How useful is the current species recognition concept for the determination of true morels? Insights from the Czech Republic

The phylogentic diversity of the genus Morchella has only been sporadically studied in Central Europe. In this study, a molecular taxonomic revision of the Morchella species of the Czech Republic was performed using available fungarium specimens, fresh collections, and axenic cultures. Molecular phylogenetic analyses based on either ITS or five-locus (ITS, LSU, RPB1, RPB2, and EF-1α) sequencing and the application of principles of the genealogical concordance phylogenetic species recognition (GCPSR) have revealed the occurrence of 11 phylogenetic species in the region, but only six of them could be assigned unequivocally to the previously published phylospecies: Mel-3 (M.semilibera), Mel-10 (M.importuna), Mel-19 (M.eohespera), Mes-4 (M.americana), Mes-5 and Mes-8 (M.esculenta). One lineage was identified as a new phylospecies and is designated as Mel-39. Four lineages grouped together with two or more previously published phylospecies: Mel-13/26 (M.deliciosa), Mel-15/16 (M.angusticeps / M.eximioides), Mel-20/34 (M.purpurascens), and Mel-23/24/31/32 (M.pulchella). Our phylogenetic analyses and literature review shed light on the pitfalls of current molecular taxonomy of morels and highlight the ambiguities of present species recognition concepts. The main source of the problems seems to be rooted in the application of different methods (multigene vs single-gene sequencing, phenotypic determination) and approaches (monophyly vs paraphyly, the application or not of GCPSR, degree of differentiation between accepted species, etc.) by various authors for the delimitation of new phylospecies. Therefore, we propose five criteria for distinguishing new phylospecies in the genus Morchella based on molecular data, and recommend a more conservative approach in species delimitation.

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High diversity of Morchella and a novel lineage of the Esculenta clade from the north Qinling Mountains revealed by GCPSR-based study

Scientific Reports ◽

10.1038/s41598-019-56321-1 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Phonepaserd Phanpadith ◽

Zhongdong Yu ◽

Tao Li

Keyword(s):

Phylogenetic Trees ◽

Species Recognition ◽

Single Gene ◽

Qinling Mountains ◽

Phylogenetic Species ◽

The North ◽

Genealogical Concordance ◽

Commercial Cultivars ◽

Commercial Farms ◽

North Qinling

AbstractChina is a mainland country rich in natural morel recourses, having records of half of the worldwide 61 morel phylospecies. In this study, 31 collections of ascocarps from the north Qinling Mountains, 4 collections of commercial cultivars from the south Qinling Mountains, and 3 Morchella mycelium clones from commercial cultivars were investigated using the genealogical concordance phylogenetic species recognition (GCPSR) method. Maximum-likelihood was employed for the construction of phylogenetic trees. A total of five phylogenetic species were found among the 38 collections, namely Morchella sp. Mes-8, Mes-9, Mes-13, and Mes-25, and Morchella chensiensis (IF556780), in addition to the false morel (Verpa bohemica). The identification of cultivated Morchella sp. Mel-2, Mel-6, Mel-10, and Mel-12 coincided with that of the commercial farms. A total of 80% (4/5) of yellow morels were new records for the Qinling region, except Mes-19; moreover, a novel monophyletic lineage, Morchella chensiensis, was found to be distinct from the previously reported phylospecies by single gene and combined genes analysis, thus being herein proposed as a new phylospecies. All collections from this study showed continental endemism, and all Qinling Mountains collections were grouped together in rDNA phylogenetic trees. The study provided insights on biodiversities in this key region of China.

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Using Genealogical Concordance and Coalescent-Based Species Delimitation to Assess Species Boundaries in the Diaporthe eres Complex

Journal of Fungi ◽

10.3390/jof7070507 ◽

2021 ◽

Vol 7 (7) ◽

pp. 507

Author(s):

Sandra Hilário ◽

Micael F. M. Gonçalves ◽

Artur Alves

Keyword(s):

Nucleotide Diversity ◽

Species Recognition ◽

Phylogenetic Analyses ◽

Single Species ◽

Diversity Indices ◽

Species Boundaries ◽

Phylogenetic Species ◽

Individual Gene ◽

Genealogical Concordance ◽

The Common

DNA sequence analysis has been of the utmost importance to delimit species boundaries in the genus Diaporthe. However, the common practice of combining multiple genes, without applying the genealogical concordance criterion has complicated the robust delimitation of species, given that phylogenetic incongruence between loci has been disregarded. Despite the several attempts to delineate the species boundaries in the D. eres complex, the phylogenetic limits within this complex remain unclear. In order to bridge this gap, we employed the Genealogical Phylogenetic Species Recognition principle (GCPSR) and the coalescent-based model Poisson Tree Processes (PTPs) and evaluated the presence of recombination within the D. eres complex. Based on the GCPSR principle, presence of incongruence between individual gene genealogies, i.e., conflicting nodes and branches lacking phylogenetic support, was evident. Moreover, the results of the coalescent model identified D. eres complex as a single species, which was not consistent with the current large number of species within the complex recognized in phylogenetic analyses. The absence of reproductive isolation and barriers to gene flow as well as the high haplotype and low nucleotide diversity indices within the above-mentioned complex suggest that D. eres constitutes a population rather than different lineages. Therefore, we argue that a cohesive approach comprising genealogical concordance criteria and methods to detect recombination must be implemented in future studies to circumscribe species in the genus Diaporthe.

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Koorchaloma oryzae sp. nov. (Stachybotryaceae, Sordariomycetes), from Oryza sativa (Poaceae) in northern Thailand

Phytotaxa ◽

10.11646/phytotaxa.524.4.4 ◽

2021 ◽

Vol 524 (4) ◽

pp. 283-292

Author(s):

XINGGUO TIAN ◽

SAMANTHA C. KARUNARATHNA ◽

AUSANA MAPOOK ◽

JIANCHU XU ◽

DANFENG BAO ◽

...

Keyword(s):

Oryza Sativa ◽

New Species ◽

Species Recognition ◽

Phylogenetic Analyses ◽

Test Results ◽

Phylogenetic Species ◽

Closely Related Species ◽

Genealogical Concordance ◽

Statistical Support ◽

A New Species

A new species of Koorchaloma is described based on morphology and multigene phylogenetic analyses of ITS, LSU and RPB2. Phylogenetic analyses showed our strain clusters with K. europaea with moderate statistical support. Koorchaloma oryzae sp. nov. is morphologically similar to K. europaea, but it can be distinguished by the conidiophores and conidia, while ITS pairwise nucleotide comparison of these two species also revealed differences. Koorchaloma oryzae is compared with all known Koorchaloma species, and a key to Koorchaloma species is provided. Genealogical concordance phylogenetic species recognition analysis (PHI test) results of the new species and closely related species are also given.

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Molecular and Morphological Assessment of Septoria Species Associated with Ornamental Plants in Yunnan Province, China

Journal of Fungi ◽

10.3390/jof7060483 ◽

2021 ◽

Vol 7 (6) ◽

pp. 483

Author(s):

Yuan-Yan An ◽

Monika C. Dayarathne ◽

Xiang-Yu Zeng ◽

Alan J. L. Phillips ◽

Kevin D. Hyde ◽

...

Keyword(s):

Yunnan Province ◽

Species Recognition ◽

Phylogenetic Analyses ◽

Single Gene ◽

Ornamental Plants ◽

Dna Barcode ◽

Botanical Garden ◽

Rapid Identification ◽

Gene Trees ◽

Genealogical Concordance

The Karst landform is the main geographic characteristic in South China. Such areas are rich in vegetation and especially suitable for growth of shrubs and herbaceous plants. In this study, 11 Septoria strains were obtained from different plants’ leaves collected in the Kunming Botanical Garden, Yunnan Province, China. Based on single-gene and multi-gene analyses of five gene loci (tef1, rpb2, tub2, ITS, and LSU) and four gene regions (without LSU), these strains were found to belong to three independent phylogenetic lineages representing five species, including four novel taxa, and one new record for China. Five single gene trees were also provided to evaluate the effectiveness of each gene for discriminating the species, as a result of which tub2 was found to have the most suitable DNA barcode for rapid identification. Morphological descriptions, illustrations, and comparisons are provided for a more comprehensive assessment. Genealogical Concordance Phylogenetic Species Recognition (GCPSR) with a pairwise homoplasy index (PHI) test was used to evaluate the conclusions of the phylogenetic analyses.

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Combined multi-gene backbone tree for the genus Coniochaeta with two new species from Uzbekistan

Phytotaxa ◽

10.11646/phytotaxa.336.1.3 ◽

2018 ◽

Vol 336 (1) ◽

pp. 43 ◽

Cited By ~ 5

Author(s):

MILAN C. SAMARAKOON ◽

YUSUFJON GAFFOROV ◽

NINGGUO LIU ◽

SAJEEWA S. N. MAHARACHCHIKUMBURA ◽

JAYARAMA D. BHAT ◽

...

Keyword(s):

New Species ◽

Sequence Data ◽

Species Recognition ◽

Phylogenetic Species ◽

Phylogenetic Studies ◽

Genealogical Concordance ◽

Two New Species ◽

Backbone Tree

The genus Coniochaeta is an important ascomycete because its members live in diversified habitats and nutritional modes. In this study, two new species, C. acaciae and C. coluteae, are introduced from dead branches of Acacia sp. and Colutea paulsenii Freyn (both Fabaceae) respectively from Uzbekistan, based on morphological and phylogenetic studies. Analyses of combined ITS and LSU sequence data with Genealogical Concordance Phylogenetic Species Recognition (GCPSR) and comparison of similar taxa, provide evidences for placement of these new species in Coniochaeta, as distinct lineages.

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Pyrenochaetopsis kuksensis (Pyrenochaetopsidaceae), a new species associated with an ornamental boxwood in the Czech Republic

Phytotaxa ◽

10.11646/phytotaxa.498.3.3 ◽

2021 ◽

Vol 498 (3) ◽

pp. 177-185

Author(s):

MILAN ŠPETÍK ◽

AKILA BERRAF-TEBBAL ◽

ROBERT POKLUDA ◽

ALEŠ EICHMEIER

Keyword(s):

Czech Republic ◽

New Species ◽

Phylogenetic Relationships ◽

Sequence Data ◽

Phylogenetic Analyses ◽

New Taxon ◽

The Czech Republic ◽

Buxus Sempervirens ◽

Fungal Microbiome ◽

A New Species

During the investigation of fungal microbiome associated with boxwood in the Czech Republic, samples from Buxus sempervirens L. (Buxaceae) plants were collected and used for isolation. Two fungal strains were proposed as a new species Pyrenochaetopsis kuksensis based on morphology as well as phylogenetic analyses of ITS, LSU, rpb2, and tub2 sequence data. Detailed descriptions and phylogenetic relationships of the new taxon are provided.

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First detection and characterisation of porcine hemagglutinating encephalomyelitis virus in the Czech Republic

Veterinární Medicína ◽

10.17221/95/2018-vetmed ◽

2019 ◽

Vol 64 (No. 02) ◽

pp. 60-66

Author(s):

R Moutelikova ◽

J Prodelalova

Keyword(s):

Czech Republic ◽

Amino Acid ◽

Amino Acid Sequence ◽

Phylogenetic Analyses ◽

Economic Losses ◽

The Czech Republic ◽

Nucleocapsid Gene ◽

Nasal Swabs ◽

Encephalomyelitis Virus ◽

Porcine Hemagglutinating Encephalomyelitis Virus

Porcine hemagglutinating encephalomyelitis virus (PHEV) is a highly neurovirulent coronavirus that invades the central nervous system in piglets. The incidence of PHEV among pigs in many countries is rising, and the economic losses to the pig industry may be significant. Serological studies suggest that PHEV is spread worldwide. However, no surveillance has been carried out in the Czech Republic. In this study, eight pig farms were screened for the presence of members of the Coronaviridae family with the use of reverse transcription PCR. A collection of 123 faecal samples and 151 nasal swabs from domestic pigs were analysed. In PHEV-positive samples, almost the complete coding sequence of the nucleocapsid gene was amplified and the acquired sequences were compared to those of geographically dispersed PHEV strains; phylogenetic analyses were also performed. PHEV was present in 7.9% of nasal swabs taken from different age categories of pigs. No other swine coronaviruses were detected. The amino acid sequence of the Czech PHEV strains showed 95.8–98.1% similarity to other PHEV reference strains in GenBank. PHEV strains collected from animals on the same farm were identical; however, strains from different farms have only exhibited only 96.7–98.7% amino acid sequence identity. Our study demonstrates the presence of PHEV in pigs in the Czech Republic. The Czech PHEV strains were evolutionarily closest to the Belgium strain VW572.

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Genealogical concordance of phylogenetic species recognition-based delimitation of Neopestalotiopsis species associated with leaf spots and fruit canker disease affected guava plants

The Pakistan Journal of Agricultural Sciences ◽

10.21162/pakjas/21.1045 ◽

2021 ◽

Vol 58 (04) ◽

pp. 1301-1313

Author(s):

Imran Ul Haq

Keyword(s):

Species Recognition ◽

Elongation Factor ◽

Plant Diseases ◽

Morphological Data ◽

Phylogenetic Species ◽

Translation Elongation ◽

Canker Disease ◽

Leaf Spots ◽

Genealogical Concordance ◽

Elongation Factor 1

Neopestalotiopsis species are known to be involved in plant diseases as associated pathogens. The taxonomic identification of the fungal group Neopestalotiopsisis little bit difficult due to its complex evolutionary history. In the present study, seven fungal isolates were investigated from canker-affected guava plants. The phylogeny for generic placement of these isolates was analyzed to validate them as Neopestalotiopsis genus by phylogenetic signals from the 28S nrRNA region (LSU). Generated morphological data was segregated as new morpho-species of the Neopestalotiopsis genus. Hence, the internal transcribed spacer (ITS), Translation elongation factor 1-α (TEF1-α) and Tubulin (TUB) genic region of these isolates were studied in juxtaposition with morphological data to resolve species limits. Both phylogenetic and morphological data revealed four novel species of the Neopestalotiopsis genus out of seven isolates studied. These Neopestalotiopsis species could be of great significance for further investigation as putative pathogens associated with canker or scabby canker disease in guava.

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Diversity within Aspergillus niger Clade and Description of a New Species: Aspergillus vinaceus sp. nov.

Journal of Fungi ◽

10.3390/jof6040371 ◽

2020 ◽

Vol 6 (4) ◽

pp. 371

Author(s):

Josué J. da Silva ◽

Beatriz T. Iamanaka ◽

Larissa S. Ferranti ◽

Fernanda P. Massi ◽

Marta H. Taniwaki ◽

...

Keyword(s):

Aspergillus Niger ◽

Secondary Metabolites ◽

Rna Polymerase Ii ◽

Random Amplified Polymorphic Dna ◽

Species Recognition ◽

Sensu Stricto ◽

Phylogenetic Species ◽

Gene Sequences ◽

Genealogical Concordance ◽

Sclerotium Production

Diversity of species within Aspergillus niger clade, currently represented by A. niger sensu stricto and A. welwitshiae, was investigated combining three-locus gene sequences, Random Amplified Polymorphic DNA, secondary metabolites profile and morphology. Firstly, approximately 700 accessions belonging to this clade were investigated using calmodulin gene sequences. Based on these sequences, eight haplotypes were clearly identified as A. niger (n = 247) and 17 as A. welwitschiae (n = 403). However, calmodulin sequences did not provide definitive species identities for six haplotypes. To elucidate the taxonomic position of these haplotypes, two other loci, part of the beta-tubulin gene and part of the RNA polymerase II gene, were sequenced and used to perform an analysis of Genealogical Concordance Phylogenetic Species Recognition. This analysis enabled the recognition of two new phylogenetic species. One of the new phylogenetic species showed morphological and chemical distinguishable features in comparison to the known species A. welwitschiae and A. niger. This species is illustrated and described as Aspergillus vinaceus sp. nov. In contrast to A. niger and A. welwitschiae, A. vinaceus strains produced asperazine, but none of them were found to produce ochratoxin A and/or fumonisins. Sclerotium production on laboratory media, which does not occur in strains of A. niger and A. welwitschiae, and strictly sclerotium-associated secondary metabolites (14-Epi-hydroxy-10,23-dihydro-24,25-dehydroaflavinine; 10,23-Dihydro-24,25-dehydroaflavinine; 10,23-Dihydro-24,25-dehydro-21-oxo-aflavinine) were found in A. vinaceus. The strain type of A. vinaceus sp. nov. is ITAL 47,456 (T) (=IBT 35556).

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Three-Locus Sequence Identification and Differential Tebuconazole Sensitivity Suggest Novel Fusarium equiseti Haplotype from Trinidad

Pathogens ◽

10.3390/pathogens9030175 ◽

2020 ◽

Vol 9 (3) ◽

pp. 175 ◽

Cited By ~ 2

Author(s):

Ria T. Villafana ◽

Sephra N. Rampersad

Keyword(s):

Rna Polymerase ◽

Species Recognition ◽

Elongation Factor ◽

Phylogenetic Species ◽

Translation Elongation Factor ◽

Translation Elongation ◽

Fusarium Equiseti ◽

Homogeneous Groups ◽

Sequence Identification ◽

Genealogical Concordance

The Fusarium incarnatum-equiseti species complex (FIESC) consists of 33 phylogenetic species according to multi-locus sequence typing (MLST) and Genealogical Concordance Phylogenetic Species Recognition (GCPSR). A multi-locus dataset consisting of nucleotide sequences of the translation elongation factor (EF-1α), calmodulin (CAM), partial RNA polymerase largest subunit (RPB1), and partial RNA polymerase second largest subunit (RPB2), was generated to distinguish among phylogenetic species within the FIESC isolates infecting bell pepper in Trinidad. Three phylogenetic species belonged to the Incarnatum clade (FIESC-15, FIESC-16, and FIESC-26), and one species belonged to the Equiseti clade (FIESC-14). Specific MLST types were sensitive to 10 µg/mL of tebuconazole fungicide as a discriminatory dose. The EC50 values were significantly different among the four MLST groups, which were separated into two homogeneous groups: FIESC-26a and FIESC-14a, demonstrating the “sensitive” azole phenotype and FIESC-15a and FIESC-16a as the “less sensitive” azole phenotype. CYP51C sequences of the Trinidad isolates, although under positive selection, were without any signatures of recombination, were highly conserved, and were not correlated with these azole phenotypes. CYP51C sequences were unable to resolve the FIESC isolates as phylogenetic inference indicated polytomic branching for these sequences. This data is important to different research communities, including those studying Fusarium phytopathology, mycotoxins, and public health impacts.

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