Variation in Botryosphaeriaceae from Eucalyptus plantations in YunNan Province in southwestern China across a climatic gradient

Diversity of Calonectria species from leaves and soils in diseased southern China Eucalyptus plantation

Calonectria leaf blight (CLB) is one of the best-known diseases of Eucalyptus spp., particularly in Asia and South America. Recently, typical symptoms of leaf and shoot blight caused by Calonectria spp. Were observed in a Eucalyptus plantation in the YunNan Province of southwestern China. Isolations were made from diseased leaves and top soil collected below the diseased trees to determine the causal agent of the disease and to consider the distribution characteristics of the Calonectria species. This resulted in 417 isolates, of which 228 were from leaves and 189 were from soil. Based on comparisons of DNA sequences for the act (actin), cmdA (calmodulin), his3 (histone H3), rpb2 (the second largest subunit of RNA polymerase), tef1 (translation elongation factor 1-alpha) and tub2 (β-tubulin) gene regions, as well as morphological characteristics, 11 Calonectria species were identified. These included Calonectria aciculata (0.7 %), Ca. colhounii (1.2 %), Ca. eucalypti (10.6 %) and Ca. honghensis (43.2 %) in the Ca. colhounii species complex, and Ca. aconidialis (15.3 %), Ca. asiatica (9.8 %), Ca. hongkongensis (1.0 %), Ca. ilicicola (6.0 %), Ca. kyotensis (0.5 %), and Ca. yunnanensis (11.3 %) in the Ca. kyotensis species complex. In addition, a novel species, accounting for 0.5 % of the isolates, was discovered and is described here as Ca. dianii sp. nov. in the Ca colhounii species complex. Most (99.1 %) of the isolates collected from the leaves resided in the Ca. colhounii species complex and a majority (95.8 %) of those from the soils were in Ca. kyotensis species complex. These results suggest that Calonectria spp. in the Ca. colhounii species complex infecting leaves might be adapted to that niche and that those in the Ca. kyotensis species complex are better adapted to a soil habitat.

Discovery of Botryosphaeria eucalypti sp. nov. from blighted Eucalyptus leaves in India

Eucalyptus spp. are undoubtedly one of the most favored plantation trees globally. Accurately identifying Eucalyptus pathogens is therefore crucial for timely disease prevention and control. Recently, symptoms of a leaf blight disease were observed on Eucalyptus trees in plantations at Jhajjar and Karnal in the state of Haryana, northern India. Asexual morphs resembling the features of the Botryosphaeriaceae were consistently isolated from the symptomatic leaves. Morphological features coupled with DNA sequence analysis confirmed a novel species, which is described and illustrated here as Botryosphaeria eucalypti sp. nov. Conidia of the new taxon are longer and wider than those of its phylogenetic neighbors. A distinct phylogenetic position for the new taxon was established through combined analysis of the internal transcribed spacer (ITS), partial translation elongation factor-1α (tef1) and partial β-tubulin (tub2) regions. Recombination analysis provided additional support for the new species hypothesis. The pathogenicity of the novel species was proved on Eucalyptus leaves, and Koch's postulates were fulfilled. The discovery of new Botryosphaeria species is important because it will help in understanding the species diversity, host range, possible threats and disease control in the long run.

Pezizomycotina species associated with rotten plant materials in Guizhou Province, China

Nine Pezizomycotina strains were isolated from rotten dead branches and leaves collected from Guizhou Province. To obtain their accurate taxonomic placement, we provided the morphological characteristics of conidiophore cells and conidia. Phylogenetic relationships, based on ITS, rpb2, SSU, LSU and tub2 gene sequences, confirmed our strains represented three novel species, Peglioniafalcata, Neoascochytapseudofusiformis and Neomicrosphaeropsiscylindrica. Peglioniafalcata produced falcate conidia and Neoa.pseudofusiformis generated fusiform conidia, while Neom.cylindrica possessed cylindrical conidia. The phylogenetic results also supported them as novel taxa. All the new species in the present study were found as saprophytic on forest litter with high rainfall, which suggest they may have a certain effect on nutrient decomposition and redistribution in forest ecosystems. Thus, it opened a way for further research on related ecological roles and their application production.

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.

Botryosphaerialean fungi associated with woody oil plants cultivated in Sichuan Province, China

Woody oil plants are important economic trees which are widely cultivated and distributed throughout China. Surveys conducted during 2020 and 2021 on several woody oil plantations from five regions of Sichuan Province, China, revealed a high diversity of Botryosphaerialean fungi. The identification of 50 botryosphaeriaceous isolates was carried out based on both morphology and multi-gene phylogenetic analysis of internal transcribed spacer region (ITS), translation elongation factor 1-alpha gene (tef1) and β-tubulin gene (tub2). This allowed the identification of twelve previously known Botryosphaeriales species: Aplosporellaprunicola, A.ginkgonis, Barriopsistectonae, Botryosphaeriadothidea, Bo.fabicerciana, Diplodiamutila, Di.seriata, Dothiorellasarmentorum, Neofusicoccumparvum, Sardiniellaguizhouensis, Sphaeropsiscitrigena, and Sp.guizhouensis, and four novel species belonging to the genera Diplodia and Dothiorella, viz. Di.acerigena, Di.pistaciicola, Do.camelliae and Do.zanthoxyli. The dominant species isolated across the surveyed regions were Botryosphaeriadothidea, Sardiniellaguizhouensis and Diplodiamutila, representing 20%, 14% and 12% of the total isolates, respectively. In addition, most isolates were obtained from Pistaciachinensis (14 isolates), followed by Camelliaoleifera (10 isolates). The present study enhances the understanding of Botryosphaeriales species diversity on woody oil plants in Sichuan Province, China.

Characterization of Pseudofusicoccum Species from Diseased Plantation-Grown Acacia mangium, Eucalyptus spp., and Pinus massoniana in Southern China

Fungi from Pseudofusicoccum (Phyllostictaceae, Botryosphaeriales) have been reported as pathogens, endophytes, or saprophytes from various woody plants in different countries. Recently, Botryosphaeriales isolates were obtained from the dead twigs of Acacia mangium, Eucalyptus spp., Pinus massoniana, and Cunninghamia lanceolata in Guangdong, Guangxi, Hainan, and Fujian Provinces in southern China. This study aimed to understand the diversity, distribution, and virulence of these Pseudofusicoccum species on these trees. A total of 126 Pseudofusicoccum isolates were obtained, and the incidences of Pseudofusicoccum (percentage of trees that yielded Pseudofusicoccum) on A. mangium, P. massoniana, Eucalyptus spp., and C. lanceolata were 21%, 2.6%, 0.5%, and 0%, respectively. Based on the internal transcribed spacer (ITS), translation elongation factor 1-alpha (tef1), and β-tubulin (tub2) loci, 75% of the total isolates were identified as P. kimberleyense, and the remaining isolates were identified as P. violaceum. For P. kimberleyense, the majority of isolates (83%) were from A. mangium, and the rest were from P. massoniana (14%) and Eucalyptus spp. (3%). Similarly, the proportion of isolates of P. violaceum from A. mangium, P. massoniana, and Eucalyptus spp. were 84%, 13%, and 3%, respectively. Inoculation trials showed that the two species produced expected lesions on the tested seedlings of A. mangium, E. urophylla × E. grandis, and P. elliottii. This study provides fundamental information on Pseudofusicoccum associated with diseases in main plantations in southern China.

Neofusicoccum cryptomeriae sp. nov. and N. parvum Cause Stem Basal Canker of Cryptomeria japonica in China

Cryptomeria japonica D. Don is a coniferous tree species widely grown in southern China for its high ornamental value. Recently, during disease surveys in China, a symptom of dieback occurred on C. japonica in Nanjing, Jiangsu Province, China. A total of 130 trees were surveyed and more than 90% showed the same symptom. The crowns of affected trees were brown when viewing from a distance, and the bark showed no difference from the healthy ones. In this study, 157 isolates were isolated from the 3 affected plants of C. japonica, and based on the living culture on PDA, the fungal isolates were preliminarily divided into 6 groups. Thirteen representative isolates were selected for the pathogenicity test, and seven of them showed obvious pathogenicity on C. japonica, causing stem basal canker. These isolates were identified based on comparisons of the DNA sequences of the internal transcribed spacer regions (ITS), partial translation elongation factor 1-alpha (tef1), β-tubulin (tub2), and DNA-directed RNA polymerase II subunit (rpb2) and combined with their morphological characteristics. Results showed that these seven isolates belong to two taxa in Neofusicoccum, including a species new to science. The new species, Neofusicoccum cryptomeriae, was hereby described and illustrated. The other species was N. parvum. Both species were pathogens of stem basal canker of Cryptomeria japonica.

Isolation, molecular characterization and first report of Dothiorella gregaria associated with fruit rot of walnuts of Jammu and Kashmir, India

Walnuts are known for their high levels of antioxidants, which are linked to various health benefits. However, challenges related to distribution and storage, as well as the risk of fungal infections, can affect the quality of walnut kernels. Fungal pathogens from the Botryosphaeriaceae family, including Dothiorella species and Diplodia species, can damage fruit and reduce its antioxidant content. To comprehend the cause of fruit rot in walnuts, Dothiorella gregaria isolates were studied using polyphasic methods, including multiple gene sequences and morphological identification, as well as analysis of polyphenol content and pathogenicity. The walnuts kernels purchased from market places of Jammu and Kashmir (J&K), India were observed to be affected by Dothiorella gregaria species causing the quality detoriation and decrease in polyphenol content thus undeniably with decreased antioxidant properties. D. gregaria Infected walnut kernels were having some brown and black spots and some were having white mycelial growth and however, most samples were asymptomatic. Pathogenicity testing revealed that the pathogen was able to develop all the symptoms under experimental conditions and the reisolated pathogen was morphologically similar to D. gregaria. The samples infected with this pathogen showed considerable decrease in polyphenol content, 10.9 ± 2.66 mgGAE/g (mean ± standard deviation) thus decreased antioxidant quality as compared to the samples which showed zero incidence of this pathogen, 52.50 ± 4.27 mgGAE/g (mean ± standard deviation). Furthermore, the pathogen was studied using polyphasic approach involving morphological, molecular and phylogenetic analysis. Combined nucleotide dataset of nuclear ribosomal ITS and tef1-α revealed that Dothiorella gregaria (NY6) formed a clade with Dothiorlla iberica (MAEC33), Dothiorella sarmentorium (MAEC28) and Dothiorella iberica (CAA905) strains with 83% bootstrap support. Besides, we observed six nucleotide changes, four were insertions or deletions and two were substitutions in the 502-bp region of the ITS rRNA gene when we compared our isolate to the most equivalent sequences submitted to NCBI GenBank. This is the first report of Dothiorella gregaria affecting walnuts purchased from various markets in J&K, India, causing fruit rot in walnuts after harvest. Given that local farmers store and export walnuts, it could pose an emerging threat to their livelihood. Thus, creating post-harvesting interventions for D. gregaria and knowing more about the fruit rot in walnuts can be benefited from morphological and molecular identification using several gene loci, genetic variability in the ITS rRNA gene, and total phenol analysis.

Re-Evaluating Botryosphaeriales: Ancestral State Reconstructions of Selected Characters and Evolution of Nutritional Modes

Botryosphaeriales (Dothideomycetes, Ascomycota) occur in a wide range of habitats as endophytes, saprobes, and pathogens. The order Botryosphaeriales has not been subjected to evaluation since 2019 by Phillips and co-authors using phylogenetic and evolutionary analyses. Subsequently, many studies introduced novel taxa into the order and revised several families separately. In addition, no ancestral character studies have been conducted for this order. Therefore, in this study, we re-evaluated the character evolution and taxonomic placements of Botryosphaeriales species based on ancestral character evolution, divergence time estimation, and phylogenetic relationships, including all the novel taxa that have been introduced so far. Maximum likelihood, maximum parsimony, and Bayesian inference analyses were conducted on a combined LSU and ITS sequence alignment. Ancestral state reconstruction was carried out for conidial colour, septation, and nutritional mode. Divergence times estimates revealed that Botryosphaeriales originated around 109 Mya in the early epoch of the Cretaceous period. All six families in Botryosphaeriales evolved in the late epoch of the Cretaceous period (66-100 Mya), during which Angiosperms also appeared, rapidly diversified and became dominant on land. Families of Botryosphaeriales diversified during the Paleogene and Neogene periods in the Cenozoic era. The order comprises the families Aplosporellaceae, Botryosphaeriaceae, Melanopsaceae, Phyllostictaceae, Planistromellaceae and Saccharataceae. Furthermore, current study assessed two hypotheses; the first one being "All Botryosphaeriales species originated as endophytes and then switched into saprobes when their hosts died or into pathogens when their hosts were under stress"; the second hypothesis states that "There is a link between the conidial colour and nutritional mode in botryosphaerialean taxa". Ancestral state reconstruction and nutritional mode analyses revealed a pathogenic/saprobic nutritional mode as the ancestral character. However, we could not provide strong evidence for the first hypothesis mainly due to the significantly low number of studies reporting the endophytic botryosphaerialean taxa. Results also showed that hyaline and aseptate conidia were ancestral characters in Botryosphaeriales and supported the relationship between conidial pigmentation and the pathogenicity of Botryosphaeriales species.

Taxonomy and Phylogeny of Fungi Associated with Mangifera indica from Yunnan, China

During investigations of saprobic fungi associated with mango (Mangifera indica) in Baoshan and Honghe of Yunnan Province (China), fungal taxa belonging to the orders Botryosphaeriales, Calosphaeriales, Chaetothyriales, Diaporthales, and Xylariales were recorded. Morphological examinations coupled with phylogenetic analyses of multigene sequences (ITS, LSU, SSU, tef1-α, rpb1, rpb2, β-tubulin and CAL) were used to identify the fungal taxa. A new genus viz. Mangifericola, four new species viz. Cyphellophora hongheensis, Diaporthe hongheensis, Hypoxylon hongheensis, and Mangifericola hongheensis, four new host and geographical records viz. Aplosporella artocarpi, Hypomontagnella monticulosa, Paraeutypella citricola and Pleurostoma ootheca, and two new collections of Lasiodiplodia are reported.

Two new Botryosphaeria (Botryosphaeriales, Botryosphaeriaceae) species in China

Five ascomycetous strains were isolated from dead branches and leaves of Salix (Salicaceae) and Osmanthusfragrans (Oleaceae), respectively. BLAST searches with ITS sequences in GenBank suggested a high degree of similarity to Botryosphaeriadothidea. To accurately identify these strains, we further analysed their morphological characteristics of asci, ascospores, all conidiophore cells and conidia. Phylogenetic relationships, based on ITS, rpb2, tef1 and tub2 gene sequences, confirmed our strains represented two novel species, which are introduced here as B.salicicola and B.osmanthuse spp. nov.

Diversity of Botryosphaeriaceae and Diaporthe Species Associated with Postharvest Apple Fruit Decay in Serbia

Family Botryosphaeriaceae and the genus Diaporthe (family Diaporthaceae) represent diverse groups of plant pathogens, which include causal agents of leaf spot, shoot blight, branch and stem cankers, dieback, and pre- and postharvest apple fruit decay. Apple fruit with symptoms of light to dark brown decay were collected during and after harvest from 2016 to 2018. Thirty selected isolates, on which pathogenicity was confirmed, were identified and characterized based on multilocus phylogeny and morphology. Five species from the family Botryosphaeriaceae and two from the genus Diaporthe (fam. Diaporthaceae) were discovered. The most commonly isolated was Diplodia seriata followed by Botryosphaeria dothidea. In this work, Diaporthe rudis is described as a new postharvest pathogen of apple fruit. Diplodia bulgarica, Diplodia sapinea, Neofusicoccum yunnanense, and Diaporthe eres are initially described as postharvest apple and D. sapinea as postharvest quince and medlar fruit pathogens in Serbia. Because species of the family Botryosphaeriaceae and the genus Diaporthe are known to cause other diseases on their hosts, have an endophytic nature, and have a wide host range, findings from this study imply that they may become a new challenge for successful fruit production.

https://botryosphaeriales.org/, an online platform for up-to-date classification and account of taxa of Botryosphaeriales

Fungi are eukaryotes that inhabit various ecosystems worldwide and have a decomposing effect that other organisms cannot replace. Fungi are divided into two main groups depending on how their sexual spores are formed, viz. Ascomycota and Basidiomycota. The members of Botryosphaeriales (Dothideomycetes, Ascomycota) are ubiquitous. They are pathogenic on a wide range of hosts, causing diverse diseases including dieback, canker, leaf spots and root rots and are also reported as saprobes and endophytes worldwide. As an important fungal group, of which most are plant pathogens, it is necessary to organize data and information on Botryosphaeriales so that scientific literature can be used effectively. For this purpose, a new website, https://botryosphaeriales.org is established to gather all published data together with updates on the present taxonomy of Botryosphaeriales. The website consists of an easy-to-operate searching system and provides an up-to-date classification together with accounts of Botryosphaeriales taxa, including colour illustrations, descriptions, notes and numbers of species in each genus, as well as their classification. Thus, readers will be able to obtain information on botryosphaerialean taxa through this platform. Database URL: https://botryosphaeriales.org/.

Novel saprobic Hermatomyces species (Hermatomycetaceae, Pleosporales) from China (Yunnan Province) and Thailand

During our survey of the diversity of woody litter fungi in China and Thailand, three Hermatomyces species were collected from dead woody twigs of Dipterocarpus sp. (Dipterocarpaceae) and Ehretiaacuminata (Boraginaceae). Both morphology and multigene analyses revealed two taxa as new species (Hermatomycesturbinatus and H.jinghaensis) and the remaining collections as new records of H.sphaericus. Hermatomycesturbinatus is characterized by 1) dimorphic conidia, having circular to oval lenticular conidia and 2) turbinate conidia consisting of two columns with two septa composed of 2–3 cells in each column. Hermatomycesjinghaensis is characterized by dimorphic conidia, having circular to oval lenticular conidia and clavate or subcylindrical to cylindrical conidia and consisting of one or two columns with 6–8 cells in each column. Phylogenetic analyses of combined LSU, ITS, tub2, tef1-α and rpb2 sequence data supports the placement of these new taxa within Hermatomycetaceae with high statistical support.

Botryosphaeria Dothidea and Neofusicoccum Yunnanense Causing Canker and Die-Back of Sequoiadendron Giganteum in Croatia

Sequoiadendron giganteum Lindl. [Buchholz] is a long-lived tree species endemic to the Sierra Nevada Mountains in California. Due to its massive size and beauty, S. giganteum is a popular ornamental tree planted in many parts of the world, including Europe. Since 2017, scattered branch die-back has been observed on S. giganteum trees in Zagreb, Croatia. Other symptoms included resinous branch cankers, reddish-brown discoloration of the sapwood and, in severe cases, crown die-back. Branches showing symptoms of die-back and cankers were collected from six S. giganteum trees in Zagreb and the aim of this study was to identify the causal agent of the disease. The constantly isolated fungi were identified using morphology and phylogenetic analyses based on the internal transcribed spacer (ITS) of the ribosomal DNA (rDNA), and partial sequencing of two housekeeping genes, i.e., translation elongation factor 1-α (TEF 1-α), and β tubulin 2 (TUB2). The fungi were identified as Botryosphaeria dothidea (Moug.) Ces. and De Not. and Neofusicoccum yunnanense G.Q. Li & S.F. Chen. The pathogenicity test was conducted in a plant growth chamber on S. giganteum seedlings and revealed that N. yunnanense was more aggressive compared to B. dothidea. N. yunnanense was able to reproduce symptoms of canker and die-back and kill plants seven weeks after inoculation whereas B. dothidea produced cankers. To the best of our knowledge, this is the first report of B. dothidea and N. yunnanense causing canker and die-back disease of S. giganteum in Croatia. It is also the first record on the identity and pathogenicity of any fungal species associated with S. giganteum in this country. The study expended the known host range of N. yunnanense to include S. giganteum, which is a valuable ornamental tree in Croatian landscapes. Disease management strategies should be developed to mitigate or reduce the impact of the disease.

Genetic Diversity and Pathogenicity of Botryosphaeriaceae Species Associated with Symptomatic Citrus Plants in Europe

This study represents the first survey studying the occurrence, genetic diversity, and pathogenicity of Botryosphaeriaceae species associated with symptomatic citrus species in citrus-production areas in five European countries. Based on morphological features and phylogenetic analyses of internal transcribed spacer (ITS) of nuclear ribosomal DNA (nrDNA), translation elongation factor 1-alpha (TEF1) and β-tubulin (TUB2) genes, nine species were identified as belonging to the genera Diplodia, Dothiorella, Lasiodiplodia, and Neofusicoccum. Isolates of Neofusicoccum parvum and Diplodia pseudoseriata were the most frequently detected, while Dothiorella viticola had the widest distribution, occurring in four of the five countries sampled. Representative isolates of the nine Botryosphaeriaceae species used in the pathogenicity tests caused similar symptoms to those observed in nature. Isolates assayed were all re-isolated, thereby fulfilling Koch's postulates. Isolates of Diplodia pseudoseriata and Diplodia olivarum are recorded for the first time on citrus and all species found in our study, except N. parvum, are reported for the first time on citrus in Europe.

Species Diversity, Mating Strategy and Pathogenicity of Calonectria Species from Diseased Leaves and Soils in the Eucalyptus Plantation in Southern China

Many Calonectria species are causal agents of diseases on several forestry, agricultural and horticultural crops. Calonectria leaf blight is one of the most important diseases associated with Eucalyptus plantations and nurseries in Asia and South America. Recently, symptoms of leaf rot and leaf blight caused by Calonectria species were observed in a one-year-old Eucalyptus experimental plantation in GuangXi Province, southern China. To better understand the species diversity, mating strategy and pathogenicity of Calonectria species isolated from diseased tissues and soils, diseased leaves and soils under the trees from ten Eucalyptus urophylla hybrid genotypes were collected. Three hundred and sixty-eight Calonectria isolates were obtained from diseased Eucalyptus leaves and soils under these trees, and 245 representative isolates were selected based on the sampling substrates and Eucalyptus genotypes and identified by DNA sequence analyses based on the translation elongation factor 1-alpha (tef1), β-tubulin (tub2), calmodulin (cmdA) and histone H3 (his3) gene regions, as well as a combination of morphological characteristics. These isolates were identified as Calonectria hongkongensis (50.2%), C. pseudoreteaudii (47.4%), C. aconidialis (1.6%), C. reteaudii (0.4%) and C. auriculiformis (0.4%). This is the first report of C. reteaudii and C. auriculiformis occurrence in China. Calonectria pseudoreteaudii was isolated from both Eucalyptus diseased leaves and soils; the other four species were only obtained from soils. MAT1-1-1 and MAT1-2-1 gene amplification and mating type assignment results showed that C. pseudoreteaudii is heterothallic and an asexual cycle represents the primary reproductive mode, C. reteaudii and C. auriculiformis are likely to be heterothallic and C. hongkongensis and C. aconidialis are homothallic. Based on the genetic diversity comparisons for C. pseudoreteaudii isolates from diseased leaves and soils, we hypothesize that C. pseudoreteaudii in soils was spread from diseased leaves. Both the mycelia plug and conidia suspension inoculations indicated that all five Calonectria species were pathogenic to the two Eucalyptus genotypes tested and the tolerance of the two genotypes differed. It is necessary to understand the ecological niche and epidemiological characteristics of these Calonectria species and to select disease resistant Eucalyptus genotypes in southern China in the future.