Multigene Phylogenetic Analyses Research Articles

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.

Contributions to the taxonomy of the mugilid genus Chelon Artedi (Teleostei: Mugilidae), with a major review of the status of C. persicus Senou, Randall & Okiyama, 1995

New data based on multigene phylogenetic analyses using the COI, 16S, and cytb genes and subsequent molecular species delimitation revealed that the mugilid genus Chelon contains 11 species. Of these, two species, Chelon sp. A and Chelon sp. B, remained unidentified in previous studies. While Chelon sp. B seemingly is a close relative to C. dumerili (Steindachner, 1870), no more detailed information were provided for Chelon sp. A which is present along the east coast of South Africa. Genetic analyses performed in this study, revealed that specimens from the Arabian/Persian Gulf and the Red Sea are nested within one genetic lineage alongside Chelon sp. A. Morphological, morphometric, and meristic analyses of specimens from all three areas demonstrated that they belong to Chelon persicus Senou, Randall & Okyiama, 1995. Chelon persicus was originally described in the genus Chelon but was later placed either in the genus Liza or Planiliza. However, results presented herein confirm its placement in Chelon and its distribution range is extended in the Western Indian Ocean from the type locality (Arabian/Persian Gulf) west to the Red Sea and south to South Africa. Further, the uncertain validity of the recently described Chelon caeruleus Deef, 2018 from the Mediterranean Sea and a previously proposed generic character distinguishing Chelon from Planiliza and Parachelon, the shape of the paired postzygapophyses of the second vertebra, are briefly discussed.

Morphology, molecular phylogenetics, and DNA barcoding revealed a new unusual species of the aphid genus Pleotrichophorus from the USA (Insecta, Hemiptera: Aphididae).

Here, we present the descriptions of a new aphid species in the genus Pleotrichophorus Brner, 1930 (Hemiptera: Aphididae: Macrosiphini), found by Kenneth L. Hibbard, inspection supervisor for the Florida Department of Agriculture and Consumer Services, Division of Plant Industry. It is associated with Euthamia graminifolia (L.) Nutt. (Asteraceae) a native plant species in Florida, USA. Apterous and alate viviparous and oviparous females of Pleotrichophorus blackmani sp. n. are described and illustrated using light and scanning electron microscopy (SEM). SEM images of apterous viviparous female of Pleotrichophorus glandulosus (Kaltenbach, 1846), type species of the genus Pleotrichophorus, are given for the first time. Taxonomic notes are given, and an updated key to the apterae of the Euthamia-feeding aphids is provided. A multigene phylogenetic analyses of two New World Pleotrichophorus species places the genus in the tribe Macrosiphini sensu stricto. Pleotrichophorus glandulosus, the type species of the genus, was described from Germany. European specimens of P. glandulosus from France had similar molecular sequences to both Florida species, strongly suggesting that the new species belongs in Pleotrichophorus. COI and gnd sequence data indicate that P. blackmani sp. n. can be identified reliably by DNA barcodes.

Characterization of Colletotrichum Isolates from Strawberry and Other Hosts with Reference to Cross-Inoculation Potential.

Colletotrichum is an important phytopathogenic fungus that causes anthracnose disease in diverse agronomically important tropical food crops. Accurate pathogen identification is critical for early diagnosis and efficient management of anthracnose. ITS is not a reliable marker for this fungal genus due to its failure to phylogenetically resolve cryptic species. In this study, 36 Colletotrichum isolates belonging to the Acutatum, Boninense and Gloeosporioides species complexes were characterized using multigene phylogenetic analyses, morphology and pathogenicity assays. Additionally, the cross-inoculation potential of a representative subset of isolates was evaluated revealing that cross-infection potential is possible among the isolates belonging to the same species complex.

Madagascaromyces cannae sp. nov. (Mycosphaerellaceae) on Canna indica (Cannaceae) from Guangdong, China

Microfungi associated with Cannaceae are distributed in tropical and subtropical regions. Even though many fungal taxa have been reported from Cannaceae hosts, Mycospharellaceae on Canna indica are less studied. In this study, a saprobic Mycosphaerellaceae species was isolated on C. indica, from Guangzhou, Guangdong province, China. To identify the species, morphological characteristics and phylogenetic analysis of LSU, ITS and rpb2 were employed. Based on multi-gene phylogenetic analyses and morphological comparisons, we introduce our collection as a new species, Madagascaromyces cannae. The novel species is characterized by the septate, pale brown conidiophores, pale brown, terminal and lateral conidiogenous cells and pale brown, clavate, guttulate conidia with 0–6 septa. In addition, a detailed comparison of morphological characters of Madagascaromyces species is provided. To our knowledge, this is the first report of a Madagascaromyces species associated with C. indica in China. Our collection will be an addition to the knowledge of fungi associated with Cannaceae.

Coprinus leucostictus Rediscovered after a Century, Epitypified, and Its Generic Position in Hausknechtia Resolved by Multigene Phylogenetic Analysis of Psathyrellaceae

About a century after the first finding in northern Vietnam (1908), Coprinus leucostictus is rediscovered on 12 localities in southern India and southern to southeastern China, growing in evergreen subtropical or tropical forests. It is morphologically a rather unique species with coprinoid basidiomata, strongly branched and diverticulate veil hyphae, and a hymeniderm pileipellis. The BLAST search of ITS and tef-1α sequences showed its close relationship to Hausknechtia floriformis, which is not clear based on morphological characters. Multigene phylogenetic analysis of a concatenated dataset of ITS, LSU, tef-1α, and β-tubulin sequences, revealed C. leucostictus and H. floriformis as separate, but sister species. Molecular phylogenetic relationships within the family Psathyrellaceae (including 17 genera) are presented in the phylogram. The genera Hausknechtia and Candolleomyces formed two well-supported lineages and were recovered as a monophyletic group. A total of 27 sequences from the genus Hausknechtia were newly generated in this study. Coprinus leucostictus is combined as Hausknechtia leucosticta, its epitype is designated, and the hitherto monotypic genus Hausknechtia is emended. A detailed morphological description of H. leucosticta supplemented with colour photographs and line drawings is provided.

A new species of Coccomyces from oak leaves in Fodingshan National Nature Reserve in China

Specimens of Coccomyces on Quercus (Cyclobalanopsis, Fagaceae) collected from Fodingshan National Nature Reserve in Guizhou Province, China, were identified as a new species and named Coccomyces fodingshanensis. A multi-gene phylogenetic analysis (ITS, LSU, mtSSU) showed that the new species is closely related to Coccomyces sinensis on Camellia species but differed by subrounded ascomata and fagaceous host.

Morphological and phylogenetic characteristics of Phaeomycocentrospora xinjangensis (Pleosporales, Dothideomycetes), a new species from China

The genus Phaeomycocentrospora (Dothidotthiaceae) is a fungal pathogen causing plant leaf spots. A new species, Phaeomycocentrospora xinjangensis sp. nov. is introduced from Xinjiang Uygur Autonomous Region, Northwest China. Multi-gene phylogenetic analyses based on a concatenated ITS, LSU, and ACT sequence dataset were used to confirm the phylogenetic position of the new species. Phaeomycocentrospora xinjangensis can easily be distinguished from the remaining species based on multi-gene phylogenetic analyses coupled with morphological characters. Morphologically, P. xinjangensis differs from other species in the genus by the presence of dark hyphae, dark brown conidiophores, few branched conidiogenous cells. Phylogenetically, our three strains were clustered together and formed a separate subclade with high support values. Moreover, we provided a description, illustrations, and phylogenetic tree for the new species.

Multi-gene phylogeny of North American clear-winged moths (Lepidoptera: Sesiidae): a foundation for future evolutionary study of a speciose mimicry complex.

Sesiids are a diverse group of predominantly diurnal moths, many of which are Batesian mimics of Hymenoptera. However, their diversity and relationships are poorly understood. A multi-gene phylogenetic analysis of 48 North American sesiid species confirmed the traditional taxonomic tribal ranks, demonstrated the paraphyly of Carmenta and Synanthedon with respect to several other genera and ultimately provided minimal phylogenetic resolution within and between North American and European groups. Character support from each gene suggested inconsistency between the phylogenetic signal of the CAD gene and that of the other four genes. However, removal of CAD from subsequent phylogenetic analyses did not substantially change the initial phylogenetic results or return Carmenta and Synanthedon as reciprocally monophyletic, suggesting that it was not impacting the overall phylogenetic signal. The lack of resolution using genes that are typically informative at the species level for other lepidopterans suggests a surprisingly rapid radiation of species in Carmenta/Synanthedon. This group also exhibits a wide range of mimicry strategies and hostplant usage, which could be fertile ground for future study.

Taxonomy and phylogeny of Smaragdinisetamusae sp. nov. and Albifimbriaverrucaria (Hypocreales, Stachybotryaceae) on Musa from Thailand.

Smaragdinisetamusae is introduced as a leaf-based novel saprobic species from Musa. Multi-gene phylogenetic analyses of internal transcribed spacer (ITS), RNA polymerase II second largest subunit (rpb2) and β-tubulin (tub2) data support the taxonomic placement of the new collection in Smaragdiniseta (Hypocreales, Stachybotryaceae). The novel species is characterised by cup-shaped sporodochia covered by numerous peripheral setae and simple hyaline, guttulate conidia produced by the ultimate branches (phialides) of conidiophores. This is the first report of Smaragdiniseta from Thailand and on Musaceae. In addition, we report Albifimbriaverrucaria for the first time from Thailand, based on morpho-molecular evidence.

Lasiodiplodia fici sp. nov., Causing Leaf Spot on Ficus altissima in China.

High temperatures and the seasonality in tropical ecosystems favours plant pathogens, which result in many fungal diseases. Among these, diseases caused by Botryosphaeriaceae species are prominent as dieback, canker and leaf spots. In this research, we isolated one leaf-spot-causing Botryosphaeriaceae species from Ficus altissima leaves, which were collected in Guangzhou, Guangdong Province, China. Isolation and identification of the pathogen were based on morphological and molecular aspects. Based on multigene phylogenetic analysis of combined internal transcribed spacer (ITS), translation elongation factor 1-α gene (tef1) and beta-tubulin gene (tub2), the fungus associated with leaf spots on F. altissima is described as Lasiodiplodia fici, a novel species. Pathogenicity assays were conducted by inoculating the fungus onto detached shoots and plants under controlled environmental conditions. The results revealed that the L. fici isolates can infect the plant tissues under stress conditions by developing disease symptoms on detached shoots within three days. However, when it was inoculated onto the leaves of the host and grown in natural conditions, the progression of the disease was slow. The putative pathogen was re-isolated, and Koch’s assumptions were satisfied. This is the first report of Lasiodiplodia species causing disease on Ficus altissima. Results from the present study will provide additional knowledge on fungal pathogens associated with forest and ornamental plant species.

Species Diversity, Distribution, and Phylogeny of Exophiala with the Addition of Four New Species from Thailand.

The genus Exophiala is an anamorphic ascomycete fungus in the family Herpotrichiellaceae of the order Chaetothyriales. Exophiala species have been classified as polymorphic black yeast-like fungi. Prior to this study, 63 species had been validated, published, and accepted into this genus. Exophiala species are known to be distributed worldwide and have been isolated in various habitats around the world. Several Exophiala species have been identified as potential agents of human and animal mycoses. However, in some studies, Exophiala species have been used in agriculture and biotechnological applications. Here, we provide a brief review of the diversity, distribution, and taxonomy of Exophiala through an overview of the recently published literature. Moreover, four new Exophiala species were isolated from rocks that were collected from natural forests located in northern Thailand. Herein, we introduce these species as E. lamphunensis, E. lapidea, E. saxicola, and E. siamensis. The identification of these species was based on a combination of morphological characteristics and molecular analyses. Multi-gene phylogenetic analyses of a combination of the internal transcribed spacer (ITS) and small subunit (nrSSU) of ribosomal DNA, along with the translation elongation factor (tef), partial β-tubulin (tub), and actin (act) genes support that these four new species are distinct from previously known species of Exophiala. A full description, illustrations, and a phylogenetic tree showing the position of four new species are provided.

Two new species of Craterellus (Cantharellales, Hydnaceae) with veined hymenophore from north-eastern China.

In this contribution to the genus Craterellus in northern China, two new species are introduced: Craterellusconnatus and C.striatus. These species and C.atrobrunneolus, initially described in south-western China, are highly similar and closely related. The species delimitation is molecularly supported by multigene phylogenetic analysis of the nr LSU and tef-1α region. Craterellusconnatus is characterised by its medium-sized basidiomata, greyish-brown and smooth pileus with an off-white margin, the hymenophore with a strongly anastomosing vein, turning khaki upon drying, connate stipe, broad ellipsoid to ellipsoid basidiospores (6.1-7.8 × 4.8-5.9 μm), slender basidia with (2)4-6 sterigmata and the absence of clamp connection. Craterellusstriatus is characterised by its small-sized basidiomata, fibrillose, greyish-brown to yellowish-brown, fully perforated pileus with a brown fringe, the hymenophore with a forking vein, the stipe inflated at the base, broad ellipsoid to ellipsoid basidiospores (6.8-8.0 × 5.1-6.0 μm), 2-6 spored basidia, encrusted hyphae and the absence of clamp connection. Detailed macroscopic and microscopic descriptions, accompanied by illustrations and a taxonomic discussion, are presented. A key to the Chinese Craterellus species is also provided.

Genomic Characteristics and Comparative Genomics Analysis of Parafenestella ontariensis sp. nov.

A new ascomycetous species of Parafenestella was isolated from Acer negundo during the survey of diseased trees in Southern Ontario, Canada. The species is morphologically similar to other taxa of Cucurbitariacea (Pleosporales). The new species is different from the extant species in the morphology of ascospores, culture characteristics and molecular data. The novel species is described as Parafenestella ontariensis sp. nov. based on morphological and multi-gene phylogenetic analyses using a combined set of ITS, LSU, tef1 and tub2 loci. Additionally, the genome of P. ontariensis was sequenced and analyzed. The phylogenomic analysis confirmed the close relationship of the species to the fenestelloid clades of Cucurbitariaceae. The comparative genomics analysis revealed that the species lifestyle appears to be multitrophic (necrotrophic or hemi-biotrophic) with a capability to turn pathogenic on a corresponding plant host.

Additions to microfungi in China: Lentithecium yunnanensis sp. nov.

We describe a new fungal species of the genus Lentithecium, collected from dead culms of Artemisia sp. in Songhua Reservoir at Kunming, Yunnan Province, China. Multi-gene phylogenetic analyses of LSU, ITS, SSU, and tef1-α sequence data showed that our new fungal strain belongs to Lentithecium and is well separated from all other extant species of Lentithecium. Lentithecium yunnanensis sp. nov. is compared with all the extant species by morphological characteristics, culture characteristics, host, and location information and is the first report of Lentithecium from China on Artemisia. A comprehensive description, a color photo plate of microcharacteristics, and a phylogenetic tree to show the position of the new species are provided.

Identification and Characterization of Calonectria Species Associated with Plant Diseases in Southern China.

Calonectria species are important plant pathogens on a wide range of hosts, causing significant losses to plant production worldwide. During our survey on phytopathogenic fungi from 2019 to 2021, diseased samples were collected from various hosts in Guangdong Province, China. In total, 16 Calonectria isolates were obtained from leaf spots, stem blights and root rots of species of Arachis, Cassia, Callistemon, Eucalyptus, Heliconia, Melaleuca and Strelitzia plants. Isolates were identified morphologically, and a multigene phylogenetic analysis of combined partial sequences of calmodulin (cmdA), translation elongation factor 1-alpha (tef1-α) and beta-tubulin (β-tubulin) was performed. These sixteen isolates were further identified as nine Calonectria species, with five new species: Ca. cassiae, Ca. guangdongensis, Ca. melaleucae, Ca. shaoguanensis and Ca. strelitziae, as well as four new records: Ca. aconidialis from Arachis hypogaea, Ca. auriculiformis from Eucalyptus sp., Ca. eucalypti from Callistemon rigidus, and Ca. hongkongensis from Eucalyptus gunnii. Moreover, we provide updated phylogenetic trees for four Calonectria species complexes viz. Ca. colhounii, Ca. cylindrospora, Ca. kyotensis and Ca. reteaudii. Our study is the first comprehensive study on Calonectria species associated with various hosts from subtropical regions in China. Results from the present study will be an addition to the biodiversity of microfungi in South China.

The first record of Metacordyceps neogunnii (Metacordyceps, Clavicipitaceae) isolated from larva of Lepidoptera in Vietnam: morphological, phylogenetic characterization and chemical constituent analysis

An entomopathogenic fungus, specimen DL0091 parasitized on the larvae of Lepidoptera, was collected from Lang Biang Biosphere Reserve, located in Lam Dong Province, Vietnam. The specimen DL0091 has been analyzed to be contained numerous chemical constituents, especially containing adenosine of 634 mg/Kg and cordycepin of 35.2 mg/Kg. Due to containing many bioactive compounds, DL0091 was promised to be a precious natural source that could be applied in fields of medicine and function food for health care. For classification, based on the morphology analysis, it was identified as Metacordyceps neogunnii (Metacordyceps, Clavicipitaceae) sharing the similar characteristics of M. neogunnii T.C. Wen & K.D. Hyde. Morphology of this species differed from Cordyceps neogunnii (Berk.) Berk., by many characteristics, such as the larger stroma of DL0091 (15–130 mm x 2–6 mm), of asci (550–680 μm × 5–8 μm), etc. Additionally, the combined multi-gene phylogenetic analysis, including ITS, Tef and Rpb1, well supported its systematic position in the clade of M. neogunnii, which was used as traditional herb in China and other Asian countries. In summary, DL0091 was identified as M. neogunnii, containing many bioactive compounds, could be used as the medicinal potential in human healthcare.

New Arthrobotrys Nematode-Trapping Species (Orbiliaceae) from Terrestrial Soils and Freshwater Sediments in China.

Arthrobotrys is the most complex genus of Orbiliaceae nematode-trapping fungi. Its members are widely distributed in various habitats worldwide due to their unique nematode-trapping survival strategies. During a survey of nematophagous fungi in Yunnan Province, China, twelve taxa were isolated from terrestrial soil and freshwater sediment habitats and were identified as six new species in Arthrobotrys based on evidence from morphological and multigene (ITS, TEF, and RPB2) phylogenetic analyses. These new species i.e., Arthrobotrys eryuanensis, A. jinpingensis, A. lanpingensis, A. luquanensis, A. shuifuensis, and A. zhaoyangensis are named in recognition of their places of origin. Morphological descriptions, illustrations, taxonomic notes, and a multilocus phylogenetic analysis are provided for all new taxa. In addition, a key to known species in Arthrobotrys is provided, and the inadequacies in the taxonomic study of nematode-trapping fungi are also discussed.

First Report of Postharvest Fruit Rot Disease of Yellow Peach Caused by Diaporthe eres in China.

The yellow peach (Amygdalus persica), is a fruit crop native to China with golden peel and pulp that is of particular interest in the fruit markets. In August of 2021, yellow peaches showing fruit rot symptoms were purchased from a commercial market in Linyi city, Shandong province, China. The symptoms included circular, tan to brown in color, rotten, necrotic lesions, and whitish mycelium mass in the center of the lesions. The infected fruit were surface disinfected with 1% NaClO for 30 s and rinsed with sterile distilled water three times. Diseased tissues from the infected fruits were cut into small segments, aseptically shifted onto potato dextrose agar media containing petri plates and incubated at 25℃ for 5 days. Eight isolates were obtained in total from two isolation experiments. Fungal colonies were initially white, aerial, fluffy at first, and gradually turned brown to gray, with black stromata at maturity. Alpha conidia were aseptate，hyaline，fusiform to ellipsoidal，and ranged in size from 4.16 to 7.76 µm × 1.95 to 3.14 µm (n=30). Beta conidia were aseptate, hyaline, filiform, curved to hamate, and 15.91 to 22.55 µm × 0.82 to 1.66 µm (n=30). The morphological characteristics were consistent with those of Diaporthe species (Gomes et al. 2013). For further identification, a multigene phylogenetic analysis was carried out. The internal transcribed spacer (ITS) region, translation elongation factor 1-α (TEF1-α), histone H3 (HIS), calmodulin (CAL), and β-tubulin (TUB) genes of two representative isolates were amplified by using primers ITS1/ITS4, EF1-728F/EF1-986R, CYLH3F/H3-1b，CAL228F/CAL737R, and Bt2a/Bt2b (Chaisiri et al. 2021), respectively. The sequences were deposited in GenBank (Accession No. OL375154 for ITS; OL406409 for TEF1-α; OL406410 for HIS; OL106407 for CAL; OL406408 for TUB). phylogenetic analyses were conducted using the concatenation of multiple sequences (ITS, TEF1-α, HIS, CAL, TUB) with Maximum Likelihood (ML) in IQtree v1.5.6 (Nguyen et al. 2015). Based on the morphological and phylogenetic characters, the isolates were identified as D. eres. A Pathogenicity test was performed by wound inoculation on harvested fruits of A. persica Variety 'Jinxiu'. Mature and healthy yellow peaches purchased from Shandong, Anhui, and Hunan Provinces in China were surface sterilized with 1% NaClO solution for 1 minute, rinsed with sterile water and dried. Each fruit was wounded with a sterile scalpel creating a 2-3 mm incision on the peel. A 5 mm agar disc with mycelium grown on PDA at 28℃ for 7 days was placed on wound and sealed with parafilm. Sterile PDA plugs were used as controls. Ten fruit were used for each treatment and the assays were repeated three times. Inoculated fruit were placed in sterilized transparent plastic cans containing wet, sterile paper towels. After 5 days of incubation at 25℃, the same rot symptoms were observed on fruits inoculated with mycelium and the control remained symptomless. D. eres was re-isolated from the lesions of inoculated fruits and the pathogen identification was confirmed by molecular analysis, thus fulfilling complete Koch's postulates. Although D. eres was previously reported on peach trees of causing shoot blight (Thomidis and Michailides 2009) and stem canker (Prencipe et al. 2017). To our knowledge, this is the first report of D. eres causing postharvest fruit rot of yellow peach in China and it may lead to considerable economic losses in the peach industry should post-harvest disease management practices not be implemented.

Bambusicolous Fungi in Pleosporales: Introducing Four Novel Taxa and a New Habitat Record for Anastomitrabeculia didymospora.

While conducting a survey of bambusicolous fungi in northern Thailand and southwestern China, several saprobic fungi were collected from dead branches, culms and twigs of bamboos, which were preliminarily identified as species belonging to Pleosporales (Dothideomycetes) based on a morphological approach. Multigene phylogenetic analyses based on ITS, LSU, SSU, rpb2, tef1-α and tub2 demonstrated four novel taxa belonging to the families Parabambusicolaceae, Pyrenochaetopsidaceae and Tetraploasphaeriaceae. Hence, Paramultiseptospora bambusae sp. et gen. nov., Pyrenochaetopsis yunnanensis sp. nov. and Tetraploa bambusae sp. nov. are introduced. In addition, Anastomitrabeculia didymospora found on bamboo twigs in terrestrial habitats is reported for the first time. Detailed morphological descriptions and updated phylogenetic trees of each family are provided herein.