Genealogical concordance phylogenetic species recognition in the Fusarium oxysporum species complex

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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Current Classification and Diversity of Fusarium Species Complex, the Causal Pathogen of Fusarium Wilt Disease of Banana in Malaysia

Agronomy ◽

10.3390/agronomy11101955 ◽

2021 ◽

Vol 11 (10) ◽

pp. 1955

Author(s):

Anysia Hedy Ujat ◽

Ganesan Vadamalai ◽

Yukako Hattori ◽

Chiharu Nakashima ◽

Clement Kiing Fook Wong ◽

...

Keyword(s):

Fusarium Oxysporum ◽

Fusarium Wilt ◽

Species Complex ◽

Phylogenetic Trees ◽

Fusarium Species ◽

Morphological Characteristics ◽

Pathogenicity Test ◽

Fusarium Spp ◽

Specific Primers ◽

Fusarium Oxysporum Species Complex

The re-emergence of the Fusarium wilt caused by Fusarium odoratissimum (F. odoratissimum) causes global banana production loss. Thirty-eight isolates of Fusarium species (Fusarium spp.) were examined for morphological characteristics on different media, showing the typical Fusarium spp. The phylogenetic trees of Fusarium isolates were generated using the sequences of histone gene (H3) and translation elongation factor gene (TEF-1α). Specific primers were used to confirm the presence of F. odoratissimum. The phylogenetic trees showed the rich diversity of the genus Fusarium related to Fusarium wilt, which consists of F. odoratissimum, Fusarium grosmichelii, Fusarium sacchari, and an unknown species of the Fusarium oxysporum species complex. By using Foc-TR4 specific primers, 27 isolates were confirmed as F. odoratissimum. A pathogenicity test was conducted for 30 days on five different local cultivars including, Musa acuminata (AAA, AA) and Musa paradisiaca (AAB, ABB). Although foliar symptoms showed different severity of those disease progression, vascular symptoms of the inoculated plantlet showed that infection was uniformly severe. Therefore, it can be concluded that the Fusarium oxysporum species complex related to Fusarium wilt of banana in Malaysia is rich in diversity, and F. odoratissimum has pathogenicity to local banana cultivars in Malaysia regardless of the genotype of the banana plants.

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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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Detection of Fusarium oxysporum f. sp. fragariae from Infected Strawberry Plants

Plant Disease ◽

10.1094/pdis-08-18-1315-re ◽

2019 ◽

Vol 103 (5) ◽

pp. 1006-1013 ◽

Cited By ~ 3

Author(s):

Alyssa Burkhardt ◽

Peter M. Henry ◽

Steven T. Koike ◽

Thomas R. Gordon ◽

Frank Martin

Keyword(s):

Fusarium Oxysporum ◽

Species Complex ◽

Plant Pathogens ◽

Genetic Locus ◽

Quantitative Polymerase Chain Reaction ◽

High Sensitivity ◽

Field Samples ◽

Pathogenicity Tests ◽

Multiple Field ◽

Fusarium Oxysporum Species Complex

Isolates of the Fusarium oxysporum species complex have been characterized as plant pathogens that commonly cause vascular wilt, stunting, and yellowing of the leaves in a variety of hosts. F. oxysporum species complex isolates have been grouped into formae speciales based on their ability to cause disease on a specific host. F. oxysporum f. sp. fragariae is the causal agent of Fusarium wilt of strawberry and has become a threat to production as fumigation practices have changed in California. F. oxysporum f. sp. fragariae is polyphyletic and limited genetic markers are available for its detection. In this study, next-generation sequencing and comparative genomics were used to identify a unique genetic locus that can detect all of the somatic compatibility groups of F. oxysporum f. sp. fragariae identified in California. This locus was used to develop a TaqMan quantitative polymerase chain reaction assay and an isothermal recombinase polymerase amplification (RPA) assay that have very high sensitivity and specificity for more than 180 different isolates of the pathogen tested. RPA assay results from multiple field samples were validated with pathogenicity tests of recovered isolates.

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Genotypic and Phenotypic Characterization of Fungi in the Fusarium oxysporum Species Complex from Soybean Roots

Phytopathology ◽

10.1094/phyto-02-14-0043-r ◽

2014 ◽

Vol 104 (12) ◽

pp. 1329-1339 ◽

Cited By ~ 19

Author(s):

Margaret L. Ellis ◽

David R. Cruz Jimenez ◽

Leonor F. Leandro ◽

Gary P. Munkvold

Keyword(s):

Fusarium Oxysporum ◽

Mating Type ◽

Species Complex ◽

Phenotypic Diversity ◽

Rflp Analysis ◽

Small Subunit ◽

Phenotypic Characterization ◽

Pcr Rflp ◽

Soybean Roots ◽

Fusarium Oxysporum Species Complex

Isolates in the Fusarium oxysporum species complex (FOSC) from soybean range from nonpathogenic to aggressive pathogens causing seedling damping-off, wilt, and root rot. The objective of this research was to characterize the genotype and phenotype of isolates within the FOSC recovered predominantly from soybean roots and seedlings. Sequence analyses of the translation elongation factor (tef1α) gene and the mitochondrial small subunit (mtSSU), polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) analysis of the intergenic spacer (IGS) region, and identification of the mating type loci were conducted for 170 isolates. Vegetative compatibility (VC) tests were conducted for 114 isolates. Isolate aggressiveness was tested using a rolled towel assay for 159 isolates. Phylogenetic analysis of the tef1α and mtSSU and PCR-RFLP analysis of the IGS region separated the FOSC isolates into five clades, including F. commune. Both mating type loci, MAT1-1 or MAT1-2, were present in isolates from all clades. The VC tests were not informative, because most VC groups consisted of a single isolate. Isolate aggressiveness varied within and among clades; isolates in clade 2 were significantly less aggressive (P < 0.0001) when compared with isolates from the other clades and F. commune. The results from this study demonstrate the high levels of genotypic and phenotypic diversity within the FOSC from soybean but further work is needed to identify characteristics associated with pathogenic capabilities.

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