Genetic and Pathogenic Relatedness of Pseudoperonospora cubensis and P. humuli

The most economically important plant pathogens in the genus Pseudoperonospora (family Peronosporaceae) are Pseudoperonospora cubensis and P. humuli, causal agents of downy mildew on cucurbits and hop, respectively. Recently, P. humuli was reduced to a taxonomic synonym of P. cubensis based on internal transcribed spacer (ITS) sequence data and morphological characteristics. Nomenclature has many practical implications for pathogen identification and regulatory considerations; therefore, further clarification of the genetic and pathogenic relatedness of these organisms is needed. Phylogenetic analyses were conducted considering two nuclear and three mitochondrial loci for 21 isolates of P. cubensis and 14 isolates of P. humuli, and all published ITS sequences of the pathogens in GenBank. There was a consistent separation of the majority of the P. humuli isolates and the P. cubensis isolates in nuclear, mitochondrial, and ITS phylogenetic analyses, with the exception of isolates of P. humuli from Humulus japonicus from Korea. The P. cubensis isolates appeared to contain the P. humuli cluster, which may indicate that P. humuli descended from P. cubensis. Host-specificity experiments were conducted with two reportedly universally susceptible hosts of P. cubensis and two hop cultivars highly susceptible to P. humuli. P. cubensis consistently infected the hop cultivars at very low rates, and sporangiophores invariably emerged from necrotic or chlorotic hypersensitive-like lesions. Only a single sporangiophore of P. humuli was observed on a cucurbit plant during the course of the studies. Together, molecular data and host specificity indicate that there are biologically relevant characteristics that differentiate P. cubensis and P. humuli that may be obfuscated if P. humuli were reduced to a taxonomic synonym of P. cubensis. Thus, we recommend retaining the two species names P. cubensis and P. humuli until the species boundaries can be resolved unambiguously.

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A revision of the Leptogium saturninum group in North America

The Lichenologist ◽

10.1017/s0024282916000323 ◽

2016 ◽

Vol 48 (5) ◽

pp. 387-421 ◽

Cited By ~ 6

Author(s):

Daphne F. STONE ◽

James W. HINDS ◽

Frances L. ANDERSON ◽

James C. LENDEMER

Keyword(s):

North American ◽

Morphological Study ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Lower Surface ◽

Molecular Data ◽

The North ◽

Molecular Phylogenetic ◽

Nrits Sequence

AbstractA revision of the North American members of the Leptogium saturninum group (i.e. species with long lower-surface hairs, isidia, and usually smooth upper surface) is presented based on molecular phylogenetic analyses of mtSSU and nrITS sequence data, together with an extensive morphological study. Three species supported by both molecular and morphological characteristics are recognized: L. acadiense sp. nov. (distinguished by granular saturninum-type isidia, medulla composed of irregularly arranged or perpendicular hyphae), L. cookii sp. nov. (distinguished by cylindrical saturninum-type isidia) and L. hirsutum (distinguished by hirsutum-type isidia and medulla composed of loosely intertwined hyphae). One species supported by morphological characteristics, but for which no molecular data could be generated, is also recognized: L. compactum sp. nov. (distinguished by hirsutum-type isidia and medulla composed of tightly packed hyphae). Finally, L. saturninum (distinguished by granular saturninum-type isidia and medulla composed of perpendicular and parallel hyphae) is supported by morphological characteristics but molecular data from geographically diverse populations, including those near the type locality, indicate that the morphologically defined species is paraphyletic. Leptogium burnetiae is excluded from North American based on morphological study of the type. The species are described and illustrated in detail, and are distinguished morphologically by their isidium development, morphology of mature isidia, and pattern of hyphae in the medulla in transverse sections near lobe margins. A key to the members of the L. saturninum group and related species is also presented.

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Additions to Karst Fungi 4: Botryosphaeria spp. associated with woody hosts in Guizhou province, China including B. guttulata sp. nov.

Phytotaxa ◽

10.11646/phytotaxa.454.3.2 ◽

2020 ◽

Vol 454 (3) ◽

pp. 186-202

Author(s):

YA-YA CHEN ◽

ASHA J. DISSANAYAKE ◽

ZUO-YI LIU ◽

JIAN-KUI (JACK) LIU

Keyword(s):

Plant Pathogens ◽

Sequence Data ◽

Morphological Characteristics ◽

Abundant Species ◽

Molecular Data ◽

Nature Reserves ◽

Guizhou Province ◽

Botryosphaeria Dothidea ◽

Wide Range ◽

One New Species

Members of Botryosphaeria encompass important plant pathogens, saprobes and endophytes on a wide range of woody hosts worldwide. Botryosphaeria species are difficult to differentiate due to the overlapping morphological characteristics and the molecular data analyses are necessary recently when species identification is carried out. In this study, 28 Botryosphaeria isolates were obtained from decaying woody hosts in six nature reserves in Guizhou province, China. Based on both morphological characteristics and molecular analysis of combined ITS and tef1-α sequence data, four known species (Botryosphaeria dothidea, B. minutispermatia, B. sinensia and B. wangensis) are identified and one new species B. guttulata is introduced. Botryosphaeria sinensia (32% of the isolates obtained from various hosts) is the abundant species, followed by B. dothidea (28.5% of the isolates), B. guttulata (28.5% of the isolates), B. minutispermatia (7% of the isolates) and B. wangensis (4% of the isolates). These results represent the first study of Botryosphaeria species associated with woody hosts from nature reserves in Guizhou province, China. Our findings indicate that there is a potential of Botryosphaeria species remain to be discovered in this unique landform (Karst formations) in Guizhou province, China.

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Morpho-phylogenetic evidence reveals Lasiodiplodia chiangraiensis sp. nov. (Botryosphaeriaceae) associated with woody hosts in northern Thailand

Phytotaxa ◽

10.11646/phytotaxa.508.2.3 ◽

2021 ◽

Vol 508 (2) ◽

Author(s):

NA WU ◽

ASHA J. DISSANAYAKE ◽

K.W. THILINI CHETHANA ◽

KEVIN D. HYDE ◽

JIAN-KUI LIU

Keyword(s):

New Species ◽

Phylogenetic Tree ◽

Sequence Data ◽

Novel Species ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Molecular Data ◽

Northern Thailand ◽

Data Support ◽

Distinct Lineage

Lasiodiplodia species are commonly as endophytes, saprobes and pathogens in tropics and subtropics. During an investigation of Botryosphaeriaceae in Thailand, two Lasiodiplodia taxa were isolated. Morphological characteristics and phylogenetic analyses based on combined ITS, tef and tub2 sequence data support the establishment of a novel species, Lasiodiplodia chiangraiensis, isolated from woody hosts. Lasiodiplodia chiangraiensis is phylogenetically close to L. iraniensis and L. thailandica, but represents a distinct lineage. The new species could be distinguished from extant Lasiodiplodia species by its mature conidial dimensions. A detailed description and illustration are provided, as well as an updated phylogenetic tree (ITS, tef and tub2) including all species (with available molecular data) of Lasiodiplodia. In addition, the accepted genera in Botryosphaeriaceae based on recent studies are given.

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Affinities of four freshwater putative “Chantransia” stages (Rhodophyta) in Southern China from molecular and morphological data

Phytotaxa ◽

10.11646/phytotaxa.441.1.4 ◽

2020 ◽

Vol 441 (1) ◽

pp. 47-59

Author(s):

JIN-FEN HAN ◽

FANG-RU NAN ◽

JIA FENG ◽

JUN-PING LV ◽

QI LIU ◽

...

Keyword(s):

Yunnan Province ◽

Sequence Data ◽

Southern China ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Morphological Characters ◽

Molecular Data ◽

Morphological Data ◽

Phylogenetic Position ◽

Morphological Description

Four putative “Chantransia” isolates were collected from four locations in Hubei and Yunnan Provinces, China. Morphological analyses were conducted on all isolates. Two specimens (HB26 and YN2) fit the morphological description of A. pygmaea, while the other two isolates (YN1 and YN3) varied in morphology, but were within the circumscription of Audouinella hermannii. Due to the fact that the morphological characters of the “Chantransia” stages of order Batrachospermales and the species of genus Audouinella are too similar to be distinguished, a molecular analysis was performed to clarify the phylogenetic position of these four isolates based on rbcL and psbA sequences. Two “pygmaea” specimens collected from Jiugong Mountain, Hubei Province (HB26) and Shimen Gorge, Yunnan Province (YN2), such as S. jiugongshanensis and S. shimenxiaensis, are proposed primarily based on the DNA sequence data generated in this study. The description of these two new species provides more molecular data for phylogenetic analysis of the genus Sheathia. In addition to these newly described species, the results strongly support that those “hermannii” isolates (YN1 and YN3) collected from Yunnan Province were the “Chantransia” of S. arcuata. However, their gametophyte stages have not been found, meaning that critical diagnostic morphological features were unavailable and molecular methods were the only means for ascertaining their phylogenetic position. Considering the extensive application of the rbcL and psbA genes in phylogenetic analyses of freshwater red algae, we recommend using these two genes to identify species when no morphological characteristics are available.

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Multi-Gene Phylogeny and Morphology Reveal Haplohelminthosporium gen. nov. and Helminthosporiella gen. nov. Associated with Palms in Thailand and A Checklist for Helminthosporium Reported Worldwide

Life ◽

10.3390/life11050454 ◽

2021 ◽

Vol 11 (5) ◽

pp. 454

Author(s):

Sirinapa Konta ◽

Kevin D. Hyde ◽

Samantha C. Karunarathna ◽

Ausana Mapook ◽

Chanokned Senwanna ◽

...

Keyword(s):

New Taxa ◽

Plant Pathogens ◽

New Genus ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Full Description ◽

New Taxon ◽

New Genera ◽

Diverse Range

Palms (Arecaceae) are substrates for a highly diverse range of fungi. Many species are known as saprobes and many are important plant pathogens. Over the course of our studies of micro-fungi from palms in Thailand, two new taxa were discovered. Morphological characteristics and phylogenetic analyses of combined ITS, LSU, SSU, and tef1-α sequence data revealed their taxonomic positions within Massarinaceae. There are currently ten genera identified and accepted in Massarinaceae, with the addition of the two new genera of Haplohelminthosporium and Helminthosporiella, that are introduced in this paper. Each new genus is provided with a full description and notes, and each new taxon is provided with an illustration for the holotype. A list of identified and accepted species of Helminthosporium with morphology, host information, locality, sequence data, and related references of Helminthosporium reported worldwide is provided based on records in Species Fungorum 2021. This work provides a micro-fungi database of Haplohelminthosporium, Helminthosporiella, and Helminthosporium which can be modified and validated as new data come to light.

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Updating species diversity of Colletotrichum, with a phylogenomic overview

Studies in Mycology ◽

10.3114/sim.2022.101.01 ◽

2022 ◽

Author(s):

F. Liu ◽

Z.Y. Ma ◽

L.W. Hou ◽

Y.Z. Diao ◽

W.P. Wu ◽

...

Keyword(s):

Species Diversity ◽

Plant Pathogens ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Single Copy ◽

Molecular Data ◽

Human Pathogens ◽

Species Complexes ◽

Backbone Tree ◽

The Uk

The genus Colletotrichum includes important plant pathogens, endophytes, saprobes and human pathogens. Even though the polyphasic approach has facilitated Colletotrichum species identification, knowledge of the overall species diversity and host distribution is largely incomplete. To address this, we examined 952 Colletotrichum strains isolated from plants representing 322 species from 248 genera, or air and soil samples, from 87 locations in China, as well as 56 strains from Saudi Arabia, Thailand, Turkey, and the UK. Based on morphological characteristics and multi-locus phylogenetic analyses, the strains were assigned to 107 species, including 30 new species described in this paper and 18 new records for China. The currently most comprehensive backbone tree of Colletotrichum, comprising 16 species complexes (including a newly introduced C. bambusicola species complex) and 15 singleton species, is provided. Based on these analyses, 280 species with available molecular data are accepted in this genus, of which 139 have been reported in China, accounting for 49.6 % of the species. Colletotrichum siamense, C. karsti, C. fructicola, C. truncatum, C. fioriniae, and C. gloeosporioides were the most commonly detected species in China, as well as the species with the broadest host range. By contrast, 76 species were currently found to be associated with a single plant species or genus in China. To date, 33 Colletotrichum species have been exclusively reported as endophytes. Furthermore, we generated and assembled whole-genome sequences of the 30 new and a further 18 known species. The most comprehensive genome tree comprising 94 Colletotrichum species based on 1 893 single-copy orthologous genes was hence generated, with all nodes, except four, supported by 100 % bootstrap values. Collectively, this study represents the most comprehensive investigation of Colletotrichum diversity and host occurrence to date, and greatly enhances our understanding of the diversity and phylogenetic relationships in this genus.

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A novel Arabidopsis phyllosphere resident Protomyces sp. and a re-examination of genus Protomyces based on genome sequence data

10.1101/2019.12.13.875955 ◽

2019 ◽

Cited By ~ 1

Author(s):

Kai Wang ◽

Timo Sipilä ◽

Kirk Overmyer

Keyword(s):

Dna Sequences ◽

Plant Pathogens ◽

Sequence Data ◽

Carbon Assimilation ◽

Morphological Characteristics ◽

Nuclear Gene ◽

Molecular Data ◽

Rapid Identification ◽

Phylogenetic Position ◽

Culture Collections

ABSTRACTProtomyces is a genus of yeast-like fungi that is currently defined as plant pathogens of only the Umbelliferae (Apiaceae) and Compositae (Asteraceae) family plants. Many Protomyces species have been proposed; however, there is a lack of molecular data and available specimens for Protomyces spp., just over ten species are officially accepted and only six species are preserved and available in public culture collections for examination. Phylogenetic relationships and species boundaries within this genus remain largely controversial. Recently, we isolated Protomyces strains from wild Arabidopsis thaliana (Arabidopsis), a Brassicaceae family plant only distantly related to the accepted Protomyces hosts. We have previously sequenced the genomes of all the currently public available Protomyces species, together with a strain (SC29) we isolated from the Arabidopsis phyllosphere. Genome-wide phylogenetic analysis suggests that SC29 occupies a unique phylogenetic position in the genus Protomyces. The SC29 genome has low average nucleotide identity values in comparison with other species genomes. As physiological evidence, SC29 has morphological characteristics and carbon assimilation patterns that distinguish it from the other six Protomyces species. Analysis with several nuclear gene phylogenetic markers further confirms SC29 as a novel Protomyces species and suggests the act1 gene DNA sequences can be used together with ITS sequences for the rapid identification of Protomyces species. In our previous study, SC29 could persist on the Arabidopsis phyllosphere in both short term laboratory and overwinter outdoor garden experiments and Protomyces spp. (or OTUs) were found in the Arabidopsis phyllosphere at multiple sites in both Finland and Germany. We conclude that SC29 is a novel Protomyces species isolated from Arabidopsis and propose the name of Protomyces arabidopsidicola sp. nov. Additionally, the genus Protomyces may not be strictly associated with only Compositae or Umbelliferae family host plants, as evidenced by SC29 and Protomyces strains previously isolated from plants in other families. The merging of two Protomyces species found to have high genomic similarity (P. inouyei and P. lactucaedebilis) is also proposed.

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Clathrosporium retortum, a novel aeroaquatic fungus in the Sordariomycetidae (Ascomycota) from Brazil

Phytotaxa ◽

10.11646/phytotaxa.239.1.2 ◽

2015 ◽

Vol 239 (1) ◽

pp. 17

Author(s):

Larissa Bernardino Moro ◽

Gregorio Delgado ◽

Iracema Helena SCHOENLEIN-CRUSIUS

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Type Specimen ◽

Molecular Data ◽

Sao Paulo ◽

São Paulo ◽

Present Fungus ◽

Broad Concept ◽

Morphological And Molecular Data ◽

First Time

Clathrosporium retortum sp. nov., collected on submerged mixed leaf litter samples at Ilha do Cardoso State Park, São Paulo state, Brazil, is described based on morphological and molecular data. The fungus is characterized by forming whitish, dense, subglobose to irregular propagules, hyaline to subhyaline when young, subhyaline to dark brown at maturity, that are formed by densely interwoven conidial filaments with each conidial cell repeatedly branching bilaterally or occasionally unilaterally. Phylogenetic analyses using partial LSU nrDNA sequence data suggest that C. retortum belongs in the Sordariomycetes (Ascomycota) where it forms a well-supported clade with Clohesia corticola in the Sordariomycetidae, but its ordinal or familial placement remains unresolved. Its phylogenetic placement confirms the polyphyletic nature of aeroaquatic fungi like Clathrosporium, as it was distantly related to one available sequence in GenBank named as C. intricatum, the type species, which is phylogenetically related to the Helotiales (Leotiomycetes). However, due to lack of authenticity of the identity of this sequence with the type specimen of C. intricatum, a broad concept of Clathrosporium is tentatively adopted here to accommodate the present fungus instead of introducing a new genus. Beverwykella clathrata, Helicoön septatissimum and Peyronelina glomerulata are recorded for the first time from Brazil. Cancellidium applanatum and Candelabrum brocchiatum are new records for the state of São Paulo.

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Morphology and phylogenetic analyses reveal Montagnula puerensis sp. nov. (Didymosphaeriaceae, Pleosporales) from southwest China

Phytotaxa ◽

10.11646/phytotaxa.514.1.1 ◽

2021 ◽

Vol 514 (1) ◽

pp. 1-25

Author(s):

TIANYE DU ◽

KEVIN D. HYDE ◽

AUSANA MAPOOK ◽

PETER E. MORTIMER ◽

JIANCHU XU ◽

...

Keyword(s):

Yunnan Province ◽

Southwest China ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Location Information ◽

Fruiting Bodies ◽

Host Genus ◽

Extant Species ◽

Culture Characteristics

A dead woody sample of Acer sp. with fungal fruiting bodies was collected in Pu’er City of Yunnan Province. Multigene phylogenetic analyses of LSU, ITS, SSU, and tef1-α sequence data showed that our collection belongs to Montagnula and is well separated from all other extant species. Montagnula puerensis is compared with all extant species by morphological characteristics, culture characteristics, host, and location information and is the first report of Montagnula from the host genus Acer.

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Introducing Chaetothyriothecium, a new genus of Microthyriales

Phytotaxa ◽

10.11646/phytotaxa.161.2.7 ◽

2014 ◽

Vol 161 (2) ◽

pp. 157 ◽

Cited By ~ 13

Author(s):

Sinang Hongsanan ◽

Putarak Chomnunti ◽

Pedro W. Crous ◽

Ekachai Chukeatirote ◽

Kevin D. Hyde

Keyword(s):

New Genus ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Plant Host ◽

Dna Sequence Data ◽

Limited Sampling ◽

Black Spots ◽

Gene Data ◽

Central Thailand

The order Microthyriales comprises foliar biotrophs, epiphytes, pathogens or saprobes that occur on plant leaves and stems. The order is relatively poorly known due to limited sampling and few in-depth studies. There is also a lack of phylogenetic data for these fungi, which form small black spots on plant host surfaces, but rarely cause any damage to the host. A "Microthyriaceae"-like fungus collected in central Thailand is described as a new genus, Chaetothyriothecium (type species Chaetothyriothecium elegans sp. nov.). Phylogenetic analyses of LSU gene data showed this species to cluster with other members of Microthyriales, where it is related to Microthyrium microscopicum the type of the order. The description of the new species is supplemented by DNA sequence data, which resolves its placement in the order. Little molecular data is available for this order, stressing the need for further collections and molecular data.

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