scholarly journals Optimal markers for the identification ofColletotrichumspecies

2019 ◽  
Author(s):  
Willie Anderson dos Santos Vieira ◽  
Priscila Alves Bezerra ◽  
Anthony Carlos da Silva ◽  
Josiene Silva Veloso ◽  
Marcos Paz Saraiva Câmara ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Species Complex ◽  
Plant Pathogens ◽  
Phylogenetic Signal ◽  
Intergenic Spacer ◽  
Internal Transcribed Spacers ◽  
Type Locus ◽  
Phylogenetic Studies ◽  
Fungal Plant Pathogens ◽  
Species Complexes

ABSTRACTColletotrichumis among the most important genera of fungal plant pathogens. Molecular phylogenetic studies over the last decade have resulted in a much better understanding of the evolutionary relationships and species boundaries within the genus. There are now approximately 200 species accepted, most of which are distributed among 13 species complexes. Given their prominence on agricultural crops around the world, rapid identification of a large collection ofColletotrichumisolates is routinely needed by plant pathologists, regulatory officials, and fungal biologists. However, there is no agreement on the best molecular markers to discriminate species in each species complex. Here we calculate the barcode gap distance and intra/inter-specific distance overlap to evaluate each of the most commonly applied molecular markers for their utility as a barcode for species identification. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone-3 (HIS3), DNA lyase (APN2), intergenic spacer between DNA lyase and the mating-type locusMAT1-2-1 (APN2/MAT-IGS), and intergenic spacer between GAPDH and a hypothetical protein (GAP2-IGS) have the properties of good barcodes, whereas sequences of actin (ACT), chitin synthase (CHS-1) and nuclear rDNA internal transcribed spacers (nrITS) are not able to distinguish most species. Finally, we assessed the utility of these markers for phylogenetic studies using phylogenetic informativeness profiling, the genealogical sorting index (GSI), and Bayesian concordance analyses (BCA). Although GAPDH, HIS3 and β-tubulin (TUB2) were frequently among the best markers, there was not a single set of markers that were best for all species complexes. Eliminating markers with low phylogenetic signal tends to decrease uncertainty in the topology, regardless of species complex, and leads to a larger proportion of markers that support each lineage in the Bayesian concordance analyses. Finally, we reconstruct the phylogeny of each species complex using a minimal set of phylogenetic markers with the strongest phylogenetic signal and find the majority of species are strongly supported as monophyletic.

Systematics of the Mesalina guttulata species complex (Squamata: Lacertidae) from Arabia with the description of two new species

Zootaxa ◽  
2018 ◽  
Vol 4429 (3) ◽  
pp. 513 ◽  
Author(s):  
ROBERTO SINDACO ◽  
MARC SIMÓ-RIUDALBAS ◽  
ROBERTO SACCHI ◽  
SALVADOR CARRANZA
Keyword(s):  
North Africa ◽  
Species Complex ◽  
Nuclear Gene ◽  
Morphological Data ◽  
Systematic Revision ◽  
Northwestern India ◽  
Phylogenetic Studies ◽  
Species Complexes ◽  
Lacertid Lizards ◽  
Phylogenetic Lineages

Mesalina are small diurnal lacertid lizards inhabiting arid areas from North Africa to northwestern India. Previous phylogenetic studies have shown the existence of several species complexes within the genus, some of them with high levels of undiscovered diversity. In the present study, we carry out an integrative systematic revision of the Mesalina guttulata species complex using both molecular and morphological data from across its entire distribution range in North Africa, the Middle East and Arabia. The results of the genetic analyses indicate that M. guttulata and M. bahaeldini are two allopatric sister taxa separated by the Suez Canal and that the species complex includes a further three unnamed deep phylogenetic lineages, two of them restricted to southern and southwestern Arabia and described herein as Mesalina austroarabica sp. nov. and Mesalina arnoldi sp. nov., respectively. As a result of the lack of enough material, the third deep lineage, distributed across Kuwait, Saudi Arabia and Jordan, is provisionally left undescribed. The two newly described species are characterized by their size, scale counts and tail coloration, as well as differences at the three mitochondrial and one nuclear gene analyzed in the present study. 

scholarly journals New endemic Fusarium species hitch-hiking with pathogenic Fusarium strains causing Panama disease in small-holder banana plots in Indonesia

2019 ◽  
Vol 43 (1) ◽  
pp. 48-69 ◽  
Author(s):  
N. Maryani ◽  
M. Sandoval-Denis ◽  
L. Lombard ◽  
P.W. Crous ◽  
G.H.J. Kema
Keyword(s):  
Rna Polymerase Ii ◽  
Fusarium Wilt ◽  
Species Complex ◽  
Plant Pathogens ◽  
Fusarium Species ◽  
Large Subunit ◽  
Fusarium Fujikuroi ◽  
Internal Transcribed Spacer Region ◽  
Species Complexes ◽  
Fusarium Wilt Of Banana

Fusarium species are well known for their abundance, diversity and cosmopolitan life style. Many members of the genus Fusarium are associated with plant hosts, either as plant pathogens, secondary invaders, saprotrophs, and/or endophytes. We previously studied the diversity of Fusarium species in the Fusarium oxysporum species complex (FOSC) associated with Fusarium wilt of banana in Indonesia. In that study, several Fusarium species not belonging to the FOSC were found to be associated with Fusarium wilt of banana. These Fusarium isolates belonged to three Fusarium species complexes, which included the Fusarium fujikuroi species complex (FFSC), Fusarium incarnatum-equiseti species complex (FIESC) and the Fusarium sambucinum species complex (FSSC). Using a multi-gene phylogeny that included partial fragments of the beta-tubulin (tub), calmodulin (cmdA), translation elongation factor 1-alpha (tef1), the internal transcribed spacer region of the rDNA (ITS), the large subunit of the rDNA (LSU), plus the RNA polymerase II large subunit (rpb1) and second largest subunit (rpb2) genes, we were able to identify and characterise several of these as new Fusarium species in the respective species complexes identified in this study.

scholarly journals Endophytic Colletotrichum Species from Aquatic Plants in Southwest China

2022 ◽  
Vol 8 (1) ◽  
pp. 87
Author(s):  
Hua Zheng ◽  
Zefen Yu ◽  
Xinwei Jiang ◽  
Linlin Fang ◽  
Min Qiao
Keyword(s):  
Aquatic Plants ◽  
Species Complex ◽  
Plant Pathogens ◽  
Fruits And Vegetables ◽  
Southwest China ◽  
Phylogenetic Analyses ◽  
Its Region ◽  
Morphological Characterization ◽  
Colletotrichum Species ◽  
Species Complexes

Colletotrichum species are plant pathogens, saprobes, and endophytes in many economically important hosts. Many studies have investigated the diversity and pathogenicity of Colletotrichum species in common ornamentals, fruits, and vegetables. However, Colletotrichum species occurring in aquatic plants are not well known. During the investigation of the diversity of endophytic fungi in aquatic plants in southwest China, 66 Colletotrichum isolates were obtained from aquatic plants there, and 26 of them were selected for sequencing and analyses of actin (ACT), chitin synthase (CHS-1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), the internal transcribed spacer (ITS) region, and β-tubulin (TUB2) genomic regions. Based on morphological characterization and multi-locus phylogenetic analyses, 13 Colletotrichum species were recognized, namely, C. baiyuense sp. nov., C. casaense sp. nov., C. demersi sp. nov., C. dianense sp. nov., C. fructicola, C. garzense sp. nov., C. jiangxiense, C. karstii, C. philoxeroidis sp. nov., C. spicati sp. nov., C. tengchongense sp. nov., C. vulgaris sp. nov., C. wuxuhaiense sp. nov. Two species complexes, the C. boninense species complex and C. gloeosporioides species complex, were found to be associated with aquatic plants. Pathogenicity tests revealed a broad diversity in pathogenicity and aggressiveness among the eight new Colletotrichum species.

scholarly journals Mating genes in Calonectria and evidence for a heterothallic ancestral state

2020 ◽  
Vol 45 (1) ◽  
pp. 163-176 ◽  
Author(s):  
J.Q. Li ◽  
B.D. Wingfield ◽  
M.J. Wingfield ◽  
I. Barnes ◽  
A. Fourie ◽  
...  
Keyword(s):  
Mating Type ◽  
Plant Pathogens ◽  
Phylogenetic Analyses ◽  
Pcr Amplification ◽  
Mating Strategies ◽  
Ancestral State ◽  
Type Locus ◽  
Species Complexes ◽  
Mating Type Genes ◽  
Heterothallic Species

The genus Calonectria includes many important plant pathogens with a wide global distribution. In order to better understand the reproductive biology of these fungi, we characterised the structure of the mating type locus and flanking genes using the genome sequences for seven Calonectria species. Primers to amplify the mating type genes in other species were also developed. PCR amplification of the mating type genes and multi-gene phylogenetic analyses were used to investigate the mating strategies and evolution of mating type in a collection of 70 Calonectria species residing in 10 Calonectria species complexes. Results showed that the organisation of the MAT locus and flanking genes is conserved. In heterothallic species, a novel MAT gene, MAT1-2-12 was identified in the MAT1-2 idiomorph;the MAT1-1 idiomorph, in most cases, contained the MAT1-1-3 gene. Neither MAT1-1-3 nor MAT1-2-12 was found in homothallic Calonectria (Ca.) hongkongensis, Ca. lateralis, Ca. pseudoturangicola and Ca. turangicola. Four different homothallic MAT locus gene arrangements were observed. Ancestral state reconstruction analysis provided evidence that the homothallic state was basal in Calonectria and this evolved from a heterothallic ancestor.

Morphological, biochemical and molecular identification of rhizobacteria isolates with potential for biocontrol of fungal plant pathogens

2021 ◽  
pp. 1-14
Author(s):  
Stephen Larbi-Koranteng ◽  
Richard Tuyee Awuah ◽  
Fredrick Kankam ◽  
Muntala Abdulai ◽  
Marian Dorcas Quain ◽  
...  
Keyword(s):  
Molecular Identification ◽  
Plant Pathogens ◽  
Fungal Plant Pathogens

scholarly journals The carbon source-dependent pattern of antimicrobial activity and gene expression in Pseudomonas donghuensis P482

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Marta Matuszewska ◽  
Tomasz Maciąg ◽  
Magdalena Rajewska ◽  
Aldona Wierzbicka ◽  
Sylwia Jafra
Keyword(s):  
Gene Expression ◽  
Antimicrobial Activity ◽  
Carbon Source ◽  
Reference Genes ◽  
Plant Pathogens ◽  
Plant Protection ◽  
Carbon Sources ◽  
Unknown Compound ◽  
Fungal Plant Pathogens ◽  
The Impact

AbstractPseudomonas donghuensis P482 is a tomato rhizosphere isolate with the ability to inhibit growth of bacterial and fungal plant pathogens. Herein, we analysed the impact of the carbon source on the antibacterial activity of P482 and expression of the selected genes of three genomic regions in the P482 genome. These regions are involved in the synthesis of pyoverdine, 7-hydroxytropolone (7-HT) and an unknown compound (“cluster 17”) and are responsible for the antimicrobial activity of P482. We showed that the P482 mutants, defective in these regions, show variations and contrasting patterns of growth inhibition of the target pathogen under given nutritional conditions (with glucose or glycerol as a carbon source). We also selected and validated the reference genes for gene expression studies in P. donghuensis P482. Amongst ten candidate genes, we found gyrB, rpoD and mrdA the most stably expressed. Using selected reference genes in RT-qPCR, we assessed the expression of the genes of interest under minimal medium conditions with glucose or glycerol as carbon sources. Glycerol was shown to negatively affect the expression of genes necessary for 7-HT synthesis. The significance of this finding in the light of the role of nutrient (carbon) availability in biological plant protection is discussed.

scholarly journals Stress-Activated Protein Kinase Signalling Regulates Mycoparasitic Hyphal-Hyphal Interactions in Trichoderma atroviride

2021 ◽  
Vol 7 (5) ◽  
pp. 365
Author(s):  
Dubraska Moreno-Ruiz ◽  
Linda Salzmann ◽  
Mark D. Fricker ◽  
Susanne Zeilinger ◽  
Alexander Lichius
Keyword(s):  
Protein Kinase ◽  
Map Kinases ◽  
Plant Pathogens ◽  
Tip Growth ◽  
Mitogen Activated Protein Kinase ◽  
Trichoderma Atroviride ◽  
Contact Phase ◽  
Fungal Plant Pathogens ◽  
Signalling Network ◽  
Mapk Signalling

Trichoderma atroviride is a mycoparasitic fungus used as biological control agent against fungal plant pathogens. The recognition and appropriate morphogenetic responses to prey-derived signals are essential for successful mycoparasitism. We established microcolony confrontation assays using T. atroviride strains expressing cell division cycle 42 (Cdc42) and Ras-related C3 botulinum toxin substrate 1 (Rac1) interactive binding (CRIB) reporters to analyse morphogenetic changes and the dynamic displacement of localized GTPase activity during polarized tip growth. Microscopic analyses showed that Trichoderma experiences significant polarity stress when approaching its fungal preys. The perception of prey-derived signals is integrated via the guanosine triphosphatase (GTPase) and mitogen-activated protein kinase (MAPK) signalling network, and deletion of the MAP kinases Trichoderma MAPK 1 (Tmk1) and Tmk3 affected T. atroviride tip polarization, chemotropic growth, and contact-induced morphogenesis so severely that the establishment of mycoparasitism was highly inefficient to impossible. The responses varied depending on the prey species and the interaction stage, reflecting the high selectivity of the signalling process. Our data suggest that Tmk3 affects the polarity-stress adaptation process especially during the pre-contact phase, whereas Tmk1 regulates contact-induced morphogenesis at the early-contact phase. Neither Tmk1 nor Tmk3 loss-of-function could be fully compensated within the GTPase/MAPK signalling network underscoring the crucial importance of a sensitive polarized tip growth apparatus for successful mycoparasitism.

Metabolites of rhizobacteria antagonistic towards fungal plant pathogens

2007 ◽  
Vol 57 (1) ◽  
pp. 127-130 ◽  
Author(s):  
Garima Jha ◽  
Vanamala Anjaiah
Keyword(s):  
Plant Pathogens ◽  
Fungal Plant Pathogens

Effectors of biotrophic fungal plant pathogens

2010 ◽  
Vol 37 (10) ◽  
pp. 913 ◽  
Author(s):  
Pamela H. P. Gan ◽  
Maryam Rafiqi ◽  
Adrienne R. Hardham ◽  
Peter N. Dodds
Keyword(s):  
Plant Tissue ◽  
Fungal Pathogen ◽  
Plant Pathogens ◽  
Plant Cells ◽  
Host Cells ◽  
Plant Proteins ◽  
Living Plant ◽  
Host Cytoplasm ◽  
Fungal Plant Pathogens ◽  
Biotrophic Fungi

Plant pathogenic biotrophic fungi are able to grow within living plant tissue due to the action of secreted pathogen proteins known as effectors that alter the response of plant cells to pathogens. The discovery and identification of these proteins has greatly expanded with the sequencing and annotation of fungal pathogen genomes. Studies to characterise effector function have revealed that a subset of these secreted pathogen proteins interact with plant proteins within the host cytoplasm. This review focuses on the effectors of intracellular biotrophic and hemibiotrophic fungal plant pathogens and summarises advances in understanding the roles of these proteins in disease and in elucidating the mechanism of fungal effector uptake into host cells.

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