Positive selection and functional diversification of transcription factor Cmr1 homologs in Alternaria.

Transcription factor Cmr1 (Colletotrichum melanin regulation 1) and its homologs in several plant fungal pathogens are the regulators of the 1,8-dihydroxynaphthalene (DHN)-melanin biosynthesis pathway and have evolved functional diversification in morphology and pathogenicity. The fungal genus Alternaria comprises the group of "black fungi" that are rich in DHN-melanin in the primary cell wall and septa of the conidia. Some Alternaria species cause many economically important plant diseases worldwide. However, the evolution and function of Cmr1 homologs in Alternaria remain poorly understood. Here, we identified a total of forty-two Cmr1 homologs from forty-two Alternaria spp. and all contained one additional diverse fungal specific transcription factor motif. Phylogenetic analysis indicated the division of these homologs into five major clades and three branches. Dated phylogeny showed the A and D clades diverged latest and earliest, respectively. Molecular evolutionary analyses revealed that three amino acid sites of Cmr1 homologs in Alternaria were the targets of positive selection. Asmr1, the homolog of Cmr1 in the potato early blight pathogen, Alternaria solani was amplified and displayed the sequence conservation at the amino acid level in different A. solani isolates. Asmr1 was further confirmed to have the transcriptional activation activity and was upregulated during the early stage of potato infection. Deletion of asmr1 led to the decreased melanin content and pathogenicity, deformed conidial morphology, and responses to cell wall and fungicide stresses in A. solani. These results suggest positive selection and functional divergence have played a role in the evolution of Cmr1 homologs in Alternaria. KEY POINTS: • Cmr1 homologs were under positive selection in Alternaria species • Asmr1 is a functional transcription factor, involved in spore development, melanin biosynthesis, pathogenicity, and responses to cell wall and fungicide stresses in A. solani • Cmr1 might be used as a potential taxonomic marker of the genus Alternaria.

First Report of Leaf Spot of Weigela florida Caused by Epicoccum layuense in China.

Weigela florida (Bunge) A. DC. is a dense, rounded, deciduous shrub commonly planted in landscapes. It is also used in Chinese medicine to treat sore throat, erysipelas, cold, and fever (Zheng et al. 2019). In May 2019, leaf spots were observed on approximately 50% of W. florida plants grown in the Wisdom Plaza Park of Anhui Agricultural University in Hefei, Anhui Province, China. Leaf spots begun as small light brown and irregular lesions, enlarged, turned reddish brown, coalesced to form large blighted areas, and eventually covered the entire leaf surface. Five pieces of tissues were removed from the lesion margins of each diseased leaf (five leaves from five different plants), chopped into several 3-4 mm2 pieces, disinfected with 1.5% NaOCl for 2 min, rinsed 3 times with sterile distilled water for 1 min, plated onto Potato Dextrose Agar (PDA) medium containing 50 µg/ml of ampicillin and kanamycin, and incubated at 25°C with a 12-hour photoperiod for 5 days. One segment of the fungal growth from the growing edge of the colony was transferred onto a fresh PDA plate for purification and incubated under the same conditions for another 5 days. The colony morphology of one representative isolate (AAU0519) was characterized by a pale orange cushion in the center surrounded by irregular pink margin, diffusing red orange pigments into the PDA medium. Isolate AAU0519 was cultured on PDA medium for 7 days at 25°C in the dark to induce sporulation. The produced conidia were globose, subglobose to pyriform, golden brown to brown, and with a diameter of 7.7 - 23.8 µm. Both cultural and morphological characteristics suggested that isolate AAU0519 was an Epicoccum species, according to the description by Chen et al. 2017. Amplification and sequencing of the internal transcribed spacer (ITS), beta-tubulin, and 28S large subunit ribosomal RNA (LSU) gene fragments from the extracted genomic DNA of AAU0519 were performed using primer sets ITS1/ITS4 (White et al. 1990), Bt2a/Bt2b (Glass and Donaldson 1995), and LSU1Fd/LR5 (Crous et al. 2009; Vilgalys and Hester 1990), respectively. A phylogenetic tree was constructed by the maximum-likelihood method with 1,000 bootstrapping replications based on the concatenated ITS, beta-tubulin, and LSU sequences from isolate AAU0519 and representative strains of 22 species of the genus Epicoccum (Chen et al. 2017). Isolate AAU0519 clustered with ex-holotype CGMCC 3.18362 of Epicoccum layuense Qian Chen, Crous & L. Cai (Chen et al. 2017). All obtained sequences were deposited into GenBank under accession numbers MK983497 (ITS), MN328723 (beta-tubulin), and MN328724 (LSU). A pathogenicity test was conducted on leaves of five 3-year-old W. florida cultivar "Red Prince" planted in the field (five leaves for each treatment and control per plant) by spraying 30 ml of a spore suspension (106 spores/ml) of isolate AAU0519 as treatment or sterilized distilled water as control. Before the inoculation, the leaves were disinfected with 70% ethanol. After inoculation, the leaves were wrapped with a plastic bag to keep high relative humidity. The average air temperature was about 28°C during the period of pathogenicity test. The experiment was repeated once. Ten days after inoculation, the fungal-inoculated leaves developed light brown lesions resembling those of naturally infected leaves, control leaves did not develop any symptoms. E. layuense was recovered from leaf lesions and its identity was confirmed by morphological and sequence analyses as described above. To our knowledge, E. layuense has been previously reported as a pathogen of Perilla sp. (Chen et al. 2017), oat (Avena sativa) (Chen et al. 2019), and tea (Camellia sinensis) plants (Chen et al. 2020), but this is the first report of E. layuense causing leaf spot on W. florida in China. This pathogen could pose a threat to the ornamental value of W. florida plants. Thus, it is necessary to adopt effective management strategies against leaf spot on W. florida.

Nigrospora oryzae Causing Leaf Spot on Asiatic Dayflower in Chongqing, China.

Asiatic dayflower (Commelina communis L.) is an annual herbaceous weed that is distributed throughout China. A foliar disease on Asiatic dayflowers was discovered in one farm field in Dianjiang County, Chongqing, China (N30°3´22″, E107°18´5″) in summer, 2019. The disease incidence was observed on about 10% (13/127) of the plants. Symptoms appeared as round-shaped tan lesions (2-5 mm) in diameter that occurred randomly and irregularly on the whole leaves. The centers of lesions become grayish white with reddish borders as the disease progressed. The leaves with typical symptoms were detached and wiped with 70% ethanol for surface disinfestation before isolating the causal agent. Subsequently, three pieces (3-4 mm2) of tissue were taken from the margin of the leaf lesion, disinfested in 1.5% NaClO for 1 min, rinsed 3 times in sterilized distilled water, and placed onto Potato Dextrose Agar (PDA) medium containing 50 µg/ml each of kanamycin and ampicillin. A fungus was exclusively and consistently isolated from the disinfested leaf lesion sections. The colonies on PDA grew rapidly and covered the entire petri dish within 5 days at 28℃. Colonies were at first grayish white, cotton wool-like, round, with abundant aerial mycelium, and later turned black as conidia produced. The abundant conidia formed on PDA were initially yellow brown and gradually became black, oblate to ellipsoidal, smooth, single-celled, and ranged in size from 4 to 10 × 3.5 to 9 µm. They were borne on a colorless, hyaline, and inverted flask-shaped cell at the tip of each conidiophore. The morphology characteristics were consistent with those of Nigrospora spp. (Wang et al. 2017). Genomic DNA was extracted from one representative isolate NDJ0819. The amplification and sequencing of the gene fragments including the internal transcribed space (ITS) region of ribosomal DNA and beta-tubulin were performed using the primers ITS1/ITS4 (White et al. 1990) and Bt2a/Bt2b (Glass and Donaldson 1995), respectively. Fragments of 536 bp for ITS and 408 bp for beta-tubulin were obtained. A phylogram of the combined ITS and beta-tubulin sequences reconstructed using the maximum likelihood bootstrapping method implemented in the software MEGA version 7.0 (Kumar et al. 2016) indicated that isolate NDJ0819 clustered with Nigrospora oryzae. Both ITS and beta-tubulin sequences were deposited into GenBank (accession no. MT140353 and MT157509, respectively). Pathogenicity test was performed by rub-inoculating needle-wounded leaves of three 4-week-old Asiatic dayflowers with spore suspension (2.6 × 106 conidia/ml) of NDJ0819 prepared in water containing 0.05% Tween-20, and holding plants at 28℃ in the growth chamber. The pathogenicity test was repeated twice. Brown, round-shaped lesions developed on leaves inoculated with spores at 15 days post-inoculation. However, the centers of the lesion did not become grayish white, compared to those of lesions seen in naturally infected leaves. No symptoms developed on leaves inoculated with sterilized distilled water. N. oryzae was re-isolated from the lesions. All results described above indicated that N. oryzae was responsible for the leaf spot of Asiatic dayflower. To our knowledge, this is the first report of N. oryzae causing leaf spot on Asiatic dayflower in China. Research into the potential use of N. oryzae as a candidate biological agent against the weed is worth being initiated.

First Report of Alternaria spp. Causing Leaf Spot on Sweet Viburnum in China.

Sweet viburnum [Viburnum odoratissimum (L.) Ker Gawl] is an evergreen shrub mainly cultivated along roadsides in urban landscapes and also in parks and residential areas. A foliar disease occurred on about 40% of sweet viburnum plants near Anhui Grand Theatre, Anhui Province of China in June 2019. In early stages of sweet viburnum infection, the symptoms appeared as small brown spots ranged in length from 2 to 3 millimeters on the leaves. The spots developed on the upper, middle, and lower leaves of the plant, however, the upper leaves got more severely affected. As the disease develops, the spots enlarged and became rectangular or oval, brown to dark-brown, and their centers became ashen gray. In later stages of infection, the diseased leaves became wilting. Diseased leaves were surface disinfested and three small sections (2-3 mm2) were cut from the margin of the lesions. Sections were placed in 1.5% NaClO for 2 min, submerged in three changes of sterilized distilled water for 1 min each, placed onto potato dextrose agar (PDA) medium amended with 50 µg/ml of ampicillin and kanamycin, and incubated at 25℃ for 3 days. The mycelium from the leading edge of colonies growing from the tissue was sub-cultured onto a PDA plate for 3 days, followed by spore induction (Simmons 2007) and single spore isolation to obtain a pure culture of the putative pathogen. Colonies of one single spore isolate HF0719 were rounded, grayish white with dense aerial mycelium viewed from above and dark brown viewed from below. On potato carrot agar (PCA) medium, conidiophores were branched or occasionally unbranched. On branched conidiophores, conidia were in dwarf tree-like branched chains of 2-5 conidia. On unbranched conidiophores, conidia were simple or in chains of 2-8 conidia. Conidia were light brown or dark brown, ovoid, ellipsoidal to fusiform, and ranged in size from 7 to 26.5 × 4.5 to 11 µm with an average size of 16 × 7 µm based on 500 spore observations, with one beak and 1-7 transverse, 0-3 longitudinal, and 0-3 oblique septa. Beaks were ranged in (1.5-)2-10(-16) µm long. Based on cultural and morphological characteristics, isolate HF0719 was identified as Alternaria spp. (Simmons 2007). For molecular identification, total genomic DNA was isolated from mycelia collected from 7 day-old colonies of isolate HF0719 using the fungal genomic DNA extraction kit (Solarbio, Beijing, China). Fragments of five genes, including those encoding glyceraldehyde-3-phosphate dehydrogenase (gpd), plasma membrane ATPase, actin, calmodulin, and the Alternaria major allergen (Alt a1) regions of isolate HF0719 were amplified and sequenced using primer pairs gpd1/gpd2 (Berbee et al. 1999), ATPDF1/ATPDR1, ACTDF1/ACTDR1, CALDF1/CALDR1 (Lawrence et al. 2013), and Alt-for/Alt-rev (Hong et al. 2005), respectively. The obtained nucleotide sequences were deposited into GenBank as accession numbers: gpd, MT614365; ATPase, MT614364; actin, MT614363; calmodulin, MN706159; and Alt a1, MN304720. Phylogenetic tree using a maximum likelihood bootstrapping method based on the five-gene combined dataset in the following order: gpd, ATPase, actin, calmodulin, Alt a1 of HF0719 and standard strains representing 120 Alternaria species (Lawrence et al. 2013) was constructed. Isolate HF0719 formed a separate branch. On the basis of morphological characteristics and phylogenetic pattern, isolate HF0719 was identified as Alternaria spp.. A pathogenicity test was performed by rubbing 32 healthy leaves of six 5-year-old sweet viburnum plants with a cotton swab dipped in spore suspension containing 2.6 × 106 spores/ml, following leaf surface disinfection with 70% ethanol in the open field. Sterilized distilled water was used as control. The average air temperature was about 28℃ during the period of pathogenicity test. Eleven days after inoculation, 100% of inoculated leaves showed the leaf spot symptom identical to symptoms observed in the field. Control leaves were symptomless. The experiment was done three times. The re-isolated pathogen from the leaf lesion had the same morphological and molecular characteristics as isolate HF0719, thus satisfying Koch's postulates. The genus Alternaria has been reported to cause leaf spot on sweet viburnum in Florida, USA (Alfieri et al. 1984). To our knowledge, this is the first report of Alternaria spp. causing leaf spot on sweet viburnum in China, a highly valued ornamental plant. Our findings will contribute to monitoring and adopting strategies for manage leaf spot disease on sweet viburnum.

Alternaria solani core effector Aex59 is a new member of the Alt a 1 protein family and is recognized as a PAMP.

Early blight caused by Alternaria solani is a destructive disease in potato production. Here, through systematically screening of an effector protein pool consisting of 115 small cysteine-containing candidate Aex (Alternariaextracellular proteins) in A. solani, we identified a core effector protein named Aex59, a pathogen-associated molecular pattern (PAMP) molecule. Aex59 is uniquely present in the Ascomycota of fungi and can activate defense responses in multiple plants. Targeted gene disruption showed that Aex59 is a virulence factor and participates in spore development. Perception of Aex59 in Nicotiana benthamiana does not depend on the receptor-like kinases Brassinosteroid-associated kinase1 (BAK1) and Suppressor of BIR1-1 (SOBIR1), which are required for multiple pattern recognition receptors (PRR) pathways. Sequence analysis revealed that Aex59 is a new member of the Alt a 1 protein family and is a potential molecular marker capable of aiding in the classification of the fungi Alternaria spp.

Multifunctionality of AsCFEM6 and AsCFEM12 effectors from the potato early blight pathogen Alternaria solani.

Plant pathogens secrete fungal-specific common in several fungal extracellular membrane (CFEM) effectors to manipulate host immunity and contribute to their virulence. Little is known about effectors and their functions in Alternaria solani, the necrotrophic fungal pathogen causing potato early blight. To identify candidate CFEM effector genes, we mined A. solani genome databases. This led to the identification of 12 genes encoding CFEM proteins (termed AsCFEM1-AsCFEM12) and 6 of them were confirmed to be putative secreted effectors. In planta expression revealed that AsCFEM6 and AsCFEM12 have elicitor function that triggers plant defense response including cell death in different botanical families. Targeted gene disruption of AsCFEM6 and AsCFEM12 resulted in a change in spore development, significant reduction of virulence on potato and eggplant susceptible cultivars, increased resistance to fungicide stress, variation in iron acquisition and utilization, and the involvement in 1,8-dihydroxynaphthalene (DHN) melanin biosynthesis pathway. Using maximum likelihood method, we found that positive selection likely caused the polymorphism within AsCFEM6 and AsCFEM12 homologs in different Alternaria spp. Site-directed mutagenesis analysis indicated that positive selection sites within their CFEM domains are required for cell death induction in Nicotiana benthamiana and are critical for response to abiotic stress in yeast. These results demonstrate that AsCFEM effectors possess additional functions beyond their roles in host plant immune response and pathogen virulence.