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Fusarium is associated with a number of wilt, blight, scab, and rot diseases in a range of economically important staple food crops worldwide. An assessment of the genetic structure and population stratification of Fusarium incarnatum-equiseti species complex (FIESC) pathogen populations is important to understand the evolutionary potential of such populations in adapting to environmental change. Based on intersimple sequence repeat polymerase chain reaction (ISSR-PCR), it was found that the pathogen population was structured into three genetic clusters for which genetic differentiation was higher within than among populations. There was high intrapopulation genetic diversity for population 1 (94.63%) which consisted largely of isolates collected from North Trinidad. Populations 2 and 3 had a low level of admixture among the populations based on overall population differentiation. Population 1 accounted for the highest amount of genetic variation (95.82%) followed by populations 2 and 3. Population stratification was reflected in the dendrogram topology, which consisted of three main genetic clusters and which coincided with the outcome of Bayesian and PCoA analyses. The populations were isolated by distance, and Voronoi tessellations indicated physical or structural barriers to gene flow which contributed to restricted admixture between two of three populations. These findings suggest a high evolutionary potential for this FIESC pathogen population, the implications of which directly affect disease management strategies.
Sephra N. Rampersad. Spatial pattern of genetic diversity in field populations of Fusarium incarnatum‐equiseti species complex. Ecology and Evolution 2021, 11, 9010 -9020.
AMA StyleSephra N. Rampersad. Spatial pattern of genetic diversity in field populations of Fusarium incarnatum‐equiseti species complex. Ecology and Evolution. 2021; 11 (13):9010-9020.
Chicago/Turabian StyleSephra N. Rampersad. 2021. "Spatial pattern of genetic diversity in field populations of Fusarium incarnatum‐equiseti species complex." Ecology and Evolution 11, no. 13: 9010-9020.
Trinidad and Tobago is the largest producer of oil and natural gas in Central America and the Caribbean. Natural crude oil seeps, in addition to leaking petroleum pipelines, have resulted in chronic contamination of the surrounding terrestrial environments since the time of petroleum discovery, production, and refinement in Trinidad. In this study, we isolated microbes from soils chronically contaminated with crude oil using a culture-dependent approach with enrichment. The sampling of eight such sites located in the southern peninsula of Trinidad revealed a diverse microbial composition and novel oil-degrading filamentous fungi and yeast as single-isolate degraders and naturally occurring consortia, with specific bacterial species not previously reported in the literature. Multiple sequence comparisons and phylogenetic analyses confirmed the identity of the top degraders. The filamentous fungal community based on culturable species was dominated by Ascomycota, and the recovered yeast isolates were affiliated with Basidiomycota (65.23%) and Ascomycota (34.78%) phyla. Enhanced biodegradation of petroleum hydrocarbons is maintained by biocatalysts such as lipases. Five out of seven species demonstrated extracellular lipase activity in vitro. Our findings could provide new insights into microbial resources from chronically contaminated terrestrial environments, and this information will be beneficial to the bioremediation of petroleum contamination and other industrial applications.
Amanda Ramdass; Sephra Rampersad. Diversity and Oil Degradation Potential of Culturable Microbes Isolated from Chronically Contaminated Soils in Trinidad. Microorganisms 2021, 9, 1167 .
AMA StyleAmanda Ramdass, Sephra Rampersad. Diversity and Oil Degradation Potential of Culturable Microbes Isolated from Chronically Contaminated Soils in Trinidad. Microorganisms. 2021; 9 (6):1167.
Chicago/Turabian StyleAmanda Ramdass; Sephra Rampersad. 2021. "Diversity and Oil Degradation Potential of Culturable Microbes Isolated from Chronically Contaminated Soils in Trinidad." Microorganisms 9, no. 6: 1167.
The variability and phylogeny among TRI5, TRI8 and TRI11 nucleotide and translated protein sequences of isolates from Trinidad belonging to Fusarium incarnatum-equiseti species complex (FIESC) were compared with FIESC reference sequences. Taxa appeared to be more divergent when DNA sequences were analyzed compared to protein sequences. Neutral and non-neutral mutations in TRI protein sequences that may correspond to variability in the function and structure of the selected TRI proteins were identified. TRI5p had the lowest amino acid diversity with zero predicted non-neutral mutations. TRI5p had potentially three protein disorder regions compared to TRI8p with five protein disorder regions. The deduced TRI11p was more conserved than TRI8p of the same strains. Amino acid substitutions that may be non-neutral to protein function were only detected in diacetoxyscirpenol (DAS) and fusarenon-X (FUS-X) producers of the reference sequence subset for TRI8p and TRI11p. The deduced TRI5 and TRI8 amino acid sequences were mapped to known 3D-structure models and indicated that variations in specific protein order/disorder regions exist in these sequences which affect the overall structural conservation of TRI proteins. Assigning single or combination non-neutral mutations to a particular toxicogenic phenotype may be more representative of potential compared to using genotypic data alone, especially in the absence of wet-lab, experimental validation.
Ria T. Villafana; Sephra N. Rampersad. Signatures of TRI5, TRI8 and TRI11 Protein Sequences of Fusarium incarnatum-equiseti Species Complex (FIESC) Indicate Differential Trichothecene Analogue Production. Toxins 2020, 12, 386 .
AMA StyleRia T. Villafana, Sephra N. Rampersad. Signatures of TRI5, TRI8 and TRI11 Protein Sequences of Fusarium incarnatum-equiseti Species Complex (FIESC) Indicate Differential Trichothecene Analogue Production. Toxins. 2020; 12 (6):386.
Chicago/Turabian StyleRia T. Villafana; Sephra N. Rampersad. 2020. "Signatures of TRI5, TRI8 and TRI11 Protein Sequences of Fusarium incarnatum-equiseti Species Complex (FIESC) Indicate Differential Trichothecene Analogue Production." Toxins 12, no. 6: 386.
There is an urgency to supplant the heavy reliance on chemical control of Fusarium diseases in different economically important, staple food crops due to development of resistance in the pathogen population, the high cost of production to the risk-averse grower, and the concomitant environmental impacts. Pathogenomics has enabled (i) the creation of genetic inventories which identify those putative genes, regulators, and effectors that are associated with virulence, pathogenicity, and primary and secondary metabolism; (ii) comparison of such genes among related pathogens; (iii) identification of potential genetic targets for chemical control; and (iv) better characterization of the complex dynamics of host–microbe interactions that lead to disease. This type of genomic data serves to inform host-induced gene silencing (HIGS) technology for targeted disruption of transcription of select genes for the control of Fusarium diseases. This review discusses the various repositories and browser access points for comparison of genomic data, the strategies for identification and selection of pathogenicity- and virulence-associated genes and effectors in different Fusarium species, HIGS and successful Fusarium disease control trials with a consideration of loss of RNAi, off-target effects, and future challenges in applying HIGS for management of Fusarium diseases.
Sephra N. Rampersad. Pathogenomics and Management of Fusarium Diseases in Plants. Pathogens 2020, 9, 340 .
AMA StyleSephra N. Rampersad. Pathogenomics and Management of Fusarium Diseases in Plants. Pathogens. 2020; 9 (5):340.
Chicago/Turabian StyleSephra N. Rampersad. 2020. "Pathogenomics and Management of Fusarium Diseases in Plants." Pathogens 9, no. 5: 340.
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.
Ria T. Villafana; Sephra N. Rampersad. Three-Locus Sequence Identification and Differential Tebuconazole Sensitivity Suggest Novel Fusarium equiseti Haplotype from Trinidad. Pathogens 2020, 9, 175 .
AMA StyleRia T. Villafana, Sephra N. Rampersad. Three-Locus Sequence Identification and Differential Tebuconazole Sensitivity Suggest Novel Fusarium equiseti Haplotype from Trinidad. Pathogens. 2020; 9 (3):175.
Chicago/Turabian StyleRia T. Villafana; Sephra N. Rampersad. 2020. "Three-Locus Sequence Identification and Differential Tebuconazole Sensitivity Suggest Novel Fusarium equiseti Haplotype from Trinidad." Pathogens 9, no. 3: 175.
Fusarium is among the top 10 most economically important plant pathogens in the world. Trichothecenes are the principal mycotoxins produced as secondary metabolites by select species of Fusarium and cause acute and chronic toxicity in animals and humans upon exposure either through consumption and/or contact. There are over 100 trichothecene metabolites and they can occur in a wide range of commodities that form food and feed products. This review discusses strategies to mitigate the risk of mycotoxin production and exposure by examining the Fusarium-trichothecene model. Fundamental to mitigation of risk is knowing the identity of the pathogen. As such, a comparison of current, recommended molecular approaches for sequence-based identification of Fusaria is presented, followed by an analysis of the rationale and methods of trichothecene (TRI) genotyping and chemotyping. This type of information confirms the source and nature of risk. While both are powerful tools for informing regulatory decisions, an assessment of the causes of incongruence between TRI genotyping and chemotyping data must be made. Reconciliation of this discordance will map the way forward in terms of optimization of molecular approaches, which includes data validation and sharing in the form of accessible repositories of genomic data and browsers for querying such data.
Ria T. Villafana; Amanda C. Ramdass; Sephra N. Rampersad. TRI Genotyping and Chemotyping: A Balance of Power. Toxins 2020, 12, 64 .
AMA StyleRia T. Villafana, Amanda C. Ramdass, Sephra N. Rampersad. TRI Genotyping and Chemotyping: A Balance of Power. Toxins. 2020; 12 (2):64.
Chicago/Turabian StyleRia T. Villafana; Amanda C. Ramdass; Sephra N. Rampersad. 2020. "TRI Genotyping and Chemotyping: A Balance of Power." Toxins 12, no. 2: 64.
Colletotrichum species complexes are among the top 10 economically important fungal plant pathogens worldwide because they can infect climacteric and nonclimacteric fruit at the pre and/or postharvest stages. C. truncatum is the major pathogen responsible for anthracnose of green and red bell pepper fruit worldwide. C. brevisporum was recently reported to be a minor pathogen of red bell pepper fruit in Trinidad, but has recently been reported as pathogenic to other host species in other countries. The ability of these phytopathogens to produce and secrete cutinase is required for dismantling the cuticle of the host plant and, therefore, crucial to the necrotrophic phase of their infection strategy. In vitro bioassays using different lipid substrates confirmed the ability of C. truncatum and C. brevisporum isolates from green and red bell peppers to secrete cutinase. The diversity, structure and organization and synteny of the cutinase gene were determined among different Colletotrichum species. Cluster analysis indicated a low level of nucleotide variation among C. truncatum sequences. Nucleotide sequences of C. brevisporum were more related to C. truncatum cutinase nucleotide sequences than to C. gloeosporioides. Cluster patterns coincided with haplotype and there was evidence of significant positive selection with no recombination signatures. The structure of the cutinase gene included two exons with one intervening intron and, therefore, one splice variant. Although amino acid sequences were highly conserved among C. truncatum isolates, diversity “hot spots” were revealed when the 66‐amino acid coding region of 200 fungal species was compared. Twenty cutinase orthologues were detected among different fungal species, whose common ancestor is Pezizomycotina and it is purported that these orthologues arose through a single gene duplication event prior to speciation. The cutinase domain was retained both in structure and arrangement among 34 different Colletotrichum species. The order of aligned genomic blocks between species and the arrangement of flanking protein domains were also conserved and shared for those domains immediately located at the N‐ and C‐terminus of the cutinase domain. Among these were an RNA recognition motif, translation elongation factor, signal peptide, pentatricopeptide repeat, and Hsp70 family of chaperone proteins, all of which support the expression of the cutinase gene. The findings of this study are important to understanding the evolution of the cutinase gene in C. truncatum as a key component of the biotrophic–necrotrophic switch which may be useful in developing gene‐targeting strategies to decrease the pathogenic potential of Colletotrichum species.
Ria T. Villafana; Sephra N. Rampersad. Diversity, structure, and synteny of the cutinase gene ofColletotrichumspecies. Ecology and Evolution 2020, 10, 1425 -1443.
AMA StyleRia T. Villafana, Sephra N. Rampersad. Diversity, structure, and synteny of the cutinase gene ofColletotrichumspecies. Ecology and Evolution. 2020; 10 (3):1425-1443.
Chicago/Turabian StyleRia T. Villafana; Sephra N. Rampersad. 2020. "Diversity, structure, and synteny of the cutinase gene ofColletotrichumspecies." Ecology and Evolution 10, no. 3: 1425-1443.
Trichothecene mycotoxins are a class of secondary metabolites produced by multiple genera of fungi, including certain plant pathogenic Fusarium species. Functional variation in the TRI1 gene produces a novel Type A trichothecene called NX-2 in strains of F. graminearum. Using a bioinformatics approach, a systematic analysis of 52 translated TRI1 sequences of Fusarium species, including five F. graminearum NX-2 producers and four F. graminearum non-NX-2 producers, was conducted to explain the functional difference of TRI1p of FGNX-2. An assessment of several signature motifs of fungal P450s revealed amino acid substitutions in addition to the post-translational N-X-S/T sequons motif, which is indicative of N-linked glycosylation of this TRI1-encoded protein characteristic of NX-2 producers. There was evidence of selection bias, where TRI1 gene sequences were found to be under positive selection and, therefore, under functional constraints. The cumulative amino acid changes in the TRI1p sequences were reflected in the phylogenetic analyses which revealed species-specific clustering with a distinct separation of FGNX-2 from FG-non-NX-2 producers with high bootstrap support. Together, our findings provide insight into the amino acid sequence features responsible for the functional diversification of this TRI1p.
Amanda C. Ramdass; Ria T. Villafana; Sephra N. Rampersad. Comparative Sequence Analysis of TRI1 of Fusarium. Toxins 2019, 11, 689 .
AMA StyleAmanda C. Ramdass, Ria T. Villafana, Sephra N. Rampersad. Comparative Sequence Analysis of TRI1 of Fusarium. Toxins. 2019; 11 (12):689.
Chicago/Turabian StyleAmanda C. Ramdass; Ria T. Villafana; Sephra N. Rampersad. 2019. "Comparative Sequence Analysis of TRI1 of Fusarium." Toxins 11, no. 12: 689.
This study was carried out towards the development of rapid PCR-based assays for detection and identification of Colletotrichum truncatum, C. gloeosporioides sensu lato and Fusarium sp. infecting green and red bell pepper seeds in Trinidad using DNA templates produced by automated grinding and robotic paramagnetic particle capture. DNA was extracted from freshly collected symptomatic green and red bell pepper seeds using Promega’s Maxwell® 16 robotic system. The PCR assay of 220 seeds harvested from field-infected bell pepper fruit compared different optimization parameters including seeds that were symptomatic and asymptomatic of infection, the relative success of two different DNA polymerase enzymes, genus-specific and species-specific primers that were pre-existing in the literature in addition to primers that were newly designed for this study and duplex PCR for the simultaneous detection of DNA templates belonging to two different fungal species. The findings indicated that seeds carried dual infections of C. truncatum and Fusarium sp. Compared to other primers that were screened, our newly designed primers, ITS219-F/ITS419-R with GoTaq® Green Master Hot Start Taq DNA Polymerase, detected C. truncatum in the highest number of symptomatic seeds of infected green and red bell pepper fruit as well as in asymptomatic seeds of infected red bell pepper fruit. Fusarium sp. was detected only in red bell pepper seeds. Duplex PCR using ITS219-F/ITS419-R and Fa/Ra primers successfully simultaneously detected and identified C. truncatum and Fusarium sp. in symptomatic seeds of infected red bell pepper fruit. None of the seeds were infected with C. gloeosporioides sensu lato which is currently considered to be a minor pathogen in bell pepper in Trinidad. PCR-based detection methods are key tools in the detection and identification of fungal plant pathogens especially where seeds are an important inoculum source. The molecular approach as optimized in this study, is faster, more sensitive and the presence of single or dual fungal infections can be assessed in one assay.
Ria T. Villafana; Amanda C. Ramdass; Sephra N. Rampersad. Development of a new methodology for the detection of Colletotrichum truncatum and Fusarium sp. in bell pepper seed. Phytoparasitica 2019, 47, 543 -555.
AMA StyleRia T. Villafana, Amanda C. Ramdass, Sephra N. Rampersad. Development of a new methodology for the detection of Colletotrichum truncatum and Fusarium sp. in bell pepper seed. Phytoparasitica. 2019; 47 (4):543-555.
Chicago/Turabian StyleRia T. Villafana; Amanda C. Ramdass; Sephra N. Rampersad. 2019. "Development of a new methodology for the detection of Colletotrichum truncatum and Fusarium sp. in bell pepper seed." Phytoparasitica 47, no. 4: 543-555.
Food security is a global concern. Fusarium are among the most economically important fungal pathogens because they are ubiquitous, disease management remains a challenge, they produce mycotoxins that affect food and feed safety, and trichothecene mycotoxin production can increase the pathogenicity of some Fusarium species depending on the host species. Although trichothecenes may differ in structure by their patterns of hydroxylation or acetylation, these small changes have a significant impact on toxicity and the biological activity of these compounds. Therefore, detecting and identifying which chemotype is present in a given population are important to predicting the specific toxins that may be produced and, therefore, to evaluating the risk of exposure. Due to the challenges of inducing trichothecene production by Fusarium isolates in vitro for subsequent chemical analysis, PCR assays using gene-specific primers, either singly or in combination, designed against specific genes of the trichothecene gene cluster of multiple species of Fusarium have been developed. The establishment of TRI genotypes that potentially correspond to a specific chemotype requires examination of an information and knowledge pipeline whose critical aspects in sequential order are: (i) understanding the TRI gene cluster organization which differs according to Fusarium species under study; (ii) knowledge of the re-arrangements to the core TRI gene cluster over evolutionary time, which also differs according to Fusarium species; (iii) the functions of the TRI genes in the biosynthesis of trichothecene analogs; and (iv) based on (i)–(iii), selection of appropriate target TRI gene(s) for primer design in PCR amplification for the Fusarium species under study. This review, therefore, explains this pipeline and its connection to utilizing TRI genotypes as a possible proxy to chemotype designation.
Ria T. Villafana; Amanda C. Ramdass; Sephra N. Rampersad. Selection of Fusarium Trichothecene Toxin Genes for Molecular Detection Depends on TRI Gene Cluster Organization and Gene Function. Toxins 2019, 11, 36 .
AMA StyleRia T. Villafana, Amanda C. Ramdass, Sephra N. Rampersad. Selection of Fusarium Trichothecene Toxin Genes for Molecular Detection Depends on TRI Gene Cluster Organization and Gene Function. Toxins. 2019; 11 (1):36.
Chicago/Turabian StyleRia T. Villafana; Amanda C. Ramdass; Sephra N. Rampersad. 2019. "Selection of Fusarium Trichothecene Toxin Genes for Molecular Detection Depends on TRI Gene Cluster Organization and Gene Function." Toxins 11, no. 1: 36.
R. T. Villafana; A. C. Ramdass; S. N. Rampersad. First Report of Colletotrichum truncatum Causing Anthracnose in Tomato Fruit in Trinidad. Plant Disease 2018, 102, 1857 -1857.
AMA StyleR. T. Villafana, A. C. Ramdass, S. N. Rampersad. First Report of Colletotrichum truncatum Causing Anthracnose in Tomato Fruit in Trinidad. Plant Disease. 2018; 102 (9):1857-1857.
Chicago/Turabian StyleR. T. Villafana; A. C. Ramdass; S. N. Rampersad. 2018. "First Report of Colletotrichum truncatum Causing Anthracnose in Tomato Fruit in Trinidad." Plant Disease 102, no. 9: 1857-1857.
The islands of the Caribbean are considered to be a “biodiversity hotspot.” Collectively, a high level of endemism for several plant groups has been reported for this region. Biodiversity conservation should, in part, be informed by taxonomy, population status, and distribution of flora. One taxonomic impediment to species inventory and management is correct identification as conventional morphology-based assessment is subject to several caveats. DNA barcoding can be a useful tool to quickly and accurately identify species and has the potential to prompt the discovery of new species. In this study, the ability of DNA barcoding to confirm the identities of 14 endangered endemic vascular plant species in Trinidad was assessed using three DNA barcodes (matK, rbcL, and rpoC1). Herbarium identifications were previously made for all species under study. matK, rbcL, and rpoC1 markers were successful in amplifying target regions for seven of the 14 species. rpoC1 sequences required extensive editing and were unusable. rbcL primers resulted in cleanest reads, however, matK appeared to be superior to rbcL based on a number of parameters assessed including level of DNA polymorphism in the sequences, genetic distance, reference library coverage based on BLASTN statistics, direct sequence comparisons within “best match” and “best close match” criteria, and finally, degree of clustering with moderate to strong bootstrap support (>60%) in neighbor-joining tree-based comparisons. The performance of both markers seemed to be species-specific based on the parameters examined. Overall, the Trinidad sequences were accurately identified to the genus level for all endemic plant species successfully amplified and sequenced using both matK and rbcL markers. DNA barcoding can contribute to taxonomic and biodiversity research and will complement efforts to select taxa for various molecular ecology and population genetics studies.
Fazeeda N. Hosein; Nigel Austin; Shobha Maharaj; Winston Johnson; Luke Rostant; Amanda C. Ramdass; Sephra N. Rampersad. Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad. Ecology and Evolution 2017, 7, 7311 -7333.
AMA StyleFazeeda N. Hosein, Nigel Austin, Shobha Maharaj, Winston Johnson, Luke Rostant, Amanda C. Ramdass, Sephra N. Rampersad. Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad. Ecology and Evolution. 2017; 7 (18):7311-7333.
Chicago/Turabian StyleFazeeda N. Hosein; Nigel Austin; Shobha Maharaj; Winston Johnson; Luke Rostant; Amanda C. Ramdass; Sephra N. Rampersad. 2017. "Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad." Ecology and Evolution 7, no. 18: 7311-7333.
Bell pepper is an economically important crop worldwide; however, production is restricted by a number of fungal diseases that cause significant yield loss. Chemical control is the most common approach adopted by growers to manage a number of these diseases. Monitoring for the development to resistance to fungicides in pathogenic fungal populations is central to devising integrated pest management strategies. Two fungal species, Fusarium incarnatum-equiseti species complex (FIESC) and Colletotrichum truncatum are important pathogens of bell pepper in Trinidad. This study was carried out to determine the sensitivity of 71 isolates belonging to these two fungal species to fungicides with different modes of action based on in vitro bioassays. There was no significant difference in log effective concentration required to achieve 50% colony growth inhibition (LogEC50) values when field location and fungicide were considered for each species separately based on ANOVA analyses. However, the LogEC50 value for the Aranguez-Antracol location-fungicide combination was almost twice the value for the Maloney/Macoya-Antracol location-fungicide combination regardless of fungal species. LogEC50 values for Benomyl fungicide was also higher for C. truncatum isolates than for FIESC isolates and for any other fungicide. Cropping practices in these locations may explain the fungicide sensitivity data obtained.
Hema Ramdial; Kathryn De Abreu; Sephra N. Rampersad. Fungicide Sensitivity among Isolates of Colletotrichum truncatum and Fusarium incarnatum-equiseti Species Complex Infecting Bell Pepper in Trinidad. The Plant Pathology Journal 2017, 33, 118 -124.
AMA StyleHema Ramdial, Kathryn De Abreu, Sephra N. Rampersad. Fungicide Sensitivity among Isolates of Colletotrichum truncatum and Fusarium incarnatum-equiseti Species Complex Infecting Bell Pepper in Trinidad. The Plant Pathology Journal. 2017; 33 (2):118-124.
Chicago/Turabian StyleHema Ramdial; Kathryn De Abreu; Sephra N. Rampersad. 2017. "Fungicide Sensitivity among Isolates of Colletotrichum truncatum and Fusarium incarnatum-equiseti Species Complex Infecting Bell Pepper in Trinidad." The Plant Pathology Journal 33, no. 2: 118-124.
The Colletotrichum gloeosporioides species complex is among the most destructive fungal plant pathogens in the world, however, identification of member species which are of quarantine importance is impacted by a number of factors that negatively affect species identification. Structural information of the rRNA marker may be considered to be a conserved marker which can be used as supplementary information for possible species identification. The difficulty in using ITS rDNA sequences for identification lies in the low level of sequence variation at the intra-specific level and the generation of artificially-induced sequence variation due to errors in polymerization of the ITS array during DNA replication. Type and query ITS sequences were subjected to sequence analyses prior to generation of predicted consensus secondary structures, including the pattern of nucleotide polymorphisms and number of indel haplotypes, GC content, and detection of artificially-induced sequence variation. Data pertaining to structure stability, the presence of conserved motifs in secondary structures and mapping of all sequences onto the consensus C. gloeosporioides sensu stricto secondary structure for ITS1, 5.8S and ITS2 markers was then carried out. Motifs that are evolutionarily conserved among eukaryotes were found for all ITS1, 5.8S and ITS2 sequences. The sequences exhibited conserved features typical of functional rRNAs. Generally, polymorphisms occurred within less conserved regions and were seen as bulges, internal and terminal loops or non-canonical G-U base-pairs within regions of the double stranded helices. Importantly, there were also taxonomic motifs and base changes that were unique to specific taxa and which may be used to support intra-specific identification of members of the C. gloeosporioides sensu lato species complex.
Sephra N Rampersad. ITS1, 5.8S and ITS2 secondary structure modelling for intra-specific differentiation among species of the Colletotrichum gloeosporioides sensu lato species complex. SpringerPlus 2014, 3, 684 .
AMA StyleSephra N Rampersad. ITS1, 5.8S and ITS2 secondary structure modelling for intra-specific differentiation among species of the Colletotrichum gloeosporioides sensu lato species complex. SpringerPlus. 2014; 3 (1):684.
Chicago/Turabian StyleSephra N Rampersad. 2014. "ITS1, 5.8S and ITS2 secondary structure modelling for intra-specific differentiation among species of the Colletotrichum gloeosporioides sensu lato species complex." SpringerPlus 3, no. 1: 684.
The Colletotrichum gloeosporioides species complex is among the most destructive fungal plant pathogens in the world, however, identification of isolates of quarantine importance to the intra-specific level is confounded by a number of factors that affect phylogenetic reconstruction. Information bias and quality parameters were investigated to determine whether nucleotide sequence alignments and phylogenetic trees accurately reflect the genetic diversity and phylogenetic relatedness of individuals. Sequence exploration of GAPDH, ACT, TUB2 and ITS markers indicated that the query sequences had different patterns of nucleotide substitution but were without evidence of base substitution saturation. Regions of high entropy were much more dispersed in the ACT and GAPDH marker alignments than for the ITS and TUB2 markers. A discernible bimodal gap in the genetic distance frequency histograms was produced for the ACT and GAPDH markers which indicated successful separation of intra- and inter-specific sequences in the data set. Overall, analyses indicated clear differences in the ability of these markers to phylogenetically separate individuals to the intra-specific level which coincided with information bias.
Sephra N Rampersad; Fazeeda N Hosein; Christine Vf Carrington. Sequence exploration reveals information bias among molecular markers used in phylogenetic reconstruction for Colletotrichum species. SpringerPlus 2014, 3, 1 -15.
AMA StyleSephra N Rampersad, Fazeeda N Hosein, Christine Vf Carrington. Sequence exploration reveals information bias among molecular markers used in phylogenetic reconstruction for Colletotrichum species. SpringerPlus. 2014; 3 (1):1-15.
Chicago/Turabian StyleSephra N Rampersad; Fazeeda N Hosein; Christine Vf Carrington. 2014. "Sequence exploration reveals information bias among molecular markers used in phylogenetic reconstruction for Colletotrichum species." SpringerPlus 3, no. 1: 1-15.
Anthracnose fruit rot of pepper (Capsicum spp.) is an economically important disease in many countries worldwide. This study was conducted to identify and characterize the pathogens responsible for anthracnose disease in bell peppers (C. annuum L.) in Trinidad. Seventy-two percent of all isolates were Colletotrichum truncatum and 28% were C. gloeosporioides. Growth rate and conidia dimensions were reliable morphological markers that allowed differentiation between C. gloeosporioides and C. truncatum isolates. Benomyl sensitivity testing also distinguished between isolates of C. gloeosporioides and C. truncatum. C. truncatum was resistant to benomyl at all concentrations tested while C. gloeosporioides sensu lato was sensitive to concentrations above 0.1 μg ml-1 . Pathogenicity tests demonstrated different levels of resistance to anthracnose in various Capsicum genotypes. C. gloeosporioides sensu lato isolates caused significantly greater damage than C. truncatum isolates regardless of pepper cultivar. PCR with taxon- and species-specific primers produced amplicons of expected band sizes for all Colletotrichum species and only for C. gloeosporioides, respectively. Molecular analysis of ITS and β-tubulin sequences positioned C. gloeosporioides sensu lato and C. truncatum isolates from bell pepper into separate species-specific clusters.
Hema Ramdial; Sephra N. Rampersad. Characterization of Colletotrichum spp. causing anthracnose of bell pepper (Capsicum annuum L.) in Trinidad. Phytoparasitica 2014, 43, 37 -49.
AMA StyleHema Ramdial, Sephra N. Rampersad. Characterization of Colletotrichum spp. causing anthracnose of bell pepper (Capsicum annuum L.) in Trinidad. Phytoparasitica. 2014; 43 (1):37-49.
Chicago/Turabian StyleHema Ramdial; Sephra N. Rampersad. 2014. "Characterization of Colletotrichum spp. causing anthracnose of bell pepper (Capsicum annuum L.) in Trinidad." Phytoparasitica 43, no. 1: 37-49.
C. gloeosporioides sensu lato is one of the most economically important post-harvest diseases affecting papaya production worldwide. There is currently no information concerning the genetic structure or demographic history of this pathogen in any of the affected countries. Knowledge of molecular demographic parameters for different populations will improve our understanding of the biogeographic history as well as the evolutionary and adaptive potential of these pathogens. In this study, sequence data for ACT, GPDH, β-TUB and ITS gene regions were analyzed for C. gloeosporioides sensu lato and C. truncatum isolates infecting papaya in Trinidad and Mexico in order to determine the genetic structure and demographic history of these populations. The data indicated that Mexico is the ancestral C. gloeosporioides sensu lato population with asymmetrical migration to Trinidad. Mexico also had the larger effective population size but, both Mexico and Trinidad populations exhibited population expansion. Mexico also had greater nucleotide diversity and high levels of diversity for each gene. There was significant sub-division of the Trinidad and Mexico populations and low levels of genetic divergence among populations for three of the four gene regions; β-TUB was shown to be under positive selection. There were also dissimilar haplotype characteristics for both populations. Mutation may play a role in shaping the population structure of C. gloeosporioides sensu lato isolates from Trinidad and from Mexico, especially with respect to the ACT and GPDH gene regions. There was no evidence of gene flow between the C. truncatum populations and it is possible that the Mexico and Trinidad populations emerged independently of each other. The study revealed relevant information based on the genetic structure as well as the demographic history of two fungal pathogens infecting papaya, C. gloeosporioides sensu lato and C. truncatum, in Trinidad and Mexico. Understanding the genetic structure of pathogen populations will assist in determining the evolutionary potential of the pathogen and in identifying which evolutionary forces may have the greatest impact on durability of resistance. Intervention strategies that target these evolutionary forces would prove to be the most practical.
Sephra N Rampersad; Daisy Pérez-Brito; Claudia Torres-Calzada; Raul Tapia-Tussell; Christine Vf Carrington. Genetic structure and demographic history of Colletotrichum gloeosporioides sensu lato and C. truncatum isolates from Trinidad and Mexico. BMC Evolutionary Biology 2013, 13, 1 -17.
AMA StyleSephra N Rampersad, Daisy Pérez-Brito, Claudia Torres-Calzada, Raul Tapia-Tussell, Christine Vf Carrington. Genetic structure and demographic history of Colletotrichum gloeosporioides sensu lato and C. truncatum isolates from Trinidad and Mexico. BMC Evolutionary Biology. 2013; 13 (1):1-17.
Chicago/Turabian StyleSephra N Rampersad; Daisy Pérez-Brito; Claudia Torres-Calzada; Raul Tapia-Tussell; Christine Vf Carrington. 2013. "Genetic structure and demographic history of Colletotrichum gloeosporioides sensu lato and C. truncatum isolates from Trinidad and Mexico." BMC Evolutionary Biology 13, no. 1: 1-17.
Colletotrichum gloeosporioides sensu lato is widely distributed throughout temperate and tropical regions and causes anthracnose disease in numerous plant species. Development of effective disease management strategies is dependent on, among other factors, an understanding of pathogen genetic diversity and population stratification at the intraspecific level. For 132 isolates of C. gloeosporioides sensu lato collected from papaya in Trinidad, inter-simple-sequence repeat-polymerase chain reaction (ISSR-PCR) generated 121 polymorphic loci from five ISSR primers selected from an initial screen of 22 ISSR primers. The mean percentage of polymorphic loci was 99.18%. Bayesian cluster analysis inferred three genetic subpopulations, where group 1 consisted exclusively of isolates collected in the southern part of Trinidad whereas groups 2 and 3, although genetically distinct, were mixtures of isolates collected from both the northern and southern parts of Trinidad. Principal coordinates analysis and unweighted pair-group method with arithmetic mean phylogeny were concordant with Bayesian cluster analysis and supported subdivision into the three subpopulations. Overall, the total mean gene diversity was 0.279, the mean within-population gene diversity was 0.2161, and genetic differentiation for the Trinidad population was 0.225. Regionally, northern isolates had a lower gene diversity compared with southern isolates. Nei's gene diversity was highest for group 1 (h = 0.231), followed by group 2 (h = 0.215) and group 3 (h = 0.202). Genotypic diversity was at or near maximum for all three subpopulations after clone correction. Pairwise estimates of differentiation indicated high and significant genetic differentiation among the inferred subpopulations (Weir's θ of 0.212 to 0.325). Pairwise comparisons among subpopulations suggested restricted gene flow between groups 1 and 2 and groups 1 and 3 but not between groups 2 and 3. The null hypothesis of random mating was rejected for all three inferred subpopulations. These results suggest that pathogen biology and epidemiology as well as certain evolutionary factors may play an important role in population substructuring of C. gloeosporioides sensu lato isolates infecting papaya in Trinidad.
Sephra N. Rampersad. Genetic Structure of Colletotrichum gloeosporioides sensu lato Isolates Infecting Papaya Inferred by Multilocus ISSR Markers. Phytopathology® 2013, 103, 182 -189.
AMA StyleSephra N. Rampersad. Genetic Structure of Colletotrichum gloeosporioides sensu lato Isolates Infecting Papaya Inferred by Multilocus ISSR Markers. Phytopathology®. 2013; 103 (2):182-189.
Chicago/Turabian StyleSephra N. Rampersad. 2013. "Genetic Structure of Colletotrichum gloeosporioides sensu lato Isolates Infecting Papaya Inferred by Multilocus ISSR Markers." Phytopathology® 103, no. 2: 182-189.
Accurate prediction of the adverse effects of test compounds on living systems, detection of toxic thresholds, and expansion of experimental data sets to include multiple toxicity end-point analysis are required for any robust screening regime. Alamar Blue is an important redox indicator that is used to evaluate metabolic function and cellular health. The Alamar Blue bioassay has been utilized over the past 50 years to assess cell viability and cytotoxicity in a range of biological and environmental systems and in a number of cell types including bacteria, yeast, fungi, protozoa and cultured mammalian and piscine cells. It offers several advantages over other metabolic indicators and other cytotoxicity assays. However, as with any bioassay, suitability must be determined for each application and cell model. This review seeks to highlight many of the important considerations involved in assay use and design in addition to the potential pitfalls.
Sephra N. Rampersad. Multiple Applications of Alamar Blue as an Indicator of Metabolic Function and Cellular Health in Cell Viability Bioassays. Sensors 2012, 12, 12347 -12360.
AMA StyleSephra N. Rampersad. Multiple Applications of Alamar Blue as an Indicator of Metabolic Function and Cellular Health in Cell Viability Bioassays. Sensors. 2012; 12 (9):12347-12360.
Chicago/Turabian StyleSephra N. Rampersad. 2012. "Multiple Applications of Alamar Blue as an Indicator of Metabolic Function and Cellular Health in Cell Viability Bioassays." Sensors 12, no. 9: 12347-12360.
Colletotrichum gloeosporioides sensu lato is one of the most common and widely distributed plant pathogens in the world. Understanding fungal biodiversity is hinged on accurate identification and delimitation at the inter- and intraspecific levels. Sequences of the ITS1-5.8S-ITS2 region (ITS), β-tubulin (TUB), actin (ACT), and glyceraldehyde-3-phosphate dehydrogenase (GPDH) genes of 30 C. gloeosporioides sensu lato isolates, collected from anthracnose infected papaya fruits grown in the main production areas in Trinidad, were analyzed by in silico PCR-RFLP analysis with the aim of identifying which gene region(s) had the highest level of intraspecific polymorphism. Restriction site polymorphisms generated from 13 restriction enzymes enabled the identification of specific enzymes that were successful at intraspecific discrimination of the C. gloeosporioides isolates. Genetic distance values were reflective of the level of polymorphisms obtained for the four different gene regions. In both cases (calculated genetic distance and percentage of polymorphic loci from RFLP profiles), ACT and ITS gene regions had the highest level of restriction site polymorphisms and genetic diversity, GPDH and TUB had the lowest. Cluster analysis based on PCR-RFLP genetic distance data revealed sub-specific placement of the isolates which appeared to be gene-dependent. The implications of these findings are discussed relative to biodiversity monitoring and the need for multilocus, polyphasic investigations which must take into account the possibility of exaggerated estimates of genetic diversity.
Stephen Ramdeen; Sephra N. Rampersad. Intraspecific Differentiation of Colletotrichum gloeosporioides sensu lato Based on In Silico Multilocus PCR-RFLP Fingerprinting. Molecular Biotechnology 2012, 53, 170 -181.
AMA StyleStephen Ramdeen, Sephra N. Rampersad. Intraspecific Differentiation of Colletotrichum gloeosporioides sensu lato Based on In Silico Multilocus PCR-RFLP Fingerprinting. Molecular Biotechnology. 2012; 53 (2):170-181.
Chicago/Turabian StyleStephen Ramdeen; Sephra N. Rampersad. 2012. "Intraspecific Differentiation of Colletotrichum gloeosporioides sensu lato Based on In Silico Multilocus PCR-RFLP Fingerprinting." Molecular Biotechnology 53, no. 2: 170-181.