isolates of the Diaporthe/Phomopsis (D/P) complex were collected in the main soybean producing area of Argentina during the 1996-97, 1997-98, and 1998-99 growing seasons. Twenty-three morphologic characters related to type of colonies, stroma, pycnidia and conidia, presence of perithecia, and asci length were studied by principal component analysis (PCA). Genomic DNA were analyzed by the random amplified polymorphic DNA (RAPD) technique. From both studies, 18 isolates were identified as D/P complex and grouped in four major taxa: (i) Diaporthe phaseolorum var. meridionalis, (ii) D. phaseolorum var. caulivora, (iii) D. phaseolorum var. sojae, and (iv) Phomopsis longicolla. In addition to distinguishing interspecific and intraspecific variability, molecular markers allowed the detection of differences among isolates within the same variety. Pathogenicity was assayed in the greenhouse, by the toothpick method, inoculating the D/P isolates to soybean genotypes carrying different resistance genes (Rdc1, Rdc2, Rdc3, and Rdc4) against soybean stem canker (SSC). Pathogenic analysis distinguished two main groups: (i) the SSC-producing isolates, including D. phaseolorum var. meridionalis and D. phaseolorum var. caulivora, and (ii) the non-SSC-producing isolates, including D. phaseolorum var. sojae and P. longicolla. Cultivar RA-702 (susceptible control) was compatible with both D. phaseolorum var. meridionalis and D. phaseolorum var. caulivora isolates; meanwhile, Tracy-M (Rdc1 and Rdc 2 genes) was incompatible with D. phaseolorum var. meridionalis but compatible with D. phaseolorum var. caulivora isolates. The fact that Rdc1 and Rdc2 together (as in Tracy-M) confer an almost immune reaction to all assayed isolates of D. phaseolorum var. meridionalis but were ineffective against the D. phaseolorum var. caulivora isolates evaluated suggests that the virulence or avirulence genes in D. phaseolorum var. meridionalis and D. phaseolorum var. caulivora are different. Moreover, physiological races of D. phaseolorum var. meridionalis were detected by using differential soybean genotypes carrying distinct single Rdc genes. As far as we know, this is the first report on the existence of physiological races of D. phaseolorum var. meridionalis in South America. Selective pressure due to deployment of resistant host cultivars may have changed the frequency of the virulence or avirulence genes within the population of D. phaseolorum var. meridionalis. On the whole, our results show that pathogenic variability of D. phaseolorum in the core soybean-producing area of Argentina is higher than previously recognized.