Abundant Genetic Diversity and Extensive Differentiation among Geographic Populations of the Citrus Pathogen Diaporthe citri in Southern China

High species diversity in Diaporthe associated with citrus diseases in China

Species in Diaporthe have broad host ranges and cosmopolitan geographic distributions, occurring as endophytes, saprobes and plant pathogens. Previous studies have indicated that many Diaporthe species are associated with Citrus. To further determine the diversity of Diaporthe species associated with citrus diseases in China, we conducted extensive surveys in major citrus-producing areas from 2017-2020. Diseased tissues were collected from leaves, fruits, twigs, branches and trunks showing a range of symptoms including melanose, dieback, gummosis, wood decay and canker. Based on phylogenetic comparisons of DNA sequences of the internal transcribed spacer regions (ITS), calmodulin (cal), histone H3 (his3), translation elongation factor 1-alpha (tef1) and beta-tubulin (tub2), 393 isolates from 10 provinces were identified as belonging to 36 species of Diaporthe, including 32 known species, namely D. apiculata, D. biconispora, D. biguttulata, D. caryae, D. citri, D. citriasiana, D. compacta, D. discoidispora, D. endophytica, D. eres, D. fusicola, D. fulvicolor, D. guangxiensis, D. hongkongensis, D. hubeiensis, D. limonicola, D. litchii, D. novem, D. passifloricola, D. penetriteum, D. pescicola, D. pometiae, D. sackstonii, D. sennicola, D. sojae, D. spinosa, D. subclavata, D. tectonae, D. tibetensis, D. unshiuensis, D. velutina and D. xishuangbanica, and four new species, namely D. gammata, D. jishouensis, D. ruiliensis and D. sexualispora. Among the 32 known species, 14 are reported for the first time on Citrus, and two are newly reported from China. Among the 36 species, D. citri was the dominant species as exemplified by its high frequency of isolation and virulence. Pathogenicity tests indicated that most Diaporthe species obtained in this study were weakly aggressive or non-pathogenic to the tested citrus varieties. Only D. citri produced the longest lesion lengths on citrus shoots and induced melanose on citrus leaves. These results further demonstrated that a rich diversity of Diaporthe species occupy Citrus, but only a few species are harmful and D. citri is the main pathogen for Citrus in China. The present study provides a basis from which targeted monitoring, prevention and control measures can be developed. Citation: Xiao XE, Liu YD, Zheng F, et al. 2023. High species diversity in Diaporthe associated with citrus diseases in China. Persoonia 51: 229-256. doi: 10.3767/persoonia.2023.51.06.

Clonal Expansion in Multiple Phyllosticta Species Causing Citrus Black Spot or Similar Symptoms in China

Phyllosticta spp. are important pathogens of citrus plants. Several Phyllosticta species associated with Citrus species grown in China have been reported; however, the relative prevalences of individual species and the distributions of their genotypes among host Citrus species remain largely unknown. In this study, we conducted an extensive survey of Phyllosticta species across 11 citrus-producing provinces in southern China. From fruits and leaves with black spots or black-spot-like symptoms, a total of 461 Phyllosticta strains were isolated. Based on molecular (ITS, actA, tef1, gapdh, LSU, and rpb2 sequences) and morphological data, the strains were systematically identified as belonging to five species: P. capitalensis, P. citrichinaensis, P. citriasiana, P. citricarpa, and P. paracitricarpa. To further understand intraspecific genetic diversity and relationships, strains of five species from different geographic and host sources were analyzed based on the multilocus sequence data. Our population genetic analyses revealed that all five Phyllosticta species on citrus showed evidence for clonal dispersals within and among geographic regions. In addition, pathogenicity tests using representative strains showed that all five species can cause disease on the tested Citrus spp. We discuss the implications of our results for the control and management of Citrus Black Spot and related diseases.

Identification of novel SSR markers for predicting the geographic origin of fungus Schizophyllum commune Fr

The fungus Schizophyllum commune is a cosmopolitan basidiomycete, which is popular as an edible, medical mushroom. It causes wood rot and often used as a model object in research. In this study, we analyzed thirty-two genomes of S. commune strains from the NCBI database and designed forty-seven unique SSR DNA markers. The detailed analysis revealed the enrichment of the S. commune genome for CG, GC, CTC, GAG, and TCG motifs. Principal components analysis confirmed the effectiveness of novel SSR DNA markers that preserve the initial heterogeneity of populations. The construction of a network between strains showed single one at a maximum similarity of 38%, and increasing the similarity to 55% breaks the linkage between large groups while separating two new groups containing strains of the population Ru and test cultures S. commune. The amplicons' presence was identified as a sufficient sign of relation of the culture to a specific population. Testing the novel SSR markers allowed to establish a clear delimitation of all groups by geographic location and to differentiate the H4-8 (GCA_000143185.1) strain from the USA population. This research is the basis for the further analysis of S. commune populations and improvement of approaches to determine its genetic diversity.

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.

Is Natural Population of Candida tropicalis Sexual, Parasexual, and/or Asexual?

Candida tropicalis is one of the most common opportunistic yeast pathogens of humans, especially prevalent in tropical and subtropical regions. This yeast has broad ecological distributions, can be found in both terrestrial and aquatic ecosystems, including being associated with a diversity of trees, animals, and humans. Evolutionary theory predicts that organisms thriving in diverse ecological niches likely have efficient mechanisms to generate genetic diversity in nature. Indeed, abundant genetic variations have been reported in natural populations (both environmental and clinical) of C. tropicalis. However, at present, our understanding on how genetic diversity is generated in natural C. tropicalis population remains controversial. In this paper, I review the current understanding on the potential modes of reproduction in C. tropicalis. I describe expectations of the three modes of reproduction (sexual, parasexual, and asexual) and compare them with the observed genotypic variations in natural populations. Though sexual and parasexual reproduction cannot be excluded, the analyses suggest asexual reproduction alone could explain all the observations reported so far. The results here have implications for understanding the evolution and epidemiology of C. tropicalis and other related human fungal pathogens.