A novel virulence gene, cviA1 of Clavibacter michiganensis for necrosis development in the Nicotiana benthamiana plant

Clavibacter michiganensis is a Gram-positive bacterium that causes diverse disease symptoms in tomatoes and Nicotiana benthamiana, a surrogate host plant, including canker, blister lesions, and wilting. Previously, we reported that C. michiganensis also causes necrosis in N. benthamiana leaves. Here, to identify novel virulence genes of C. michiganensis required for necrosis development in N. benthamiana leaves, we screened 1,862 transposon-inserted mutants and identified a mutant strain that exhibited weak and delayed necrosis, whereas there was no discernible difference in blister lesions, canker, or wilting symptoms. Notably, this mutant caused canker similar to that of the wild-type strain, but caused mild wilting in tomato. This mutant carried a transposon in a chromosomal gene, called Clavibactervirulence gene A1 (cviA1). CviA1 encodes a 180-amino acid protein with a signal peptide (SP) at the N-terminus and two putative transmembrane domains (TMs) at the C-terminus. Interestingly, deletion of the SP or the C-terminus, including the two putative TMs, in CviA1 failed to restore full necrosis in the mutant, highlighting the importance of protein secretion and the putative TMs for necrosis. A paralog of cviA1, cviA2 is located on the large plasmid pCM2 of C. michiganensis. Despite its high similarity to cviA1, the introduction of cviA2 into the cviA1 mutant strain did not restore virulence. Similarly, the introduction of cviA1 into the Clavibacter capsici type strain PF008, which initially lacks cviA1, did not enhance necrosis symptoms. These results reveals that the chromosomal cviA1 gene in C. michiganensis plays an important role in necrosis development in N. benthamiana leaves.

First Report of Cytospora ailanthicola Causing Canker on cherry blossom (Cerasus serrulata) in China

Cherry blossom (Cerasus serrulata) is a plant with important garden applications. It is a newly introduced exotic plants in the Arar region of Xinjiang, China (40°41'18.19″N,81°43'50.55″E). In October 2022, it was discovered that about 30% of cherry blossoms had a canker disease. The leaves of the sick branches were dired, the branches themselves were damaged, with dark brown color inside. Orange-yellow conidia horns were produced in humid condition. Samples were collected from fifteen trees exhibiting notable symptoms. The diseased junctions of the infected shoots were chopped into small pieces and subjected to surface sterilization by using 70% ethanol for 30s, 1% NaClO solution for one minute, and sterile distilled water three times (Chen et al. 2016). The representative strain YINGHUA-1 was chosen for identification by molecular biology and morphology. After five days of incubation at 26℃ on PDA media, colonies of white fluffy mycelium were produced from the YINGHUA-1 strain. After 25 days of PDA culture, the production of pycnidia was first observed, circular, black. The pycnidia began to produce conidia at 30 days. The conidia was translucent without septum, with a slightly curved single cell and smooth surface. Pycnidia was spherical and flat, with a single black aperture at the top that resembles a nearly round hole, the chamber was made up of several tiny chambers separated by a shared wall, and its diameter ranges from 900-1900 µm. The size of the conidium was 3.7-6.6×1.1-1.9 μm (n=20). The intrinsic transcriptional spacer (ITS), transcriptional elongation factor (tef-1α), and β-tubulin (tub2) gene moieties of rDNA were sequenced using ITS1/ITS4, EF1-728F/EF1-986R, and Bt2a/Bt2b primers, respectively(Zhang et al. 2014). The amplified sequences of ITS region (Accession No. OR855907), tub2 (Accession No. OR865863) and tef-1α (Accession No. OR865864) were deposited in the GenBank. BLAST searches of the sequences revealed 99.59% identity (474/476 bp) of the ITS sequence, 98.63% identity (216/219 bp) of the tef-1α sequence, and 98.55% identity of the tub2 sequence (339/344 bp) with C. ailanthicola CFCC59446 (accessions OR826163, OR832040, and OR832062, respectively.) Phylogenetic analyses were performed with Iqtree v.1.6.12 for maximum likelihood (ML). Confidence levels for the nodes were determined using 1000 replicates of bootstrapping methods. Based on phylogenetic analysis and morphological characteristics, the pathogen was identified as C. ailanthicola. The pathogenicity of C. ailanthicola was confirmed by inoculation of 1-year-old shoots (5 replicates of this experiment). After 7 days, symptoms of inner bark discoloration were visible on xylem of branches and the same fungus was re-isolated from the inoculated shoots, with no lesions on the control shoots. C. ailanthicola is only known from a single host plant, Ailanthus altissima,in China (Fan et al.2020). As far as we know, this is the first report of C. ailanthicola harmings C. serrulata in China.

High-quality genome resource of Lasiodiplodia pseudotheobromae associated with die-back on Eucalyptus trees

OBJECTIVES

Lasiodiplodia pseudotheobromae is an important fungal pathogen associated with die-back, canker and shoot blight in many plant hosts with a wide geographic distribution. The aim of our study was to provide high-quality genome assemblies and sequence annotation resources of L. pseudotheobromae, to facilitate future studies on the systematics, population genetics and genomics of the fungal pathogen L. pseudotheobromae.

DATA DESCRIPTION

High-quality genomes of five L. pseudotheobromae isolates were sequenced based on Oxford Nanopore technology (ONT) and Illumina HiSeq sequencing platform. The total size of each assembly ranged from 43 Mb to 43.86 Mb and over 11,000 protein-coding genes were predicted from each genome. The proteins of predicted genes were annotated using multiple public databases, among the annotated protein-coding genes, more than 4,300 genes were predicted as potential virulence genes by the Pathogen Host Interactions (PHI) database. Moreover, the genome comparative analysis among L. pseudotheobromae and other closely related species revealed that 7,408 gene clusters were shared among them and 152 gene clusters unique to L. pseudotheobromae. This genome and associated datasets provided here will serve as a useful resource for further analyses of this fungal pathogen species.

First Report of Valsa nivea (Hoffm.) Fr. Causing Valsa Canker on Korla Pear (Pyrus sinkiangensis Yü) in the World

Korla pear (Pyrus sinkiangensis Yü) is an important commercial fruit tree that originated in China (Zhou et al. 2020). In April 2020, a survey was conducted in Aksu region, Xinjiang (40°55'37"N, 80°28'42"E), China. Some Korla pear trees (>15 years old) exhibited symptoms of branch dieback and branch cankers. Cankers observed on the trunk and branches of the tree were sunken, dark ulcerative lesions sometimes exhibiting signs of stromata erumpent through the bark and exuding yellow to reddish-orange spore tendrils. Of the 180 plants surveyed, 80% were symptomatic. Thirty samples of symptomatic tissues of infected branches were taken to the laboratory. Bark and cortical wood samples containing necrotic and healthy tissue were excised with flame-sterilized scalpels, surface disinfected with 75% ethanol and 1% NaClO, placed on PDA plates, and incubated at 25°C. A total of 30 fungal isolates were obtained. Among them, 28 isolates were identified as Valsa mali var. pyri (Lu. 1992) based on morphological and molecular identification, and two isolates (ALE6T-GP21 and ALE7T-GP23) were identified as Valsa nivea (Hoffm.) Fr. Valsa nivea isolates had a fine villi form mycelium that was initially white, turned grayish-green over time and grew close to the medium surface. Cultures also contained black ostiolate pycnidia in a stroma that consisted of multiple irregular locules. Conidiophores were hyaline, occasionally branched at the bases and (15.50-)16.48-17.94(-18.50)×(1.00-)1.13-1.37(-1.50) μm (n=20). Conidiogenous cells were phialidic and subcylindrical that taper towards the apex. Conidia were hyaline, banana-like and (5.47-)6.13-6.97(-7.64)×(1.02-)1.06-1.20(-1.23) μm (n=10). The molecular characteristics are consistent with the previous description of V. nivea (Adams et al. 2006). The internal transcribed spacer (ITS), transcription elongation factor (tef-1α) and β-tubulin (Tub2) gene were sequenced using ITS1/ITS4, EF1-728F/EF1-986R and Bt2a/Bt2b primers, respectively (Zhang et al. 2014). BLAST (Basic Local Alignment Search Tool) searches against the NCBI database revealed that the ITS sequence had 99.83% homology (ON843984.1 and ON843987.1), tef-1α gene had 99.22% homology (MH015266.1 and MH015267.1), and the Tub2 sequence had 99.57% and 100% homologies (KT934364.1 and KT934364.1) with V. nivea sequences. The amplified sequences of ITS region (OK442665 and OK442666), tef-1α (OK510871 and OK510872) and Tub2 (OK510869 and OK510870) were deposited in the GenBank. A phylogenetic analysis was performed using MEGA7 that shows 100% bootstrap support that ALE6T-GP21 and ALE7T-GP23 were V. nivea. A pathogenicity trial was conducted with isolate ALE6T-GP21 inoculated onto 1-year-old shoots of 15-year-old Korla pear trees in Alar city, Xinjiang, China. Five shoots were inoculated by making 5-mm deep wounds using a sterile scalpel then inoculating with a 50 μL conidia suspension (1×106 mL-1). Additionally, five shoots served as the negative control and were inoculated in the same way using 50 μL ddH2O. The trees were kept under ambient conditions. Inoculated branches developed symptoms 18 days post inoculation, whereas the control branches showed no symptoms. V. nivea was re-isolated from the symptomatic areas and the isolate confirmed as ALE6T-GP21 by sequence analysis. Currently, the proven hosts of V. nivea are Populus, Elaeagnus, Juglans, Malus and Salix (Adams et al. 2006; Wang et al. 2020). To our knowledge, this is the first report of pathogenic V. nivea occurring on P. sinkiangensis in the world. It will provide a basis for research into the occurrence, distribution of V. nivea on Korla Pear.

Detection and molecular characterization of Trichomonas gallinae recovered from domestic pigeons in Egypt

Trichomonas gallinae is a protozoan parasite that causes canker in pigeons. Squabs (young pigeons) are frequently infected with T. gallinae and can die because of the infection, while adult pigeons can act as carriers showing no clinical signs. In the present study, 50 squabs, up to 1-month-old, were purchased from pigeon markets in different regions of the Giza governorate, Egypt. Direct wet mount preparations of the oral excretions of the squabs (mouth wash) and Giemsa staining revealed that 64% (32/50) were positive for T. gallinae. Experimental infection of ten squabs with 10³ T. gallinae trophozoites/ml resulted in oral lesions on the mouth, tongue, and soft palate, with the presence of yellowish-white nodules (cheese-like) in the oral cavity on the sixth day post-infection in all squabs. A subset of five samples were cultured in modified Diamond's media, their DNA was extracted, and a portion of the ribosomal internal transcribed spacer region (ITS1/5.8S/ITS2) was amplified by polymerase chain reaction (PCR) followed by sequencing. Phylogenetic analysis of the five isolates revealed 64-91% homology with some reference isolates circulating in Egypt and related countries.

First report of Neoscytalidium dimidiatum causing stem canker on yellow dragon fruit (Hylocereus megalantus) in Ecuador

Dragon fruit cultivation is an emerging industry in Ecuador. In August of 2020, yellow dragon fruit plants (Hylocereus megalantus) showing brown hardened scabs on cladodes and fruits were observed in a field in Guayas, a coastal province of Ecuador (Fig. 1A). Symptoms were observed in ~ 40% of the assessed plants (n=100) with damage varying from mild (necrotic spots) to severe (canker). Ten cladode sections of ~ 10 cm2 with signs of canker were collected from five affected plants (two from each plant). Symptomatic cladode sections were sliced, surface-sterilized with a solution of 1% sodium hypochlorite, rinsed with sterile water, transferred into potato dextrose agar (PDA) media, and incubated at 28°C for five days in the dark. Three fungal isolates recovered from the cladodes produced colonies with dense dark aerial mycelia that matched the morphological description for Neoscytalidium dimidiatum (Crous et al 2006) (Fig 1B, 1C). Arthric chains of cylindrical conidia were observed under the microscope and presented zero or one septum with sizes between 10.9 ± 0.27 x 4.97 ± 0.36 µm (n=50). Pycnidia produced ellipsoid-shaped conidia, and sizes ranged from 4.5 ± 0.3 x 11.02 ± 0.5 µm (n=50). Cultured isolates were subjected to DNA extractions using the fungal DNA mini kit (Omega, Bio-Tek, Inc) for molecular identification by amplifying the 5.8S rDNA and adjacent internal transcriber spacer (ITS) 1 and 2 regions using primers (ITS1 / ITS4) as described (White et al., 1990). In addition, the β-tubulin and elongation factor 1-α targets were amplified by primers Bt2a / Bt2b (Glass and Donaldson, 1995) and EF1-728 F / EF1-986R (Carbone and Kohn, 1999), respectively, following the recommended PCR conditions. Amplified products were cloned using a pGEMT-easy kit (Promega, USA) and sequenced. Sequence comparisons for each target revealed that the three isolates were 100% identical to each other. Sequences obtained from a single plant were submitted to NCBI Genbank and assigned acc. Numbers OP377444, OP381216, and OP381217, for the ITS, β-tubulin, and elongation factor, respectively. BLAST analyses of the three amplified targets confirmed homology to counterparts from N. dimitiatum, with 99-100 % identities to isolates from China (JX524168), United Arab Emirates (MN447201), and Israel (KF020895). To fulfill Koch´s postulates, thirteen 4-month-old healthy plants were inoculated either with the pathogen (n=10) or mock-inoculated (n=3). In addition, two detached yellow dragon fruits and a mock were inoculated following the same protocol as stems. Inoculation was performed by making small wounds on cladodes or fruits using a sterile needle and placing a 2-mm agar plug containing mycelia from a 7-day-old colony. For mock inoculations, 2-mm plugs with clean PDA media were used. The inoculated area was wrapped with black plastic film for seven days at 27 to 32°C. At ten days post-inoculation, brown scab lesions with an orange halo were observed in the inoculated plants but not in the mock-inoculated plants and fruit (Fig. 1D, 1E). N. dimidiatum was re-isolated from experimentally-induced canker lesions, and morphologically identified. Stem canker caused by N. dimidiatum is a severe disease affecting dragon fruit production worldwide (Chuang et al., 2021). In Ecuador, this pathogen was found affecting yellow dragon fruit (H. megalantus) under natural conditions; however, under experimental conditions, red dragon fruit (H. undatus), which is widely produced in several coastal provinces of the country, was also found to be susceptible. Further studies are needed to investigate epidemiological aspects of this important pathogen, which threatens dragon fruit production in Ecuador.

First Report of Bacterial Canker of Pecan Caused by Pseudomonas syringae pv. syringae in China

Pecan (Carya illinoinensis) is a world-famous nut tree that is widely cultivated in China, especially in Jiangsu Province (Zhang et al. 2015). In April 2022, cankers on trunks were recorded in pecan (cv. Pawnee) fields located in Taizhou (32°27'58″ N, 120°0'49″ E), Jiangsu. Cankers on the trunks resulted in wilt of the plants. Usually, the color of infected bark on the trunk became darker than the healty bark. When the outer bark was peeled away, the inner tissues were water-soaked, often with reddish streaks. In the surveyed orchards, disease incidence ranged from 10 to 20% among young saplings (about 200 three-year-old trees). While no fungal mycelium or spores were found in the diseased areas by microscope, bacterial colonies were isolated by surface-sterilizing small fragments (25 mm2) of symptomatic tissue in 0.5% NaOCl, rinsing the sections twice in sterilized water, and then streaking them on Luria-Bertani (LB) plates. More than 20 bacterial isolates were obtained and all isolates induced a hypersensitive response on Nicotiana tabacum. All isolates were fluorescent on King's medium B, and were gram-negative based on lysis by KOH. Isolates were positive for levan formation, negative for oxidase and arginine dihydrolase, and did not cause soft rot on potato slices. Based on above information, the isolates thus belonged to Lelliot's LOPAT group 1, P. syringae (Lelliott and Stead 1988). The 16S rRNA sequences of five representative isolates (accession numbers OP175939-OP175943) were amplified by PCR, sequenced, and compared with the NCBI GenBank database (Weisburg et al. 1991; Sarkar and Guttman 2004), finding a 99.92% genetic similarity with a previously reported 16S rRNA sequence of a Pseudomonas syringae pv. syringae (Pss) isolate (accession numbers NW389777). Additional housekeeping genes gap1(accession numbers OP186937-OP186941), rpoD (accession numbers OP186952-OP186956), gyrB (accession numbers OP186947-OP186951), and gltA (accession numbers OP186942-OP186946) were PCR-amplified and sequenced as reported by Hwang et al. (2005), followed by multilocus sequence typing analysis (MLSA). Molecular phylogenetic trees (MEGA vesion 6.0, maximum likelihood with Jukes-Cantor model, 1,000 bootstraps) were generated based on each of these five DNA regions and revealed that all five isolates were clustered together with the strains in P. syringae genomospecies 2, and grouped these isolates with Pss in the PAMDB database (Hwang et al. 2005). As a result, these isolates were identified as Pss. Pathogenicity on pecan (cv. Pawnee) was confirmed by cutting the trunks of two-year-old pecan trees with sterilized blades dipped in cell suspensions containing 107 CFU/ml of each isolate. Plants inoculated in a similar manner with sterile water served as negative controls. The inoculated plants were incubated in a greenhouse maintained at 25°C and 80% relative humidity. After 7 to 8 days, all inoculated plants showed the symptoms of necrosis previously described for the original field plants, while the control plants did not show symptoms. The bacteria reisolated from the inoculated plants were identified as Pss using the LOPAT tests. These results and the sequence analysis of the 16S rRNA and four housekeeping genes described above, fulfilled Koch's postulates. No target bacteria were isolated from the control plants. To our knowledge, this is the first report of Pseudomonas syringae pv. syringaecausing bacterial canker of pecan worldwide. The identification of this pathogen will allow the study of strategies for managing the disease. References: Hwang, M. S., et al. 2005. Applied and Environmental Microbiology, 71:5182-5191. Lelliott, R. A., and Stead, D. E. 1988. Blackwell Scientific, Sussex, UK. Sarkar, S. F., and Guttman, D. S. 2004. Applied and Environmental Microbiology, 70:1999. Weisburg, W. G., et al. 1991. Journal of Bacteriology, 173: 697. Zhang, R., et al. 2015. Scientia Horticulturae, 197: 719-727. The author(s) declare no conflict of interest. Keywords: Carya illinoinensis, Pseudomonas syringae, Canker, Identification †Indicates the corresponding author.Y. Q. Zhao; zhaoyuqiang123@126.com.

First Report of Stem Canker Caused by Diaporthe tulliensis on jasmine in Taiwan

Diaporthe species can infect forest trees, ornamentals, and crops, causing root and fruit rots, stem cankers, leaf spots, etc. (Yang et al. 2018). In February 2021, about 10-20% of jasmine plants showing stem canker, foot rot, and wilting were observed in Changhua (24°01'57.7"N 120°34'54.7"E), Taiwan. The diseased plants initially showed chlorosis, leaf drop, and dieback. Sunken lesions were observed on the infected stem and kept expanding gradually. Eventually, plants wilted and black spots formed on the lesions. The margin of healthy and infected tissues of six samples were cut into 4 pieces, disinfected with 10% NaOCl for 30 seconds, rinsed twice in sterilized distilled water for 1 minute, and cultured on water agar at 28℃ under 12 h light / 12 h dark cycle. Hyphae grown out from isolated tissues were sub-cultured on potato dextrose agar (PDA). All tissues grown out of fungi showed similar colony morphology. Two hyphal tips from different tissues were isolated as representatives and deposited in Bioresource Collection and Research Center, Hsinchu, Taiwan, under BCRC numbers FU31566 and FU31567. The colonies on PDA were white to pale gray and produced black pycnidial conidiomata. The two-week-old conidiomata scattered or aggregated in small groups, exuded cream to pale yellow conidial droplets, 0.3-1.1 mm (n=50). The α-conidia were one-celled, hyaline, ovoid to cylindrical with one or two droplets, 3.8-6.3 × 2.5-3.8 μm (n=50). β-conidia were absent. The internal transcribed spacer (ITS), translational elongation factor subunit 1-α (EF1α), and β-tubulin of the two isolates were amplified using primer pairs ITS1/ITS4 (White et al. 1990), EF1-728F/EF1-986R (Carbone and Kohn 1999), and Bt2a/Bt2b (Glass and Donaldson, 1995), respectively. The ITS (MZ389113, MZ389114), EF1α (MZ419338, MZ419339), and β-tubulin (MZ408893, MZ408894) sequences of two isolates showed 98.55-98.56% (KR936130), 98.82% (KR936133), and 99.11-99.33% (KR936132) match to those of Diaporthe tulliensis R.G. Shivas, Vawdery & Y.P. Tan ex-type isolate BRIP 62248a (Dissanayake et al. 2017), respectively. Based on the morphological and molecular characters, this fungus is identified as D. tulliensis. To confirm the pathogenicity, the needle-wounded stem bases of eight-month-old cutting jasmine seedlings were inoculated with BCRC FU31566 by two PDA disks with actively grown fungal edges or conidial suspension at the concentration of approximately 2 × 105 conidia/ml. Each method inoculated five seedlings, performed in the greenhouse at 25 ± 2°C. Non-inoculated plants served as control. Two weeks after inoculation, three plants inoculated with PDA disks of the fungal culture showed wilting, and conidiomata formed on the stem base. The same symptoms were observed in one plant inoculated with the conidial suspension 3 weeks after inoculation. By contrast, the controls remained symptomless. Koch's postulates were completed by re-isolating the fungus from the inoculated plant. The re-isolated pathogen showed similar morphology and molecular characteristics to the original. D. tulliensis has been reported to cause cocoa rotted stem in Australia, kiwifruit stem canker in China, and Boston ivy leaf spot in Taiwan (Crous et al. 2015; Bai et al. 2017; Huang et al. 2021; Farr and Rossman 2021). To our knowledge, this is the first report of stem canker on jasmine associated with D. tulliensis in Taiwan. Furthermore, this is the first record of jasmine as a host of D. tulliensis worldwide.

Survey and Monitoring of Phytophthora Species in Natural Ecosystems: Methods for Sampling, Isolation, Purification, Storage, and Pathogenicity Tests

Phytophthora species can be found in multiple substrates. Due to dormancy of resting structures and presence of faster-growing antagonists, direct isolation of Phytophthora can be difficult to achieve, and indirect baiting methods often reach higher isolation frequencies. In this chapter, different methodologies are described for sampling and for the successful isolation of Phytophthora species from natural ecosystems. Sampling methods for soil, roots, bark cankers, and waterbodies are described. Agar recipes and guidance on the selection of suitable tissue to perform direct isolations are provided. A range of different baiting techniques are described for isolation of Phytophthora from different substrates. Purification methods to obtain clean and non-mixed cultures and conservation methods for pure cultures are shown. Two pathogenicity test methods for soil infestation and for under-bark inoculation, respectively, are described in detail.

Photodynamic control of citrus crop diseases

Citrus are economically important fruit crops to which infectious diseases like citrus canker caused by Xanthomonas citri subs. citri, citrus variegated chlorosis caused by Xylella fastidiosa, "huanglongbing" associated with the presence of Candidatus liberibacter species, anthracnose caused by Colletotrichum gloeosporioides and citrus black spot caused by Phyllosticta citricarpa, impose significant losses. Control measures involve chemical treatment of orchards but often, eradication of infected plants is unavoidable. To circumvent the environmental impacts of pesticides and the socio-economic impacts of eradication, innovative antimicrobial approaches like photodynamic inactivation are being tested. There is evidence of the susceptibility of Xanthomonas citri subs. citri and C. gloeosporioides to photodynamic damage. However, the realistic assessment of perspectives for widespread application of photodynamic inactivation in the control of citrus diseases, necessarily implies that other microorganisms are also considered. This review intends to provide a critical summary of the current state of research on photodynamic inactivation of citrus pathogens and to identify some of the current limitations to the widespread use of photodynamic treatments in citrus crops.

Identification and validation of miRNA reference genes in poplar under pathogen stress

Quantitative real time polymerase chain reaction (qRT-PCR) is a common method to analyze gene expression. Due to differences in RNA quantity, quality, and reverse transcription efficiency between qRT-PCR samples, reference genes are used as internal standards to normalize gene expression. However, few universal genes, especially miRNAs, have been identified as reference so far. Therefore, it is essential to identify reference genes that can be used across various experimental conditions, stress treatments, or tissues. In this study, 14 microRNAs (miRNAs) and 5.8S rRNA were assessed for expression stability in poplar trees infected with canker pathogen. Using geNorm, NormFinder and Bestkeeper reference gene analysis programs, we found that miR156g and miR156a exhibited stable expression throughout the infection process. miR156g, miR156a and 5.8S rRNA were then tested as internal standards to measure the expression of miR1447 and miR171c, and the results were compared to small RNA sequencing (RNA-seq) data. We found that when miR156a and 5.8S rRNA were used as the reference gene, the expression of miR1447 and miR171c were consistent with the small RNA-seq expression profiles. Therefore, miR156a was the most stable miRNAs examined in this study, and could be used as a reference gene in poplar under canker pathogen stress, which should enable comprehensive comparisons of miRNAs expression and avoid the bias caused by different length between detected miRNAs and traditional reference genes. The present study has expanded the miRNA reference genes available for gene expression studies in trees under biotic stress.

Inonotus rickii (Agaricomycetes, Hymenochaetaceae) in Brazilian Cerrado: Expanding Its Geographic Distribution and Host List

Inonotus rickii (Pat.) Reid (Agaricomycetes: Hymenochaetaceae) is a poroid fungus characterized by the expressive production of chlamydospores, in vivo and in vitro, especially during its anamorphic stage. The species plays important ecological roles, standing out as a phytopathogen, affecting several species of ornamental and wild trees, mainly in tropical and subtropical regions. The infected trees develop canker and white rot of the wood, showing symptoms of reduced vegetative vigor and decline of leaves and branches which causes death in some cases. The first record of I. rickii for the Cerrado biome (Brazilian Savanna) and the first record as causal agent of canker in Schinus molle L. in Brazil is reported here. In addition, we present a checklist of its worldwide geographical distribution and known hosts, from an extensive bibliographic search in Google Scholar, SciELO, Scopus, and Web of Science databases. The species is widespread in tropical and subtropical zones; common in the American continent, especially in Central and South America and the Mediterranean region, and rare in temperate zones. We found specimens growing in both living and dead hosts, totalizing 70 species of hosts, distributed in 43 genera and 22 families. Of these, Acer negundo L. (10.5%), Celtis australis L. (6.5%), and Platanus acerifolia (Aiton) Willd. (4.8%), and the Fabaceae (30%), Fagaceae (10%), and Sapindaceae (8.6%) families were the most frequent. We present morphological descriptions and illustrations, as well as the growth characteristics in culture medium. Our study expands the known geographical distribution of I. rickii, including the Cerrado biome, as well as its structural, physiological characteristics, and its hosts.

Fungi associated with galleries of the emerald ash borer

The emerald ash borer (EAB) is an exotic forest pest that has killed millions of ash trees in the United States and Canada, resulting in an ecological disaster and billions of dollars in economic losses of urban landscape and forest trees. The beetle was first detected in Michigan in 2002 and has spread through much of the Eastern and Midwestern U.S., reaching Minnesota in 2009. Since then, it has spread across the state and poses a great risk to the more than 1 billion ash trees in Minnesota. The larval stage of EAB creates wounds on trees as they feed on the inner bark, causing disruption of water and sap flow that results in tree death. The fungal community associated with EAB larval galleries is poorly understood and the role these fungi may play in tree death is not known. This study describes fungi isolated from EAB larval galleries sampled throughout the main geographic areas of Minnesota where ash is affected by EAB. Fungal cultures were identified by extracting genomic DNA and sequencing the ITS region of the rDNA. Results from 1126 isolates reveal a diverse assemblage of fungi and three functional guilds comprised of canker pathogens, wood decay, and entomopathogenic fungi. The most common canker-associated genera were Cytospora followed by Phaeoacremonium, Paraconiothyrium, Coniothyrium, Nectria, Diplodia, and Botryosphaeria. Fungi in the Basidiomycota were nearly all wood decay causing fungi and many were species of pioneer colonizing genera including Sistotrema, Irpex, Peniophora, Phlebia and Ganoderma. Some of these fungi seriously affect urban trees, having the potential to cause rapid wood decay resulting in hazardous tree situations. Several entomopathogenic genera with the potential for biological control of EAB were also isolated from galleries. Purpureocillium was the most commonly isolated genus, followed by Beauveria, Clonostachys, Lecanicillium, Akanthomyces, Cordyceps, Microcera, Tolypocladium, and Pochonia. The results identify important fungal functional guilds that are occupying a new niche in ash trees resulting from EAB and include fungi that may accelerate decline in tree health, increase hazard tree situations, or may provide options for biological control of this destructive invasive insect.

First report of Diaporthe eres causing branch canker on Cinnamomum camphora (camphor tree) in Jiangxi Province, China

In September 2019, approximately 75 to 90% of camphor trees (Cinnamomum camphora) were observed with cankers and branch dieback symptoms in Anyi (N28°32'54'', E115°37'52'') and Xinyu (N27°37'38'', E114°50'25'') county (Jiangxi Province, China). The symptoms included dark brown to dark, oval-shaped canker lesions, sunken and cracked longitudinally, cracked and evenly swelling, or reddish brown (Figure 1 A-D). Samples were collected from symptomatic branches and were cut into small pieces (ca. 0.5 cm × 0.5 cm × 0.5 cm). Sections were surface sterilized as described by Zhang et al. (2020), then placed on potato dextrose agar amended with 0.01% penicillin and 0.015% streptomycin sulfate and incubated in the laboratory at 25℃ with darkness. After 3 to 5 days, mycelium growing out from tissues were transferred onto PDA medium. In total, 68 fungal isolates including 22 isolates of Diaporthe sp. were obtained from cankers and then were classified into five categories based on morphological characteristics and sequencing of the ITS for morphological representative strains. Pathogenicity tests were conducted in the greenhouse (Figure 1 E-M) and field (Figure 1 N-Q). Branches were surface sterilized and inoculated as described by Prencipe et al. (2017). In the greenhouse, a total of 13 representative isolates (including 6 isolates of Diaporthe sp., 2 isolates of Neofusicoccum sp., 2 isolates of Botryosphaeria sp. and 3 isolates of Colletotrichum sp.) were selected and evaluated using 2-year-old seedlings of camphor tree in pots with 5 replicates per isolate, in which 3 isolates of Collectotrichum sp. had no pathogenicity. Then, two isolates of Diaporthe sp. (Z4 and Z7) were selected for field experiment. In field tests, the same method was used as in the greenhouse. The inoculated and control branches were collected 40 days after inoculation and the fungi were isolated and placed on PDA plates to recover the inoculated fungi and complete Koch's postulates. Both isolates of Diaporthe sp. produced canker symptoms on the branches. Isolate Z4 caused discoloration also on the branch without wounding. Both isolates produced pycnidia scattered in PDA plates supplemented with stems of alfalfa, were dark brown to black, globose to subglobose (Figure 1 T). Alpha conidia were cylindrical, 5.72-9.98 µm (mean 7.64 µm) × 2.15-3.13 µm (mean 2.69 µm) (n = 30) (Figure 1 S, red arrow), while beta conidia were biguttulate, one-celled, hyaline, non-septate, and 16.21-25.52 µm (mean 21.60 µm) × 0.76~1.65 µm (mean 1.14 µm) (n = 30, green arrow) (Figure 1 S). Five isolates (Z4, S-Z4, P-Z4, Z7 and S-Z7) including those used for pathogenicity test were selected for multi-locus phylogenetic analyses of ITS (White et al., 1990), TEF1-α and TUB2 (Glass et al. 1995) gene sequences, which the accession number was MW036358- MW036362 for ITS, MW052267- MW052271 for TEF1- α, MW052276-MW052280 for TUB2. Based on the phylogenetic tree analysis using IQ-TREE 2, all five isolates were identified as D. eres (Figure 2). D. eres has been reported to cause canker on many different woody plants, such as almond (Holland et al. 2020), peach (Prencipe et al. 2017), hazelnut (Wiman et al. 2019), and so on. However, this is the first report worldwide of D. eres causing disease on Cinnamomum camphora in China.

Improved subtyping affords better discrimination of Trichomonas gallinae strains and suggests hybrid lineages

Trichomonas gallinae is a protozoan pathogen that causes avian trichomonosis typically associated with columbids (canker) and birds of prey (frounce) that predate on them, and has recently emerged as an important cause of passerine disease. An archived panel of DNA from North American (USA) birds used initially to establish the ITS ribotypes was reanalysed using Iron hydrogenase (FeHyd) gene sequences to provide an alphanumeric subtyping scheme with improved resolution for strain discrimination. Thirteen novel subtypes of T. gallinae using FeHyd gene as the subtyping locus are described. Although the phylogenetic topologies derived from each single marker are complementary, they are not entirely congruent. This may reflect the complex genetic histories of the isolates analysed which appear to contain two major lineages and several that are hybrid. This new analysis consolidates much of the phylogenetic signal generated from the ITS ribotype and provides additional resolution for discrimination of T. gallinae strains. The single copy FeHyd gene provides higher resolution genotyping than ITS ribotype alone. It should be used where possible as an additional, single-marker subtyping tool for cultured isolates.

Species of Dendrostoma (Erythrogloeaceae, Diaporthales) associated with chestnut and oak canker diseases in China

Dendrostoma was recently proposed in Erythrogloeaceae (Diaporthales, Sordariomycetes), with all known members recorded as being plant pathogenic on economically important tree hosts. During our collections of Dendrostoma species in China, mild to severe canker symptoms were observed on sweet chestnut (Castaneamollissima) and oak (Quercus spp.) trees. Dead and dying plant tissues exhibiting Dendrostoma canker symptoms were sampled for fungal isolation. A total of 37 Dendrostoma isolates were obtained and analysed using morphological characteristics and molecular data (ITS, LSU, RPB2, TEF1-α). Based on these data, 10 novel clades could be distinguished, which also proved to represent morphologically distinct species described here as Dendrostomaaurorae, D.castaneae, D.castaneicola, D.chinense, D.dispersum, D. parasiticum, D.qinlingense, D.quercus, D.shaanxiense and D.shandongense spp. nov. A key to species of the genus is also provided.

Emerging citrus diseases in Europe caused by species of Diaporthe

Species of Diaporthe are considered important plant pathogens, saprobes, and endophytes on a wide range of plant hosts. Several species are well-known on citrus, either as agents of pre- or post-harvest infections, such as dieback, melanose and stem-end rot on fruit. In this study we explored the occurrence, diversity and pathogenicity of Diaporthe species associated with Citrus and allied genera in European orchards, nurseries, and gardens. Surveys were carried out during 2015 and 2016 in Greece, Italy, Malta, Portugal, and Spain. A total of 79 Diaporthe strains were isolated from symptomatic twigs, branches and trunks. A multi-locus phylogeny was established based on five genomic loci (ITS, tef1, cal, his3 and tub2), and the morphological characters of the isolates determined. Preliminary pathogenicity tests were performed on lemon, lime, and orange plants with representative isolates. The most commonly isolated species were D. foeniculina and D. baccae, while only four isolates of D. novem were collected. Two new Diaporthe species, described here as D. limonicola and D. melitensis spp. nov. were found associated with a new devastating dieback disease of lemon plants. Furthermore, one cluster of sterile Diaporthe isolates was renamed as D. infertilis. Pathogenicity tests revealed most of the Citrus species as susceptible to D. baccae, D. foeniculina, and D. novem. Moreover, D. limonicola and D. melitensis caused serious cankers affecting all the Citrus species tested. This study is the first report of D. baccae and D. novem on citrus in Europe, and the first detection of a new Diaporthe canker disease of citrus in Europe. However, no isolates of D. citri were found. The study improves our understanding of the species associated with several disease symptoms on citrus plants, and provides useful information for effective disease management.

The genetic landscape of Ceratocystis albifundus populations in South Africa reveals a recent fungal introduction event

Geographical range expansion or host shifts is amongst the various evolutionary forces that underlie numerous emerging diseases caused by fungal pathogens. In this regard, Ceratocystis albifundus, the causal agent of a serious wilt disease of Acacia mearnsii trees in Africa, was recently identified killing cultivated Protea cynaroides in the Western Cape (WC) Province of South Africa. Protea cynaroides is an important native plant in the area and a key component of the Cape Floristic Region. The appearance of this new disease outbreak, together with isolates of C. albifundus from natural ecosystems as well as plantations of nonnative trees, provided an opportunity to consider questions relating to the possible origin and movement of the pathogen in South Africa. Ten microsatellite markers were used to determine the genetic diversity, population structure, and possible gene flow in a collection of 193 C. albifundus isolates. All populations, other than those from the WC, showed high levels of genetic diversity. An intermediate level of gene flow was found amongst populations of the pathogen. The results suggest that a limited number of individuals have recently been introduced into the WC, resulting in a novel disease problem in the area.

First Report and Characterization of Pestalotiopsis ellipsospora Causing Canker on Acanthopanax divaricatus

Acanthopanax divaricatus, a member of the Araliaceae family, has been used as an invigorant in traditional Korean medicine. During disease monitoring, a stem with small, irregular, brown lesions was sampled at a farm in Cheonan in 2011. The symptoms seen were sunken cankers and reddish-brown needles on the infected twig. The isolated fungal colonies were whitish, having crenated edges and aerial mycelium on the surface, and with black gregarious fruiting bodies. The reverse plate was creamy white. Conidia were 17~22 × 3.5~4.2 µm, fusiform, 4-septate, and straight to slightly curved. The nucleotide sequence of the partial translation elongation factor 1 alpha gene of the fungal isolate, shares 99% sequence identity with that of known Pestalotiopsis ellipsospora. Based on the results of the morphological and molecular analyses, the fungal isolate was identified as P. ellipsospora. In Korea, this is the first report of canker on A. divaricatus.

The dual nature of trehalose in citrus canker disease: a virulence factor for Xanthomonas citri subsp. citri and a trigger for plant defence responses

Xanthomonas citri subsp. citri (Xcc) is a bacterial pathogen that causes citrus canker in susceptible Citrus spp. The Xcc genome contains genes encoding enzymes from three separate pathways of trehalose biosynthesis. Expression of genes encoding trehalose-6-phosphate synthase (otsA) and trehalose phosphatase (otsB) was highly induced during canker development, suggesting that the two-step pathway of trehalose biosynthesis via trehalose-6-phosphate has a function in pathogenesis. This pathway was eliminated from the bacterium by deletion of the otsA gene. The resulting XccΔotsA mutant produced less trehalose than the wild-type strain, was less resistant to salt and oxidative stresses, and was less able to colonize plant tissues. Gene expression and proteomic analyses of infected leaves showed that infection with XccΔotsA triggered only weak defence responses in the plant compared with infection with Xcc, and had less impact on the host plant's metabolism than the wild-type strain. These results suggested that trehalose of bacterial origin, synthesized via the otsA-otsB pathway, in Xcc, plays a role in modifying the host plant's metabolism to its own advantage but is also perceived by the plant as a sign of pathogen attack. Thus, trehalose biosynthesis has both positive and negative consequences for Xcc. On the one hand, it enables this bacterial pathogen to survive in the inhospitable environment of the leaf surface before infection and exploit the host plant's resources after infection, but on the other hand, it is a tell-tale sign of the pathogen's presence that triggers the plant to defend itself against infection.

Luteocirrhus shearii gen. sp. nov. (Diaporthales, Cryphonectriaceae) pathogenic to Proteaceae in the South Western Australian Floristic Region

Morphological and DNA sequence characteristics of a pathogenic fungus isolated from branch cankers in Proteaceae of the South West Australian Floristic Region elucidated a new genus and species within Cryphonectriaceae (Diaporthales). The pathogen has been isolated from canker lesions in several Banksia species and Lambertia echinata subsp. citrina, and is associated with a serious decline of the rare B. verticillata. Lack of orange pigment in all observed structures except cirrhi, combined with pulvinate to globose black semi-immersed conidiomata with paraphyses, distinguishes the canker fungus from other genera of Cryphonectriaceae. This was confirmed by DNA sequence analysis of the ITS regions, β-tubulin, and LSU genes. The fungus (sexual morph unknown) is described as Luteocirrhus shearii gen. sp. nov. Lesions in seedlings of Banksia spp. following wound inoculation and subsequent recovery confirm Koch's postulates for pathogenicity. This pathogen of native Proteaceae is currently an emerging threat, particularly toward B. baxteri and B. verticillata.

Morphological and Molecular Characteristics of the Oak Tree Canker Pathogen, Annulohypoxylon truncatum

Cankers are localized dead areas in the bark of stems, branches or twigs of many types of trees and shrubs, and are usually caused by fungi. We observed severe canker symptoms in oak trees located in Gyeongnam province in 2011. A total 31 trees were discovered with cankers of varied size, with an average of 48.5 × 15.2 cm. Black, half-rounded globular mound shaped stromata were associated with the cankers, and the asci of the fungi associated with the cankers were cylindrical shaped with their spore-bearing parts being up to 84 µm in length. The average fungal ascospores size was 7.59 × 4.23 µm. The internal transcribed spacer sequence for the canker causing fungus showed 99% similarity to the sequence of Annulohypoxylon truncatum. In this study, the isolated fungus was precisely described and then compared with fungi of similar taxa.