Diaporthe amygdali, a species complex or a complex species?

Species of Diaporthe (Diaporthaceae, Diaporthales) associated with Alnusnepalensis leaf spot and branch canker diseases in Xizang, China

Alnusnepalensis is an important tree species in the Himalayas with significant ecological and economic roles. During disease surveys in Xizang, China, we observed leaf spot and branch canker symptoms on this tree. Fungal isolates associated with these diseases were collected and identified based on morphological characteristics and phylogenetic analysis of ITS, cal, his3, tef1, and tub2 sequences. As a result, Diaporthealnicola sp. nov. and D.amygdali were identified from the leaf spots, while D.linzhiensis was identified to be associated with the cankered branches. This study identifies pathogenic species from alder trees, providing a foundation for future disease management and forest health research.

Effect of temperature on in vitro germination and growth of Colletotrichum fioriniae, a new emerging pathogen of olive fruits

Olive anthracnose induced by different Colletotrichum species causes dramatic losses of fruit yield and oil quality. The increasing incidence of Colletotrichum fioriniae (Colletotrichum acutatum species complex) as causal agent of olive anthracnose in Italy, is endorsing new studies on its biology, ecology, and environmental factors such as temperature. Five isolates from different sampling sites in Lazio region (Central Italy) were studied under controlled laboratory conditions aiming to better understand the differences of thermal development among the isolates and to lay the foundations of a future mathematical model able to describe the key aspects of the pathogen's life cycle. The mycelial growth rate and the conidial germination rate were assessed at seven different constant temperatures (5, 10, 15, 20, 25, 30, and 35°C) and fixed relative humidity (100% RH). The obtained dataset was analysed to estimate the parameters of mathematical functions that connect the mycelial growth rate and the spore germination with the environmental temperature. The parameters set provided as the result of this study constitute a key step forward in the biological knowledge of the species and the basis for future formulations of mathematical models that might be the core of decision support systems in an integrated pest management framework.

New species of Diaporthe (Diaporthaceae, Diaporthales) from Bauhiniavariegata in China

Diaporthe species are known as endophytes, saprobes and pathogens infecting a wide range of plants and resulting in important crop diseases. In the present study, four strains of Diaporthe were obtained from diseased leaves of Bauhiniavariegata in Guangdong Province, China. Phylogenetic analyses were conducted to identify these strains using five gene regions: internal transcribed spacer (ITS), calmodulin (cal), histone H3 (his3), translation elongation factor 1-α (tef1) and β-tubulin (tub2). The results combined with morphology revealed two new species of Diaporthe named D.bauhiniicola in D.arecae species complex and D.guangzhouensis in D.sojae species complex.

Revision of Alternaria sections Pseudoulocladium and Ulocladioides: Assessment of species boundaries, determination of mating-type loci, and identification of Russian strains

Alternaria is a large genus within Pleosporaceae and consists of fungi that have up to recently been considered to be 15 separate genera, including Ulocladium. The majority of Ulocladium species after incorporation into Alternaria were placed in three sections: Ulocladioides, Pseudoulocladium, and Ulocladium. In this study, phylogeny of 26 reference strains of 22 species and 20 Russian Ulocladium-like isolates was recovered. The partial actin gene (act), Alternaria major allergen (alta1), calmodulin (cal), glyceraldehyde-3-phosphate dehydrogenase (gapdh), RNA polymerase II second largest subunit (rpb2), and translation elongation factor 1-α (tef1) were sequenced for Russian isolates. All these fungi were examined using multilocus phylogenetic analysis according to the genealogical concordance phylogenetic species recognition (GCPSR) principle and the coalescent-based model Poisson tree processes (PTP, mPTP) and evaluated for the presence of recombination. All strains were combined into two clades that corresponded to the Pseudoulocladium and Ulocladioides sections. The Pseudoulocladium clade included four reference strains and nine local isolates and considered to be a single species, whereas the Ulocladioides section comprises 11 species, instead of 17 names previously adopted. Nine species were abolished by joining four other species. Species A. atra and A. multiformis were combined into the single species A. atra. Five species, A. brassicae-pekinensis, A. consortialis, A. cucurbitae, A. obovoidea, and A. terricola, were united in the species A. consortialis. Alternaria heterospora and A. subcucurbitae were combined into one species, A. subcucurbitae. Alternaria aspera, A. chartarum, A. concatenata, and A. septospora were combined into a single species, A. chartarum. Also, amplification with two different primer sets was performed to define mating-type locus 1 (MAT1) idiomorph. All studied isolates were heterothallic, contradicting some prior studies. Twenty Russian Ulocladium-like isolates were assigned to five species of two sections, A. atra, A. cantlous, A. chartarum, A. consortialis, and A. subcucurbitae. Species A. cantlous and A. subcucurbitae were found in Russia for the first time.

Hidden diversity of Pestalotiopsis and Neopestalotiopsis (Amphisphaeriales, Sporocadaceae) species allied with the stromata of entomopathogenic fungi in Taiwan

Pestalotiopsissensu lato, commonly referred to as pestalotiopsis-like fungi, exhibit a broad distribution and are frequently found as endophytes, saprobes and pathogens across various plant hosts. The taxa within pestalotiopsis-like fungi are classified into three genera viz. Pestalotiopsis, Pseudopestalotiopsis and Neopestalotiopsis, based on the conidial colour of their median cells and multi-locus molecular phylogenies. In the course of a biodiversity investigation focusing on pestalotiopsis-like fungi, a total of 12 fungal strains were identified. These strains were found to be associated with stromata of Beauveria, Ophiocordyceps and Tolypocladium in various regions of Taiwan from 2018 to 2021. These strains were evaluated morphologically and multi-locus phylogenetic analyses of the ITS (internal transcribed spacer), tef1-α (translation elongation factor 1-α) and tub2 (beta-tubulin) gene regions were conducted for genotyping. The results revealed seven well-classified taxa and one tentative clade in Pestalotiopsis and Neopestalotiopsis. One novel species, Pestalotiopsismanyueyuanani and four new records, N.camelliae-oleiferae, N.haikouensis, P.chamaeropis and P.hispanica, were reported for the first time in Taiwan. In addition, P.formosana and an unclassified strain of Neopestalotiopsis were identified, based on similarities of phylogeny and morphology. However, the data obtained in the present study suggest that the currently recommended loci for species delimitation of pestalotiopsis-like fungi do not deliver reliable or adequate resolution of tree topologies. The in-vitro mycelial growth rates of selected strains from these taxa had an optimum temperature of 25 °C, but growth ceased at 5 °C and 35 °C, while all the strains grew faster under alkaline than acidic or neutral pH conditions. This study provides the first assessment of pestalotiopsis-like fungi, associated with entomopathogenic taxa.

Diaporthe Species on Palms: Molecular Re-Assessment and Species Boundaries Delimitation in the D. arecae Species Complex

Due to cryptic diversification, phenotypic plasticity and host associations, multilocus phylogenetic analyses have become the most important tool in accurately identifying and circumscribing species in the Diaporthe genus. However, the application of the genealogical concordance criterion has often been overlooked, ultimately leading to an exponential increase in novel Diaporthe spp. Due to the large number of species, many lineages remain poorly understood under the so-called species complexes. For this reason, a robust delimitation of the species boundaries in Diaporthe is still an ongoing challenge. Therefore, the present study aimed to resolve the species boundaries of the Diaporthe arecae species complex (DASC) by implementing an integrative taxonomic approach. The Genealogical Phylogenetic Species Recognition (GCPSR) principle revealed incongruences between the individual gene genealogies. Moreover, the Poisson Tree Processes' (PTPs) coalescent-based species delimitation models identified three well-delimited subclades represented by the species D. arecae, D. chiangmaiensis and D. smilacicola. These results evidence that all species previously described in the D. arecae subclade are conspecific, which is coherent with the morphological indistinctiveness observed and the absence of reproductive isolation and barriers to gene flow. Thus, 52 Diaporthe spp. are reduced to synonymy under D. arecae. Recent population expansion and the possibility of incomplete lineage sorting suggested that the D. arecae subclade may be considered as ongoing evolving lineages under active divergence and speciation. Hence, the genetic diversity and intraspecific variability of D. arecae in the context of current global climate change and the role of D. arecae as a pathogen on palm trees and other hosts are also discussed. This study illustrates that species in Diaporthe are highly overestimated, and highlights the relevance of applying an integrative taxonomic approach to accurately circumscribe the species boundaries in the genus Diaporthe.

Four new endophytic species of Diaporthe (Diaporthaceae, Diaporthales) isolated from Cameroon

The genus Diaporthe (Diaporthaceae, Diaporthales) is a large group of fungi frequently reported as phytopathogens, with ubiquitous distribution across the globe. Diaporthe have traditionally been characterized by the morphology of their ana- and teleomorphic state, revealing a high degree of heterogeneity as soon as DNA sequencing was utilized across the different members of the group. Their relevance for biotechnology and agriculture attracts the attention of taxonomists and natural product chemists alike in context of plant protection and exploitation for their potential to produce bioactive secondary metabolites. While more than 1000 species are described to date, Africa, as a natural habitat, has so far been under-sampled. Several endophytic fungi belonging to Diaporthe were isolated from different plant hosts in Cameroon over the course of this study. Phylogenetic analyses based on DNA sequence data of the internal transcribed spacer region and intervening 5.8S nrRNA gene, and partial fragments of the calmodulin, beta-tubulin, histone and the translation elongation factor 1-α genes, demonstrated that these isolates represent four new species, i.e. D.brideliae, D.cameroonensis, D.pseudoanacardii and D.rauvolfiae. Moreover, the description of D.isoberliniae is here emended, now incorporating the morphology of beta and gamma conidia produced by two of our endophytic isolates, which had never been documented in previous records. Moreover, the paraphyletic nature of the genus is discussed and suggestions are made for future revision of the genus.

Genome Analyses of Two Blueberry Pathogens: Diaportheamygdali CAA958 and Diaporthe eres CBS 160.32

The genus Diaporthe includes pathogenic species distributed worldwide and affecting a wide variety of hosts. Diaporthe amygdali and Diaporthe eres have been found to cause cankers, dieback, or twig blights on economically important crops such as soybean, almond, grapevine, and blueberry. Despite their importance as plant pathogens, the strategies of species of Diaporthe to infect host plants are poorly explored. To provide a genomic basis of pathogenicity, the genomes of D. amygdali CAA958 and D. eres CBS 160.32 were sequenced and analyzed. Cellular transporters involved in the transport of toxins, ions, sugars, effectors, and genes implicated in pathogenicity were detected in both genomes. Hydrolases and oxidoreductases were the most prevalent carbohydrate-active enzymes (CAZymes). However, analyses of the secreted proteins revealed that the secretome of D. eres CBS 160.32 is represented by 5.4% of CAZymes, whereas the secreted CAZymes repertoire of D. amygdali CAA958 represents 29.1% of all secretomes. Biosynthetic gene clusters (BGCs) encoding compounds related to phytotoxins and mycotoxins were detected in D. eres and D. amygdali genomes. The core gene clusters of the phytotoxin Fusicoccin A in D. amygdali are reported here through a genome-scale assembly. Comparative analyses of the genomes from 11 Diaporthe species revealed an average of 874 CAZymes, 101 secondary metabolite BGCs, 1640 secreted proteins per species, and genome sizes ranging from 51.5 to 63.6 Mbp. This study offers insights into the overall features and characteristics of Diaporthe genomes. Our findings enrich the knowledge about D. eres and D. amygdali, which will facilitate further research into the pathogenicity mechanisms of these species.

Susceptibility of Almond (Prunus dulcis) Cultivars to Twig Canker and Shoot Blight Caused by Diaporthe amygdali

Twenty-five almond cultivars were assessed for susceptibility to Diaporthe amygdali, causal agent of twig canker and shoot blight disease. In laboratory experiments, growing twigs were inoculated with four D. amygdali isolates. Moreover, growing shoots of almond cultivars grafted onto INRA 'GF-677' rootstock were used in 4-year field inoculations with one D. amygdali isolate. In both types of experiments, inoculum consisted of agar plugs with mycelium, which were inserted underneath the bark, and the lesion lengths caused by the fungus were measured. Necrotic lesions were observed in the inoculated almond cultivars in both laboratory and field tests, confirming the susceptibility of all evaluated cultivars to all inoculated isolates of D. amygdali. Cultivars were grouped as susceptible or very susceptible according to a cluster analysis. The relationship between some agronomic traits and cultivar susceptibility was also investigated. Blooming and ripening times were found to be relevant variables explaining cultivar performance related to D. amygdali susceptibility. Late and very late blooming and early and medium ripening cultivars were highly susceptible to D. amygdali. Our results may provide valuable information that could assist in ongoing breeding programs of this crop and in the selection of cultivars for new almond plantations.

Diaporthe citri: A Fungal Pathogen Causing Melanose Disease

Citrus melanose is a fungal disease caused by Diaporthe citri F.A. Wolf. It is found in various citrus-growing locations across the world. The host range of D. citri is limited to plants of the Citrus genus. The most economically important hosts are Citrus reticulata (mandarin), C. sinensis (sweet orange), C. grandis or C. maxima (pumelo), and C. paradisi (grapefruit). In the life cycle of D. citri throughout the citrus growing season, pycnidia can be seen in abundance on dead branches, especially after rain, with conidia appearing as slimy masses discharged from the dead twigs. Raindrops can transmit conidia to leaves, twigs, and fruits, resulting in disease dispersion throughout small distances. Persistent rains and warm climatic conditions generally favor disease onset and development. The melanose disease causes a decline in fruit quality, which lowers the value of fruits during marketing and exportation. High rainfall areas should avoid planting susceptible varieties. In this article, information about the disease symptoms, history, geographic distribution, epidemiology, impact, and integrated management practices, as well as the pathogen morphology and identification, was reviewed and discussed.

Caveats of the internal transcribed spacer region as a barcode to resolve species boundaries in Diaporthe

Species in Diaporthe are largely reported as important plant pathogens. Identification of species in this genus has been complemented by morphological and molecular features. However, one important factor delaying this process is the struggle to formulate robust species concepts to create adequate international phytosanitary measures. Regardless of the wide use of the internal transcribed spacer (ITS) rDNA region, established as the primary DNA barcode for fungi, the tendency for intraspecific variation has been reported, misleading interpretation of phylogenetic analyses. Therefore, the present study aimed to illustrate, using specific examples, how the ITS region may be problematic for species delimitation. We showed that the ITS region is highly variable, with strains of Diaporthe malorum and Diaporthe novem falling into more than one clade, which if analyzed on their own, would be likely recognized as distinct taxa. Divergent ITS paralogs were also proven to coexist within the genome of D. novem. We also suggest that ITS may have escaped from concerted evolution or has undergone a duplication event. Furthermore, this study reports for the first time the existence of a putative hybrid in the genus Diaporthe. Our findings offer new clues towards the intraspecific and intragenomic variation in the ITS region, raising questions about its value for barcoding, i.e., identifying species in the genus Diaporthe. Therefore, we recommend that the ITS region be analyzed cautiously and always compared for congruence prior to description of novel taxa.

Endophytes of Brazilian Medicinal Plants With Activity Against Phytopathogens

Plant diseases caused by phytopathogens are responsible for significant crop losses worldwide. Resistance induction and biological control have been exploited in agriculture due to their enormous potential. In this study, we investigated the antimicrobial potential of endophytic fungi of leaves and petioles of medicinal plants Vochysia divergens and Stryphnodendron adstringens located in two regions of high diversity in Brazil, Pantanal, and Cerrado, respectively. We recovered 1,304 fungal isolates and based on the characteristics of the culture, were assigned to 159 phenotypes. One isolate was selected as representative of each phenotype and studied for antimicrobial activity against phytopathogens. Isolates with better biological activities were identified based on DNA sequences and phylogenetic analyzes. Among the 159 representative isolates, extracts from 12 endophytes that inhibited the mycelial growth (IG) of Colletotrichum abscissum (≥40%) were selected to expand the antimicrobial analysis. The minimum inhibitory concentrations (MIC) of the extracts were determined against citrus pathogens, C. abscissum, Phyllosticta citricarpa and Xanthomonas citri subsp. citri and the maize pathogen Fusarium graminearum. The highest activity against C. abscissum were from extracts of Pseudofusicoccum stromaticum CMRP4328 (IG: 83% and MIC: 40 μg/mL) and Diaporthe vochysiae CMRP4322 (IG: 75% and MIC: 1 μg/mL), both extracts also inhibited the development of post-bloom fruit drop symptoms in citrus flowers. The extracts were promising in inhibiting the mycelial growth of P. citricarpa and reducing the production of pycnidia in citrus leaves. Among the isolates that showed activity, the genus Diaporthe was the most common, including the new species D. cerradensis described in this study. In addition, high performance liquid chromatography, UV detection, and mass spectrometry and thin layer chromatography analyzes of extracts produced by endophytes that showed high activity, indicated D. vochysiae CMRP4322 and P. stromaticum CMRP4328 as promising strains that produce new bioactive natural products. We report here the capacity of endophytic fungi of medicinal plants to produce secondary metabolites with biological activities against phytopathogenic fungi and bacteria. The description of the new species D. cerradensis, reinforces the ability of medicinal plants found in Brazil to host a diverse group of fungi with biotechnological potential.

Using Genealogical Concordance and Coalescent-Based Species Delimitation to Assess Species Boundaries in the Diaporthe eres Complex

DNA sequence analysis has been of the utmost importance to delimit species boundaries in the genus Diaporthe. However, the common practice of combining multiple genes, without applying the genealogical concordance criterion has complicated the robust delimitation of species, given that phylogenetic incongruence between loci has been disregarded. Despite the several attempts to delineate the species boundaries in the D. eres complex, the phylogenetic limits within this complex remain unclear. In order to bridge this gap, we employed the Genealogical Phylogenetic Species Recognition principle (GCPSR) and the coalescent-based model Poisson Tree Processes (PTPs) and evaluated the presence of recombination within the D. eres complex. Based on the GCPSR principle, presence of incongruence between individual gene genealogies, i.e., conflicting nodes and branches lacking phylogenetic support, was evident. Moreover, the results of the coalescent model identified D. eres complex as a single species, which was not consistent with the current large number of species within the complex recognized in phylogenetic analyses. The absence of reproductive isolation and barriers to gene flow as well as the high haplotype and low nucleotide diversity indices within the above-mentioned complex suggest that D. eres constitutes a population rather than different lineages. Therefore, we argue that a cohesive approach comprising genealogical concordance criteria and methods to detect recombination must be implemented in future studies to circumscribe species in the genus Diaporthe.

First Report of Diaporthe amygdali Associated with Twig Canker and Shoot Blight of Nectarine in Spain

Nectarine (Prunus persica (L.) Batsch var. nucipersica (Suckow) C. K. Schneid.) is a fruit crop widely cultivated throughout the Mediterranean basin. In Spain, it is mainly grown in eastern regions of the country. In March 2018, 5-year-old nectarine trees showing twig canker symptoms were observed after a rainy spring period in a 0.5 ha orchard located at Alaior, Menorca island (Spain). Cankers were frequent on affected trees (approximately, 80% of the total trees), thus leading to shoot blight. Ten twig segments of one-year old wood with cankers were cut, washed under running tap water, surface disinfected for 1 min in a 1.5% sodium hypochlorite solution and rinsed twice in sterile distilled water. Small pieces (2 mm) of affected tissues were taken from the margin of the cankers and plated on potato dextrose agar (PDA) supplemented with 0.5 g/L of streptomycin sulphate (PDAS). The plates were then incubated at 25 ºC in the dark for 7 to 10 d. Actively growing colonies were first hyphal-tipped and then transferred to PDA and 2% water agar supplemented with sterile pine needles and incubated at 21-22ºC under a 12h/12h near UV / darkness cycle during 21 d (León et al. 2020). Colonies were white at first, becoming light cream, with visible solitary and aggregate pycnidia at maturity. Alpha conidia were aseptate, fusiform, hyaline, multi-guttulated (mean ± SD = 7.4 ± 0.7 × 2.8 ± 0.4 µm, n = 100). Beta and gamma conidia were not observed. The morphological and cultural characteristics of the isolates were congruent with those of Diaporthe spp. (Gomes et al. 2013). The ITS1-5.8S-ITS2 (ITS) region and fragments of β-tubulin (tub2), the translation elongation factor 1-alpha (tef1-α) gene regions, histone H3 (his3) and calmodulin (cal) genes of representative isolate DAL-59 were amplified and sequenced (Santos et al. 2017). The BLASTn analysis revealed 100% similarity with sequences of D. mediterranea (Synonym D. amygdali) (Hilário et al. 2021) isolate DAL-34 from almond (ITS: MT007489, tub2: MT006686, tef1-α: MT006989, his3: MT007095 and cal: MT006761). Sequences of isolate DAL-59 were deposited in GenBank Database (ITS: MT007491, tub2: MT006688, tef1-α: MT006991, his3: MT007097 and cal: MT006763). Pathogenicity tests were conducted using one-year-old potted plants of nectarine cv. Boreal, which were inoculated with isolate DAL-59. In each plant, a 3 mm wound was made in the center of the main branch (about 30 cm length) with a scalpel. Colonized agar plugs with 3 mm diameter, which were obtained from active 10-day-old colonies growing on PDA, were inserted underneath the epidermis and the wounds sealed with Parafilm. Inoculated plants were incubated in a growth chamber at 23 ºC with 12 h of light per day. Controls were inoculated with uncolonized PDA plugs. There were twelve plants per treatment, which were arranged in a completely randomized design. Five days after inoculation necrosis development was observed in the area of inoculation. Wilting and twig blight symptoms over the lesion occurred 3-wk after inoculation and pycnidia were detected, while the controls remained asymptomatic. Diaporthe amygdali was re-isolated from symptomatic tissues and identified as described above to satisfy Koch's postulates. To our knowledge, this is the first report of D. amygdali causing twig canker and shoot blight disease on nectarine in Spain.