Colletotrichum shisoi sp. nov., an anthracnose pathogen of Perilla frutescens in Japan: molecular phylogenetic, morphological and genomic evidence

First report of Colletotrichum shisoi causing anthracnose of Perilla frutescens in the United States

Perilla mint (Perilla frutescens (L.) Britt.) is an annual plant native to Asia and considered invasive in North America where it has escaped cultivation as an ornamental (Miller 1947; Swearingen et al. 2010). In August 2021, an anthracnose disease was observed on invasive perilla found along the disturbed margins of a forest in Frederick County, Maryland, United States. Symptoms included necrotic lesions with chlorotic halos, were concentrated in the lower canopy, and caused premature defoliation of lower leaves (Figure S1). Leaves from four plants were surface sterilized by rinsing for 30 s in 70% ethanol, 60 s in 0.8% NaClO, and 60 s in sterile water and then incubated on 2% water agar under ambient laboratory conditions to permit sporulation. After three days, spores that exuded from individual lesions were streaked onto acidified potato dextrose agar. Two single-conidium isolates were recovered from each plant. All eight isolates were identified to species using DNA sequences. A single isolate (21-067) was selected at random for morphological characterization and completion of Koch's postulates. Morphological features were recorded after seven days of growth on synthetic low-nutrient agar (SNA) and potato dextrose agar (PDA) incubated at 22°C under 12 hr UV-B and white fluorescent lighting. Measurements were based on a minimum of 20 observations per structure. Cultures on SNA were flat, hyaline to pale salmon, lacked sporodochia and grew at a rate of 1.3 mm day-1 (n = 3). Vegetative hyphal width was (minimum-maximum) 1.5-4.0 μm, (average ± standard deviation) 2.7 ± 0.9 μm. Conidiophores arose directly from hyphae, were hyaline, smooth, unbranched and measured 40.0-180.0 x 1.5-4.5 μm, 102.3 ± 33.9 x 2.7 ± 0.8 μm. Conidia were single celled, straight, hyaline, glabrous, rounded at both ends and measured 10.0-20.0 x 3.8-6.3 μm, 15.4 ± 2.5 x 4.9 ± 0.7 μm. Setae, observed only on PDA, were pale brown, 1-2 septate, straight, blunt tipped and measured 42.5-97.5 μm, 70.8 ± 13.4 μm. Appressoria formed on PDA were single-celled, pigmented, smooth, and obovoid with entire margins, measuring 5.2-7.7 x 8.6-13.8 μm, 6.8 ± 0.6 x 10.8 ± 1.4 μm. These characteristics were consistent with members of the Colletotrichum destructivum species complex. Partial DNA sequences from five loci were amplified following the procedures of Damm et al. 2014: internal transcribed spacer region of rDNA (ITS), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), chitin synthase 1 (CHS-1), actin (ACT), and beta-tubulin (TUB2). Pairwise sequence comparisons to references using the Blastn algorithm found 99.8% similarity between isolate 21-067 and ex-type C. shisoi isolate JCM 31818: MH660930 (ITS, 545/546 bp), MH660931 (GAPDH,192/192 bp), MH660929 (CHS-1, 278/280 bp), MH660928 (ACT, 262/262 bp), and MH660932 (TUB2, 511/511 bp) (Altschul et al. 1990; Gan et al. 2019). Subsequently, sequences from all eight isolates were aligned with Clustal Omega (Sievers and Higgins 2018), concatenated, and used in a Bayesian phylogenetic reconstruction (Huelsenbeck and Ronquist 2001) of the C. destructivum species complex (Figure S2), confirming the species identity as C. shisoi. Sequences were deposited in NCBI GenBank under accession numbers OM865277-OM865284 and OM885059-OM885090. Koch's postulates were fulfilled using perilla grown in a greenhouse until second true leaves emerged. Inoculum washed from two-week-old fungal cultures grown on potato dextrose agar was adjusted to 4 x 104 conidia mL-1 and applied to three replicate plants with an aspirator until runoff. Three plants were sprayed with sterile water as a negative control. Plants were covered with plastic bags for 72 hrs and maintained in a growth chamber at 20°C and 80% RH for 14 days. Inoculated plants displayed disease symptoms similar to those observed under field conditions, and control plants did not develop symptoms. Colletotrichum shisoi was reisolated from symptomatic tissue and reidentified based on morphology. The experiment was completed twice. To the authors' knowledge, this is the first report of C. shisoi on P. frutescens in the United States. Colletotrichum shisoi has not been reported as a pathogen on other plants in the United States and may have potential use as a biological control agent for invasive perilla.

Colletotrichumchinense sp. nov. from Yuccagloriosa and C.quercicola sp. nov. from Quercusvariabilis in China

Colletotrichum is an important plant pathogenic genus causing anthracnose on a wide range of host plants. During 2019 and 2021, Colletotrichum isolates were obtained during surveys of anthracnose on garden plants in China. Multi-gene phylogenetic analyses of internal transcribed spacer (ITS), glyceraldehyde-3-phosphate dehydrogenase (gapdh), chitin synthase 1 (chs-1), actin (act) and beta-tubulin (tub2) sequences coupled with morphological evidence support the introduction of two novel species namely Colletotrichumchinense sp. nov. from Yuccagloriosa in Beijing and C.quercicola sp. nov. from Quercusvariabilis in Shaanxi Province. Phylogenetic inference revealed that two isolates of C.chinense belonged to the agaves species complex and were closely related to C.agaves, and differed from the other species within this species complex by shorter conidia and the host association. Molecular identification showed that two isolates of C.quercicola formed a highly supported lineage close to C.tanaceti in the destructivum species complex, which could be distinguished from C.tanaceti by straighter conidia. In pathogenicity tests, yellow spots and orange conidial masses displayed on the inoculated Y.gloriosa leaves and brown spots appeared on the inoculated Q.variabilis leaves. In addition, C.chinense and C.quercicola were re-isolated from spots of the tested leaves of Y.gloriosa and Q.variabilis.

Identification and Comparison of Colletotrichum Secreted Effector Candidates Reveal Two Independent Lineages Pathogenic to Soybean

Colletotrichum is one of the most important plant pathogenic genus of fungi due to its scientific and economic impact. A wide range of hosts can be infected by Colletotrichum spp., which causes losses in crops of major importance worldwide, such as soybean. Soybean anthracnose is mainly caused by C. truncatum, but other species have been identified at an increasing rate during the last decade, becoming one of the most important limiting factors to soybean production in several regions. To gain a better understanding of the evolutionary origin of soybean anthracnose, we compared the repertoire of effector candidates of four Colletotrichum species pathogenic to soybean and eight species not pathogenic. Our results show that the four species infecting soybean belong to two lineages and do not share any effector candidates. These results strongly suggest that two Colletotrichum lineages have acquired the capability to infect soybean independently. This study also provides, for each lineage, a set of candidate effectors encoding genes that may have important roles in pathogenicity towards soybean offering a new resource useful for further research on soybean anthracnose management.

A nuclear-targeted effector of Rhizophagus irregularis interferes with histone 2B mono-ubiquitination to promote arbuscular mycorrhisation

Arguably, symbiotic arbuscular mycorrhizal (AM) fungi have the broadest host range of all fungi, being able to intracellularly colonise root cells in the vast majority of all land plants. This raises the question how AM fungi effectively deal with the immune systems of such a widely diverse range of plants. Here, we studied the role of a nuclear-localisation signal-containing effector from Rhizophagus irregularis, called Nuclear Localised Effector1 (RiNLE1), that is highly and specifically expressed in arbuscules. We showed that RiNLE1 is able to translocate to the host nucleus where it interacts with the plant core nucleosome protein histone 2B (H2B). RiNLE1 is able to impair the mono-ubiquitination of H2B, which results in the suppression of defence-related gene expression and enhanced colonisation levels. This study highlights a novel mechanism by which AM fungi can effectively control plant epigenetic modifications through direct interaction with a core nucleosome component. Homologues of RiNLE1 are found in a range of fungi that establish intimate interactions with plants, suggesting that this type of effector may be more widely recruited to manipulate host defence responses.

Identification, Virulence and Fungicide Sensitivity of Colletotrichum gloeosporioides s.s. Responsible for Walnut Anthracnose Disease in China

Walnut (Juglans regia L.) is an economically important woody nut and edible oil tree all over the world. However, walnut production is limited by walnut anthracnose, which is a disastrous disease that causes significant yield losses. Studying the etiology of anthracnose on walnut and the pathogens' virulence and sensitivities to fungicides would be beneficial for effective control. This study was conducted to identify the pathogen of walnut anthracnose and reveal the population diversity of pathogens through virulence, sensitivities to fungicides, and genetic variation. A total of 13 single-spore Colletotrichum isolates were collected from walnut anthracnose-diseased fruits and leaves from 13 walnut commercial orchards in Henan, Hubei, Shandong, and Shaanxi provinces in China. The isolates were identified as Colletotrichum gloeosporioides sensu stricto (s.s.) according to multilocus phylogenetic analyses (internal transcribed spacer, actin, glyceraldehyde-3-phosphate dehydrogenase, and chitin synthase), morphological as well as cultural characters, and pathogenicity. When the same walnut tissue was inoculated with different isolates, the disease lesion size was different. The results showed that the virulence of all isolates was considerably different, and the differences were not correlated with geographic origins. The virulence to walnut leaves and fruits inoculated with the same isolate was significantly different. Based on the virulence to walnut leaves and fruits, the 13 isolates were divided into three groups. Virulence of 69.2% of the isolates to walnut fruits was higher than that to leaves; 15.4% of isolates had no difference in pathogenicity, and the virulence to walnut leaves was higher for 15.4% of isolates. Tebuconazole, difenoconazole, flusilazole, and carbendazim inhibited the growth of fungal mycelia, and the concentration for 50% of maximal effect (EC₅₀) values were 0.4 to 20.5, 0.6 to 2.6, 0.2 to 1.6, and 0.002 to 0.2 µg/ml, respectively, with average values of 6.5 ± 6.9, 1.5 ± 0.6, 0.9 ± 0.4, and 0.1 ± 0.05 µg/ml, respectively. All isolates were more sensitive to difenoconazole, flusilazole, and carbendazim than tebuconazole (P < 0.01). Isolate sensitivities to the same fungicide were different. Isolates SL-31 and TS-09 were the least sensitive to carbendazim and tebuconazole, respectively, and the resistance ratios were 87.3 and 51.6, respectively. Sensitivities to difenoconazole and flusilazole were largely consistent among all isolates, and the resistance ratios were from 1 to 4.6 and from 1 to 7, respectively. Therefore, difenoconazole and flusilazole could be chosen for disease control. The differences of pathogenicity and fungicide sensitivity were not correlated with geographic regions. These results indicated that there was high intraspecific diversity of populations in C. gloeosporioides s.s. that caused walnut anthracnose. For effective management, the targeted control strategy should be implemented based on the different geographic regions.

Colletotrichum: species complexes, lifestyle, and peculiarities of some sources of genetic variability

The genus Colletotrichum comprises species with different lifestyles but is mainly known for phytopathogenic species that infect crops of agronomic relevance causing considerable losses. The fungi of the genus Colletotrichum are distributed in species complexes and within each complex some species have particularities regarding their lifestyle. The most commonly found and described lifestyles in Colletotrichum are endophytic and hemibiotrophic phytopathogenic. Several of these phytopathogenic species show wide genetic variability, which makes long-term maintenance of resistance in plants difficult. Different mechanisms may play an important role in the emergence of genetic variants but are not yet fully understood in this genus. These mechanisms include heterokaryosis, a parasexual cycle, sexual cycle, transposable element activity, and repeat-induced point mutations. This review provides an overview of the genus Colletotrichum, the species complexes described so far and the most common lifestyles in the genus, with a special emphasis on the mechanisms that may be responsible, at least in part, for the emergence of new genotypes under field conditions.

Method for Assessing Virulence of Colletotrichum higginsianum on Arabidopsis thaliana Leaves Using Automated Lesion Area Detection and Measurement

The plant pathogenic fungus, Colletotrichum higginsianum is widely used to understand infection mechanisms, as it infects the model plant Arabidopsis thaliana. To determine the virulence of C. higginsianum, several methods have been developed, such as disease reaction scoring, lesion measurement, entry rate assays, and relative fungal biomass assays using real-time quantitative PCR. Although many studies have taken advantage of these methods, they have shortcomings in terms of objectivity, time, or cost. Here, we show a lesion area detection method applying ImageJ color thresholds to images of A. thaliana leaves infected by C. higginsianum. This method can automatically detect multiple lesions in a short time without the requirement for special equipment and measures lesion areas in a standardized way. This high throughput technique will aid better understanding of plant immunity and pathogenicity and contribute to reproducibility of assays.