scholarly journals Updating species diversity of Colletotrichum, with a phylogenomic overview

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.

Cryptic species complexes in manipulative echinostomatid trematodes: when two become six

Parasitology ◽  
2008 ◽  
Vol 136 (2) ◽  
pp. 241-252 ◽  
Author(s):  
T. L. F. LEUNG ◽  
D. B. KEENEY ◽  
R. POULIN
Keyword(s):  
Cryptic Species ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Single Species ◽  
Distinct Species ◽  
Molecular Data ◽  
Spatial Segregation ◽  
Small Scale ◽  
Intermediate Hosts ◽  
Species Complexes

SUMMARYRecent studies have shown that some digenean trematodes previously identified as single species due to the lack of distinguishing morphological characteristics actually consist of a number of genetically distinct cryptic species. We obtained mitochondrial 16S and nuclear ITS1 sequences for the redial stages of Acanthoparyphium sp. and Curtuteria australis collected from snails and whelks at various locations around Otago Peninsula, New Zealand. These two echinostomes are well-known host manipulators whose impact extends to the entire intertidal community. Using phylogenetic analyses, we found that Acanthoparyphium sp. is actually composed of at least 4 genetically distinct species, and that a cryptic species of Curtuteria occurs in addition to C. australis. Molecular data obtained for metacercariae dissected from cockle second intermediate hosts matched sequences obtained for Acanthoparyphium sp. A and C. australis rediae, respectively, but no other species. The various cryptic species of both Acanthoparyphium and Curtuteria also showed an extremely localized pattern of distribution: some species were either absent or very rare in Otago Harbour, but reached far higher prevalence in nearby sheltered inlets. This small-scale spatial segregation is unexpected as shorebird definitive hosts can disperse trematode eggs across wide geographical areas, which should result in a homogeneous mixing of the species on small geographical scales. Possible explanations for this spatial segregation of the species include sampling artefacts, local adaptation by first intermediate hosts, environmental conditions, and site fidelity of the definitive hosts.

scholarly journals Genetic and Pathogenic Relatedness of Pseudoperonospora cubensis and P. humuli

2011 ◽  
Vol 101 (7) ◽  
pp. 805-818 ◽  
Author(s):  
Melanie N. Mitchell ◽  
Cynthia M. Ocamb ◽  
Niklaus J. Grünwald ◽  
Leah E. Mancino ◽  
David H. Gent
Keyword(s):  
Host Specificity ◽  
Plant Pathogens ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Species Boundaries ◽  
Pseudoperonospora Cubensis ◽  
Biologically Relevant ◽  
Practical Implications

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.

A revision of the Leptogium saturninum group in North America

2016 ◽  
Vol 48 (5) ◽  
pp. 387-421 ◽  
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.

Two species of Agaricus subg. Minoriopsis from Mexico

Phytotaxa ◽  
2019 ◽  
Vol 404 (3) ◽  
pp. 91
Author(s):  
JIE CHEN ◽  
PHILIPPE CALLAC ◽  
RÉGULO CARLOS LLARENA-HERNÁNDEZ ◽  
GERARDO GERARDO MATA
Keyword(s):  
New Species ◽  
New Record ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Edible Fungi ◽  
The World ◽  
Wild Edible Fungi ◽  
A New Species ◽  
Taxonomic System

Agaricus is a species-rich genus with more than 500 species over the world. Recent studies on tropical Agaricus revealed new tropical clades and a revised taxonomic system was consequently developed. Agaricus subg. Minoriopsis, a sixth subgenus was recently added, comprising species exclusively from the Americas. The diversity of Agaricus is little studied in Mexico, despite this country has a long history in the consumption of wild edible fungi. In this paper, we introduce a new species A. guzmanii and a new record for A. globocystidiatus from Mexico based on morphological characteristics and molecular data. Phylogenetic analyses indicate that they belong to A. subg. Minoriopsis.

Molecular data reveal unexpected species diversity of tapeworms of Australasian reptiles: revision of Kapsulotaenia (Cestoda: Proteocephalidae)

Zootaxa ◽  
2020 ◽  
Vol 4869 (4) ◽  
pp. 529-561
Author(s):  
ALAIN DE CHAMBRIER ◽  
JAN BRABEC ◽  
TOMÁŠ SCHOLZ
Keyword(s):  
Species Diversity ◽  
Phylogenetic Analyses ◽  
Relative Size ◽  
Interdisciplinary Approach ◽  
Molecular Data ◽  
Lower Number ◽  
Width Ratio ◽  
Molecular Phylogenetic ◽  
Three New Species ◽  
Australasian Region

Species diversity and interrelationships of tapeworms of the genus Kapsulotaenia Freze, 1963 (Proteocephalidae: Acanthotaeniinae), parasites of lizards, especially monitors (Varanus spp.) in the Australasian region, were re-assessed using an interdisciplinary approach. Molecular phylogenetic analyses of newly characterized lsrDNA and cox1 sequences confirmed monophyly of the genus, which is typified by the presence of eggs in capsules, and also indicated a strict (oioxenous) level of host specificity of its species thus revealing unexpected species diversity. Diagnoses of insufficiently described species were amended based on a study of the types and freshly collected specimens and, in addition, three new species were described. A list of ten species of the genus recognized as valid is provided, including illustrations of taxonomically important structures of poorly known taxa. Kapsulotaenia beveridgei n. sp. from V. rosenbergi in Australia differs from all other species of Kapsulotaenia but K. frezei and K. saccifera by having a lower number of testes and an absence of banana-shaped clusters of eggs. Kapsulotaenia cannoni n. sp. from V. gouldii can be distinguished from all species but K. chisholmae by a smaller scolex diameter and from all remaining species by its bigger cirrus-sac ratio and a bigger Mehlis’ gland/proglottid width ratio. Kapsulotaenia cannoni n. sp. differs from K. chisholmae, by the presence of an armed cirrus and a lower number of eggs in cluster (3–7 versus 8–13). Kapsulotaenia nybelini n. sp., which also occurs in V. gouldii, differs from K. tidswelli, K. frezei and K. beveridgei by having a greater number of testes, and it differs from K. varia by having a smaller relative size of the ovary. It differs from K. saccifera by the absence of banana-shaped cluster, and from K. pythonis by the number of eggs in clusters. Identification keys for all species of Kapsulotaenia and genera of the Acanthotaeniinae are also provided, together with SEM micrographs of three species, including two newly described species. 

Species diversity and genetic differentiation of stygofauna (Syncarida:Bathynellacea) across an alluvial aquifer in north-eastern Australia

2012 ◽  
Vol 60 (3) ◽  
pp. 152 ◽  
Author(s):  
B. D. Cook ◽  
K. M. Abrams ◽  
J. Marshall ◽  
C. N. Perna ◽  
S. Choy ◽  
...  
Keyword(s):  
Species Diversity ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Alluvial Aquifer ◽  
Species Level ◽  
Coi Gene ◽  
Generic Level ◽  
Alluvial Aquifers ◽  
Eastern Australia ◽  
North Eastern

Recent research suggests that alluvial aquifers in southern and eastern Australia may contain a diverse subterranean aquatic fauna (i.e. stygofauna). However, to date only a limited number of alluvial aquifers have been studied and little molecular data are available to assess species-level diversity and spatial patterns of genetic variation within stygofaunal species. In this paper, we present the initial results of a stygofaunal survey of the Burdekin River alluvial aquifer in Queensland, extending the northern range of alluvial aquifers along the east coast of Australia that have been investigated. The survey resulted in the collection of bathynellid stygofauna (Syncarida: Bathynellacea) and genetic analyses were conducted to determine species level diversity using the mitochondrial cytochrome oxidase subunit I (COI) gene. We further investigated the phylogenetic relationships of the species with bathynellids from western and southern Australia to assess the generic status of species. Four highly divergent COI lineages within the Parabathynellidae and one lineage within the Bathynellidae were found. These lineages did not group within any described genera, and phylogenetic analyses indicated that both local radiations and the retention of a lineage that was more apical in the genealogy account for the diversity within the Parabathynellidae in the Burdekin River alluvial aquifer. Most COI lineages were sampled from only a single bore, although one taxon within the Parabathynellidae was found to be more widespread in the aquifer. Haplotypes within this taxon were not shared among bores (ΦST = 0.603, P < 0.001). Overall, the high species diversity for bathynellaceans from an alluvial aquifer reported here, and surveys of bathynellaceans in several other alluvial systems in south-eastern Australia, suggests that groundwater ecosystems of eastern Australia may contain high stygofaunal diversity by Australian and world standards, particularly at the generic level for parabathynellids.

scholarly journals High species diversity of the soft coral family Xeniidae (Octocorallia, Alcyonacea) in the temperate region of Japan revealed by morphological and molecular analyses

ZooKeys ◽  
2019 ◽  
Vol 862 ◽  
pp. 1-22 ◽  
Author(s):  
Tatsuki Koido ◽  
Yukimitsu Imahara ◽  
Hironobu Fukami
Keyword(s):  
Species Diversity ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Soft Coral ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Temperate Region ◽  
High Species Diversity ◽  
Molecular Phylogenetic ◽  
Traditional Taxonomy

The soft coral family Xeniidae, commonly found in tropical and subtropical regions, consists of 20 genera and 162 species. To date, few studies on this family have been conducted in Japan, especially at higher latitudes. Although molecular phylogenetic analyses have recently been used to distinguish soft coral species, it is difficult to identify species and genera in this family due to the limited taxonomic indices and high morphological variation. In this study, we found a large Xeniidae community off the coast of Oshima Island (31°31.35'N, 131°24.27'E) at Miyazaki, Kyushu Island, located in the temperate region of Japan. The species composition and molecular phylogenetic relationships were investigated to uncover the species diversity of Xeniidae in this community. A total of 182 xeniid specimens were collected and identified to the species level, after which the samples were molecularly analyzed using a mitochondrial marker (ND2) and a nuclear marker (ITS) to infer the phylogenetic relationships. A total of 14 xeniid species were identified, including five undescribed species from five genera (Anthelia, Heteroxenia, Sympodium, Xenia, and Yamazatum). Miyazaki was identified as having the highest xeniid species diversity in Japan. The molecular phylogenetic trees inferred from each marker recovered very similar topologies: four genera (Anthelia, Heteroxenia, Sympodium, and Yamazatum) were monophyletic, whereas one (Xenia) was polyphyletic. Thus, except for Xenia, the morphological characteristics used for traditional taxonomy well reflected the phylogeny of the Xeniidae at the genus level. On the other hand, our results show that further taxonomic revisions of Xenia are needed.

scholarly journals Four new species in the Tremella fibulifera complex (Tremellales, Basidiomycota)

MycoKeys ◽  
2021 ◽  
Vol 82 ◽  
pp. 33-56
Author(s):  
Long-Fei Fan ◽  
Renato Lúcio Mendes Alvarenga ◽  
Tatiana Baptista Gibertoni ◽  
Fang Wu ◽  
Yu-Cheng Dai
Keyword(s):  
New Species ◽  
Rna Polymerase Ii ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Elongation Factor ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Small Subunit ◽  
Molecular Evidence ◽  
Rrna Gene

Samples of species close to Tremella fibulifera from China and Brazil are studied, and T. fibulifera is confirmed as a species complex including nine species. Five known species (T. cheejenii, T. fibulifera s.s., T. “neofibulifera”, T. lloydiae-candidae and T. olens) and four new species (T. australe, T. guangxiensis, T. latispora and T. subfibulifera) in the complex are recognized based on morphological characteristics, molecular evidence, and geographic distribution. Sequences of eight species of the complex were included in the phylogenetic analyses because T. olens lacks molecular data. The phylogenetic analyses were performed by a combined sequence dataset of the internal transcribed spacer (ITS) and the partial nuclear large subunit rDNA (nLSU), and a combined sequence dataset of the ITS, partial nLSU, the small subunit mitochondrial rRNA gene (mtSSU), the translation elongation factor 1-α (TEF1), the largest and second largest subunits of RNA polymerase II (RPB1 and RPB2). The eight species formed eight independent lineages with robust support in phylogenies based on both datasets. Illustrated description of the six species including Tremella fibulifera s.s., T. “neofibulifera” and four new species, and discussions with their related species, are provided. A table of the comparison of the important characteristics of nine species in the T. fibulifera complex and a key to the whitish species in Tremella s.s. are provided.

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

Phytotaxa ◽  
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.

Three new species of Micropsalliota (Agaricaceae, Agaricales) from China

Phytotaxa ◽  
2021 ◽  
Vol 491 (2) ◽  
pp. 167-176
Author(s):  
JIA-XIN LI ◽  
MAO-QIANG HE ◽  
RUI-LIN ZHAO
Keyword(s):  
New Species ◽  
Species Diversity ◽  
Phylogenetic Tree ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Southwestern China ◽  
Molecular Phylogenetic ◽  
Three New Species

Species diversity of Micropsalliota in China remains poorly known, especially in southwestern China, a hotspot of biodiversity. Based on morphological characteristics and molecular phylogenetic analyses using ITS and nrLSU sequences, three new species named Micropsalliota delicatula, M. dentatomarginata and M. digitatocystis are introduced from China. Phylogenetc analyses results indicated the unique phylogenetic positions of three new species in Micropsalliota. Full descriptions, photo plates, illustrations and a phylogenetic tree to show the placement of three new species are presented.

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