Discovery of a Cryptic Species, Erysiphe Salicina Sp. Nov., and Reconstruction of The Phylogeny of Powdery Mildews On Populus and Salix Spp.

Recently performed phylogenetic-taxonomic analyses of species belonging to Erysiphe sect. Uncinula on willows (Salix spp.) demonstrated a much higher diversity than previously assumed. Phylogenetic analyses and morphological examinations of Chinese Erysiphe collections on Salix abscondita (= S. raddeana), S. sinica and S. taraikensis, all belonging to Salix subgen. Vetrix sect. Vetrix, revealed an additional cryptic species in sister position to the E. salicis clade, which is described as Erysiphe salicina. The new species clearly distinguished from all allied species in morphological and genetical results. The phylogeny of the new species and closely related species on Populus and Salix spp. (Salicaceae) was reconstructed and discussed using a combined alignment of the internal transcribed spacer (ITS) regions and 28S rDNA sequences. The present phylogenetic analyses suggest that the recently described E. salicicola (on Salix gracilistyla in South Korea) has to be reduced to synonymy with E. salicis var. salicis-gracilistylae (º Uncinula salicis-gracilistylae).

Identification of Pueraria spp. through DNA barcoding and comparative transcriptomics

Background Kudzu is a term used generically to describe members of the genus Pueraria. Kudzu roots have been used for centuries in traditional Chinese medicine in view of their high levels of beneficial isoflavones including the unique 8-C-glycoside of daidzein, puerarin. In the US, kudzu is seen as a noxious weed causing ecological and economic damage. However, not all kudzu species make puerarin or are equally invasive. Kudzu remains difficult to identify due to its diverse morphology and inconsistent nomenclature. Results We have generated sequences for the internal transcribed spacer 2 (ITS2) and maturase K (matK) regions of Pueraria montana lobata, P. montana montana, and P. phaseoloides, and identified two accessions previously used for differential analysis of puerarin biosynthesis as P. lobata and P. phaseoloides. Additionally, we have generated root transcriptomes for the puerarin-producing P. m. lobata and the non-puerarin producing P. phaseoloides. Within the transcriptomes, microsatellites were identified to aid in species identification as well as population diversity. Conclusions The barcode sequences generated will aid in fast and efficient identification of the three kudzu species. Additionally, the microsatellites identified from the transcriptomes will aid in genetic analysis. The root transcriptomes also provide a molecular toolkit for comparative gene expression analysis towards elucidation of the biosynthesis of kudzu phytochemicals.

Biological Trace Information Extracted from Bioaerosols Using NGS Analysis

Bioaerosols are atmospheric particles with a biological trace, such as viruses, bacteria, fungi, and plant material such as pollen and plant debris. In this study, we analyzed the biological information in bioaerosols using next generation sequencing of the trace DNA. The samples were collected using an Andersen air sampler and separated into two groups according to particulate matter (PM) size: small (PM2.5) and large (PM10). Amplification and sequencing of the bacterial 16S rDNA gene, prokaryotic internal transcribed spacer 1 (ITS1) region and DNA sequence of a plant chloroplast gene (rbcL) were carried out using several sets of specific primers targeting animal and plant sequences. Lots of bacterial information was detected from the bioaerosols. The most abundant bacteria in several samples were of the Actinobacteria (class), Alphaproteobacteria, Bacilli, and Clostridia. For the animal detection using internal transcribed spacer 1, only uncultured fungi were detected in more than half of the hits, with a high number of Cladosporium sp. in the samples. For the plant identification, the ITS1 information only matched fungal species. However, targeting of the rbcL region revealed diverse plant information, such as Medicago papillosa. In conclusion, traces of bacteria, fungi, and plants could be detected in the bioaerosols, but not of animals using our primers.

The first detection of Botryosphaeria sinensis on white lupine

Fungal strain MF KP-12.1, which is similar in morphological and cultural characteristics to Botryosphaeria fungi, was isolated from the seeds of white lupine variety Dega grown in Oryol region in 2018. Phylogenetic analysis of the large rRNA subunit (LSU), elongation factor-1α (TEF) and internal transcribed spacer (ITS) fragments was used to accurately identify the isolated strain as B. sinensis. When 2-week-old white lupine plants were treated under laboratory conditions with mycelial suspension of B. sinensis MF KP-12.1, plant damage reached 67 % on day 3, and 100 % plant death was observed on day 10. Pathogenicity of B. sinensis MF KP-12.1 was confirmed by re-isolation of the strain from damaged plant tissue. This is the first detection of B. sinensis on white lupine, which has not been previously reported as a host for this fungus. It is also the first detection of B. sinensis in Russia.

Evidences of Colletotrichum fructicola Causing Anthracnose on Passiflora edulis Sims in China

Passion fruit (Passiflora edulis) is a tropical and subtropical plant that is widely cultivated in China due to its high nutritional value, unique flavor and medicinal properties. In August 2020, typical anthracnose symptoms with light brown and water-soaked lesions on Passiflora edulis Sims were observed, which result in severe economic losses. The incidence of this disease was approximately 30%. The pathogens from the infected fruit were isolated and purified by the method of tissue isolation. Morphological observations showed that the colony of isolate BXG-2 was gray to celadon and grew in concentric circles. The orange conidia appeared in the center after 14 days of incubation. The pathogenicity was verified by Koch’s postulates. The internal transcribed spacer (ITS), chitin synthase (CHS-1), actin (ACT), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were amplified by relevant PCR programs. The multi-gene (ITS, GAPDH, ACT, CHS-1) phylogeny analysis confirmed that isolate BXG-2 belongs to Colletotrichum fructicola. The inhibitory effect of six synthetic fungicides on the mycelial growth of the pathogen was investigated, among which difenoconazole 10% WG showed the best inhibitory effect against C. fructicola with an EC50 value of 0.5579 mg·L−1. This is the first report of anthracnose on Passiflora edulis Sims caused by Colletotrichum fructicola in China.

Endosymbiont Communities in Pachyseris speciosa Highlight Geographical and Methodological Variations

Reef-building corals live in symbiosis with the phototrophic dinoflagellate family Symbiodiniaceae, which comprises diverse genera such as Cladocopium and Durusdinium. Pachyseris speciosa, a widely distributed Indo-Pacific coral found in a variety of reef habitats, is known to be associated with these two Symbiodiniaceae genera, but little is known about the biogeographic variability of the endosymbiont communities across the region. In this study, the diversity and dominance patterns of Symbiodiniaceae at the western and eastern areas of the Central Indo-Pacific region were examined. We sampled Pachyseris speciosa colonies at seven and six sites in Singapore and Papua New Guinea, respectively, and genotyped their endosymbionts based on the internal transcribed spacer (ITS) markers using two distinct methods, quantitative polymerase chain reaction (qPCR) and high-throughput sequencing (HTS). Results showed 92% of all colonies in Singapore exhibiting Cladocopium dominance. There was a higher abundance of Durusdinium compared to Cladocopium in certain colonies from one site, Pulau Hantu (mean Durusdinium abundance of 90%, compared to 0–14% among all other sites). In contrast, variation in the endosymbiont communities was generally higher among sites in Papua New Guinea. Cladocopium expectedly dominated most colonies (75%), although colonies from Kimbe Bay (85%) and Kavieng (65%) showed Durusdinium dominance. Between localities, relative genus abundances based on qPCR were not significantly different, but HTS showed that the ratio of Durusdinium over Cladocopium was significantly higher in Papua New Guinea corals. Notably, 6% of colonies from Singapore and 15% from Papua New Guinea showed endosymbiont dominance patterns that were inconsistent between the two methods, underscoring the need for further validation of symbiotic algal quantification based on HTS. The richness of ITS2 type profiles was clearly lower among colonies from the impacted and turbid reefs of Singapore compared to the less urbanized reefs of Papua New Guinea. These coral intraspecific variations of Symbiodiniaceae communities within and among localities suggest that local conditions are important drivers of endosymbiosis and may ultimately influence corals’ resilience against global stressors such as ocean warming.

Identification of Monilia species in Tibet and characterization of M. yunnanensis in China

Samples of peach and plum fruits with brown rot symptoms were collected from Tibet in 2019 and 2020, and the causal agent was identified as Monilia yunnanensis, which represents the first characterization of Monilia spp. on peach and plum in Tibet. Morphological investigation showed that some conidia from naturally diseased fruits were larger than those observed in previously isolated M. yunnanensis. Some conidia of M. yunnanensis isolates from Tibet produced more than two, even up to six germ tubes from different parts of each conidium, instead of one or two germ tubes developing from the pointy sides of each conidium. The alignment of ribosomal internal transcribed spacer region (ITS) sequences revealed that some isolates from Tibet displayed a mutation at the 374th position from adenine (A) to cytosine (C). Although above-mentioned differences were observed between isolates from Tibet and other regions, phylogenetic analysis indicated that all of the M. yunnanensis isolates from different stone fruits and different regions in China were clustered together without obvious genetic differentiation. These results revealed that hosts and geographical environments did not play a major role in the evolution of M. yunnanensis.

Analysis of thrips (Thysanoptera: Thripidae) diversity in avocado shows the presence of a new species and limitations of using the COI gene for differentiation of two species

Thrips are important pests of avocados causing damage to the fruits, making themunsuitable for exportation. Many of them are quarantine species and their identification isnecessary. Despite their importance, not many studies describe thrips diversity on avocado,especially in Colombia, partly because identification of some of the species is difficult usingclassical taxonomic keys. In this study, 93 adult thrips specimens were collected on avocadoand adventitious dandelion plants from plantations in the department of Antioquia, Colombia. Morphological characters were used to classify 62 of them and all of them were analyzed by PCR amplification and sequencing of cytochrome c oxidase subunit I (COI) gene and internal transcribed spacer (ITS) region. The species identified by morphological features were Frankliniella gardeniae Moulton, F. gossypiana Hood, F. panamensis Hood, Liothrips perseae Watson, Thrips palmi Karny, T. simplex (Morison), T. trehernei Priesner, Microcephalothrips abdominalis (Crawford DL), and Scirtothrips hansoni Mound & Hoddle (Tubulifera), being F. panamensis, M. abdominalis, and S. hansoni reported for the first time on avocado in Colombia. Thrips simplex and T. trehernei were also found on adventitious dandelion plants, but not on avocado. Phylogenetic analysis of COI and ITS sequences showed that most species, except for F. gardeniae and F. gossypiana were mainly identified with the COI gene. Furthermore, FST values obtained between them suggest no genetic differentiation at COI level. The results obtained here contribute to the knowledge of the diversity of thrips species found on the avocado crop in Colombia and are meaningful for pest management.

Fungal Diversity and Composition of the Continental Solar Saltern in Añana Salt Valley (Spain)

The Añana Salt Valley in Spain is an active continental solar saltern formed 220 million years ago. To date, no fungal genomic studies of continental salterns have been published, although DNA metabarcoding has recently expanded researchers’ ability to study microbial community structures. Accordingly, the aim of this present study was to evaluate fungal diversity using the internal transcribed spacer (ITS) metabarcoding at different locations along the saltern (springs, ponds, and groundwater) to describe the fungal community of this saline environment. A total of 380 fungal genera were detected. The ubiquity of Saccharomyces was observed in the saltern, although other halotolerant and halophilic fungi like Wallemia, Cladosporium, and Trimmatostroma were also detected. Most of the fungi observed in the saltern were saprotrophs. The fungal distribution appeared to be influenced by surrounding conditions, such as the plant and soil contact, cereal fields, and vineyards of this agricultural region.