scholarly journals Genome-wide characterization deciphers distinct properties of major intrinsic proteins in six Phytophthora species

2018 ◽  
Author(s):  
Abul Kalam Azad ◽  
Jahed Ahmed ◽  
Al Hakim ◽  
Md. Mahbub Hasan ◽  
Md. Asraful Alum ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Phytophthora Species ◽  
Membrane Diffusion ◽  
Transmembrane Helices ◽  
Consensus Sequences ◽  
Major Intrinsic Proteins ◽  
Genome Wide ◽  
Polar Solutes ◽  
Distinct Lineage ◽  
Eukaryotic Microbes

ABSTRACTMajor intrinsic proteins (MIPs), commonly known as aquaporins, facilitate the membrane diffusion of water and some other non- polar solutes. MIPs might be involved in host-pathogen interactions. Herein, we identified 17, 24, 27, 19, 19, and 22 full-length MIPs, respectively, in the genomes of six Phytophthora species, P. infestans, P. parasitica, P. sojae, P. ramorum, P. capsici, and P. cinnamomi. These Phytophthora species are devastating plant pathogens and members of oomycetes, a distinct lineage of fungus-like eukaryotic microbes. Phylogenetic analysis showed that the Phytophthora MIPs (PMIPs) formed a completely distinct clade from their counterparts in other taxa and were clustered into nine subgroups. Sequence and structural properties indicated that the primary selectivity-related constrictions, including aromatic arginine (ar/R) selectivity filter and Froger’s positions in PMIPs were distinct from those in other taxa. The substitutions in the conserved Asn-Pro-Ala motifs in loops B and E of many PMIPs were also divergent from those in plants. We further deciphered group-specific consensus sequences/motifs in different loops and transmembrane helices of PMIPs, which were distinct from those in plants, animals, and microbes. The data collectively supported the notion that PMIPs might have novel functions.

Genome-wide Characterization Deciphers Distinct Properties of Aquaporins in Six Phytophthora species

2021 ◽  
Vol 16 ◽  
Author(s):  
Abul Kalam Azad ◽  
Jahed Ahmed ◽  
Al Hakim ◽  
Md. Mahbub Hasan ◽  
Md. Asraful Alum ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Structural Properties ◽  
Phytophthora Species ◽  
Likelihood Method ◽  
Membrane Diffusion ◽  
Consensus Sequences ◽  
Physiological Processes ◽  
Stereochemical Quality ◽  
Domains Of Life ◽  
Plant Pathogen Interactions

Background: Aquaporins, also known as major intrinsic proteins (MIPs), facilitate the membrane diffusion of water and some other small solutes. The role of MIPs in plant physiological processes is established and now their roles in plant-pathogen interactions are getting more attention. Objective: To investigate the evolution, diversity, and structural insights of Phytophthora MIPs (PhyMIPs) and to compare them to those in other domains of life. Methods: Bioinformatics approaches were used to identify and characterize the PhyMIPs. The phylogenetic analysis was done with MEGA7.0 using maximum likelihood method. The prediction of transmembrane α-helices was done by using SOSUI and TMpred servers, and that of subcellular localization was performed with WoLF PSORT and Cello prediction system. The structure of PhyMIP genes was predicted by GeneMark.hmm ES-3.0 program. The 3D homology models were generated using the Molecular Operating Environment software and the stereochemical quality of the templates and models was assessed by PROCHECK. The PoreWalker server was used to detect and characterize PhyMIP channels from their 3D structural models. Results: Herein, we identified 17, 24, 27, 19, 19, and 22 full-length MIPs, respectively, in the genomes of six Phytophthora species, P. infestans, P. parasitica, P. sojae, P. ramorum, P. capsici,and P. cinnamomi. Phylogenetic analysis showed that the PhyMIPs formed a completely distinct clade from their counterparts in other taxa and were clustered into nine subgroups. Sequence and structural properties indicated that the primary selectivity-related constrictions, including aromatic arginine (ar/R) selectivity filter and Froger's positions in PhyMIPs were distinct from those in other taxa. The substitutions in the conserved Asn-Pro-Ala motifs in loops B and E of many PhyMIPs were also divergent from those in other taxonomic domains. The group-specific consensus sequences/motifs deciphered in different loops and transmembrane α-helices of PhyMIPs were distinct from those in plants, animals, and other microbes. Conclusion: This study represents PhyMIPs with distinct evolutionary and structural properties, and the data collectively indicates that PhyMIPs might have novel functions.

scholarly journals High-Quality Genome Resource of the Pathogen of Diaporthe (Phomopsis) phragmitis Causing Kiwifruit Soft Rot

2020 ◽  
Author(s):  
Pu Liu ◽  
Wang Xiaojie ◽  
Dong Hongjie ◽  
Jianbin Lan ◽  
Kuan Liang ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Management Strategies ◽  
Soft Rot ◽  
Fruit Rot ◽  
Economic Plant ◽  
High Quality ◽  
Total Size ◽  
Genome Wide ◽  
Solid Foundation ◽  
High Quality Genome

Diaporthe spp. are critical plant pathogens that cause wood cankers, wilt, dieback, and fruit rot in a wide variety of economic plant hosts and are regarded as one of the most acute threats faced by kiwifruit industry worldwide. Diaporthe phragmitis strain NJD1 is a highly pathogenic isolate of soft rot of kiwifruit. Here, we present a high-quality genome-wide sequence of D. phragmitis NJD1 that was assembled into 28 contigs containing a total size of 58.33 Mb and N50 length of 3.55 Mb. These results lay a solid foundation for understanding host–pathogen interaction and improving disease management strategies.

scholarly journals Comparative Genomic and Proteomic Analyses of Three Widespread Phytophthora Species: Phytophthora chlamydospora, Phytophthora gonapodyides and Phytophthora pseudosyringae

2020 ◽  
Vol 8 (5) ◽  
pp. 653 ◽  
Author(s):  
Jamie McGowan ◽  
Richard O’Hanlon ◽  
Rebecca A. Owens ◽  
David A. Fitzpatrick
Keyword(s):  
Mass Spectrometry ◽  
Plant Pathogens ◽  
Genome Structure ◽  
Draft Genome ◽  
Phytophthora Species ◽  
Comparative Genomic ◽  
Tandem Gene Duplication ◽  
Widespread Species ◽  
Forest Pathogen ◽  
Extracellular Proteome

The Phytophthora genus includes some of the most devastating plant pathogens. Here we report draft genome sequences for three ubiquitous Phytophthora species—Phytophthora chlamydospora, Phytophthora gonapodyides, and Phytophthora pseudosyringae. Phytophthora pseudosyringae is an important forest pathogen that is abundant in Europe and North America. Phytophthora chlamydospora and Ph. gonapodyides are globally widespread species often associated with aquatic habitats. They are both regarded as opportunistic plant pathogens. The three sequenced genomes range in size from 45 Mb to 61 Mb. Similar to other oomycete species, tandem gene duplication appears to have played an important role in the expansion of effector arsenals. Comparative analysis of carbohydrate-active enzymes (CAZymes) across 44 oomycete genomes indicates that oomycete lifestyles may be linked to CAZyme repertoires. The mitochondrial genome sequence of each species was also determined, and their gene content and genome structure were compared. Using mass spectrometry, we characterised the extracellular proteome of each species and identified large numbers of proteins putatively involved in pathogenicity and osmotrophy. The mycelial proteome of each species was also characterised using mass spectrometry. In total, the expression of approximately 3000 genes per species was validated at the protein level. These genome resources will be valuable for future studies to understand the behaviour of these three widespread Phytophthora species.

scholarly journals Validation of a Preformulated, Field Deployable, Recombinase Polymerase Amplification Assay for Phytophthora Species

Plants ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 466
Author(s):  
Austin G. McCoy ◽  
Timothy D. Miles ◽  
Guillaume J. Bilodeau ◽  
Patrick Woods ◽  
Cheryl Blomquist ◽  
...  
Keyword(s):  
Plant Extract ◽  
Plant Pathogens ◽  
Limit Of Detection ◽  
Quantitative Polymerase Chain Reaction ◽  
Phytophthora Species ◽  
Recombinase Polymerase Amplification ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Liquid Form ◽  
Crude Plant Extract

Recombinase polymerase amplification (RPA) assays are valuable molecular diagnostic tools that can detect and identify plant pathogens in the field without time-consuming DNA extractions. Historically, RPA assay reagents were commercially available as a lyophilized pellet in microfuge strip tubes, but have become available in liquid form more recently—both require the addition of primers and probes prior to use, which can be challenging to handle in a field setting. Lyophilization of primers and probes, along with RPA reagents, contained within a single tube limits the risk of contamination, eliminates the need for refrigeration, as the lyophilized reagents are stable at ambient temperatures, and simplifies field use of the assays. This study investigates the potential effect of preformulation on assay performance using a previously validated Phytophthora genus-specific RPA assay, lyophilized with primers and probes included with the RPA reagents. The preformulated lyophilized Phytophthora RPA assay was compared with a quantitative polymerase chain reaction (qPCR) assay and commercially available RPA kits using three qPCR platforms (BioRad CFX96, QuantStudio 6 and Applied Biosystems ViiA7) and one isothermal platform (Axxin T16-ISO RPA), with experiments run in four separate labs. The assay was tested for sensitivity (ranging from 500 to 0.33 pg of DNA) and specificity using purified oomycete DNA, as well as crude extracts of Phytophthora-infected and non-infected plants. The limit of detection (LOD) using purified DNA was 33 pg in the CFX96 and ViiA7 qPCR platforms using the preformulated kits, while the Axxin T16-ISO RPA chamber and the QuantStudio 6 platform could detect down to 3.3 pg with or without added plant extract. The LOD using a crude plant extract for the BioRad CFX96 was 330 pg, whereas the LOD for the ViiA7 system was 33 pg. These trials demonstrate the consistency and uniformity of pathogen detection with preformulated RPA kits for Phytophthora detection when conducted by different labs using different instruments for measuring results.

scholarly journals Towards on-site testing of Phytophthora species

2015 ◽  
Vol 7 (1) ◽  
pp. 211-217 ◽  
Author(s):  
Lydia Schwenkbier ◽  
Sibyll Pollok ◽  
Stephan König ◽  
Matthias Urban ◽  
Sabine Werres ◽  
...  
Keyword(s):  
Rapid Detection ◽  
Plant Pathogens ◽  
Phytophthora Species ◽  
Site Testing ◽  
Accurate Identification

Rapid detection and accurate identification of plant pathogens in the field is an ongoing challenge.

scholarly journals A Lucid Key to the Common Species of Phytophthora

Plant Disease ◽  
2012 ◽  
Vol 96 (6) ◽  
pp. 897-903 ◽  
Author(s):  
Jean Beagle Ristaino
Keyword(s):  
Plant Pathogens ◽  
Common Species ◽  
Morphological Characters ◽  
Phytophthora Species ◽  
Molecular Characteristics ◽  
Character State ◽  
Disease Symptoms ◽  
Fact Sheet ◽  
The Common ◽  
Simple Search

The Key to the Common Phytophthora species (Lucid v 3.4) is a matrix-based computerized identification key and includes important morphological and molecular characters that are useful for identification of 55 common species of Phytophthora. A set of 20 features are used to make a correct species identification. Once a culture is obtained, the user enters responses to known character state options into Lucid Player, and the correct species is identified. Illustrations of each character state for a feature are included in the key. The main morphological features included in the key are: asexual structures, sexual structures, and chlamydospore, hyphae, and cultural characteristics. The user can read an illustrated “Fact Sheet” on each species that includes pictures of morphological characters, disease symptoms, host range, and relevant references. A cross-linked glossary of terminology is included in each fact sheet. In addition, a DNA search function that contains a simple search of internal transcribed spacer (ITS) and Barcode of Life (BOL, 5′ end of the cox 1 gene) sequences for each species can be queried. The key was created to provide teachers, diagnosticians, and regulatory personnel with easily accessible tools to distinguish common species in the genus Phytophthora based on a number of important morphological and molecular characteristics. The key is available for purchase from APS Press and should provide another useful tool for the identification of members of this destructive group of Oomycete plant pathogens.

scholarly journals Effectors as Tools in Disease Resistance Breeding Against Biotrophic, Hemibiotrophic, and Necrotrophic Plant Pathogens

2014 ◽  
Vol 27 (3) ◽  
pp. 196-206 ◽  
Author(s):  
Vivianne G. A. A. Vleeshouwers ◽  
Richard P. Oliver
Keyword(s):  
Fungicide Resistance ◽  
Plant Pathogens ◽  
Functional Characterization ◽  
Resistance Breeding ◽  
World Population ◽  
Breeding Programs ◽  
Genome Wide ◽  
Disease Resistance Breeding ◽  
Pathogen Populations ◽  
New Strategies

One of most important challenges in plant breeding is improving resistance to the plethora of pathogens that threaten our crops. The ever-growing world population, changing pathogen populations, and fungicide resistance issues have increased the urgency of this task. In addition to a vital inflow of novel resistance sources into breeding programs, the functional characterization and deployment of resistance also needs improvement. Therefore, plant breeders need to adopt new strategies and techniques. In modern resistance breeding, effectors are emerging as tools to accelerate and improve the identification, functional characterization, and deployment of resistance genes. Since genome-wide catalogues of effectors have become available for various pathogens, including biotrophs as well as necrotrophs, effector-assisted breeding has been shown to be successful for various crops. “Effectoromics” has contributed to classical resistance breeding as well as for genetically modified approaches. Here, we present an overview of how effector-assisted breeding and deployment is being exploited for various pathosystems.

scholarly journals Phytophthora methylomes modulated by expanded 6mA methyltransferases are associated with adaptive genome regions

2017 ◽  
Author(s):  
Han Chen ◽  
Haidong Shu ◽  
Liyuan Wang ◽  
Fan Zhang ◽  
Xi Li ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
Plant Pathogens ◽  
Phytophthora Sojae ◽  
Genome Architecture ◽  
Epigenetic Mark ◽  
Gene Body ◽  
Gene Body Methylation ◽  
Methylated Dna ◽  
Genome Wide

AbstractFilamentous plant pathogen genomes often display a bipartite architecture with gene sparse, repeat-rich compartments serving as a cradle for adaptive evolution. However, the extent to which this “two-speed” genome architecture is associated with genome-wide epigenetic modifications is unknown. Here, we show that the oomycete plant pathogens Phytophthora infestans and Phytophthora sojae possess functional adenine N6- methylation (6mA) methyltransferases that modulate patterns of 6mA marks across the genome. In contrast, 5-methylcytosine (5mC) could not be detected in the two Phytophthora species. Methylated DNA IP Sequencing (MeDIP-seq) of each species revealed that 6mA is depleted around the transcriptional starting sites (TSS) and is associated with low expressed genes, particularly transposable elements. Remarkably, genes occupying the gene-sparse regions have higher levels of 6mA compared to the remainder of both genomes, possibly implicating the methylome in adaptive evolution of Phytophthora. Among three putative adenine methyltransferases, DAMT1 and DAMT3 displayed robust enzymatic activities. Surprisingly, single knockouts of each of the 6mA methyltransferases in P. sojae significantly reduced in vivo 6mA levels, indicating that the three enzymes are not fully redundant. MeDIP-seq of the damt3 mutant revealed uneven patterns of 6mA methylation across genes, suggesting that PsDAMT3 may have a preference for gene body methylation after the TSS. Our findings provide evidence that 6mA modification is an epigenetic mark of Phytophthora genomes and that complex patterns of 6mA methylation by the expanded 6mA methyltransferases may be associated with adaptive evolution in these important plant pathogens.

scholarly journals Inference of Population Genetic Structure and High Linkage Disequilibrium Among Alternaria spp. Collected from Tomato and Potato Using Genotyping by Sequencing

2019 ◽  
Author(s):  
Tika B. Adhikari ◽  
Brian J. Knaus ◽  
Niklaus J. Grünwald ◽  
Dennis Halterman ◽  
Frank J. Louws
Keyword(s):  
Population Structure ◽  
Linkage Disequilibrium ◽  
Plant Pathogens ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Allelic Association ◽  
Nucleotide Polymorphisms ◽  
Entire Genome ◽  
Genome Wide ◽  
A Genome

ABSTRACTGenotyping by sequencing (GBS) is considered a powerful tool to discover single nucleotide polymorphisms (SNPs), which are useful to characterize closely related genomes of plant species and plant pathogens. We applied GBS to determine genome-wide variations in a panel of 187 isolates of three closely related Alternaria spp. that cause diseases on tomato and potato in North Carolina (NC) and Wisconsin (WI). To compare genetic variations, reads were mapped to both A. alternata and A. solani draft reference genomes and detected dramatic differences in SNPs among them. Comparison of A. linariae and A. solani populations by principal component analysis revealed the first (83.8% of variation) and second (8.0% of variation) components contained A. linariae from tomato in NC and A. solani from potato in WI, respectively, providing evidence of population structure. Genetic differentiation (Hedrick’s G’ST) in A. linariae populations from Haywood, Macon, and Madison counties in NC were little or no differentiated (G’ST 0.0 - 0.2). However, A. linariae population from Swain county appeared to be highly differentiated (G’ST > 0.8). To measure the strength of the linkage disequilibrium (LD), we also calculated the allelic association between pairs of loci. Lewontin’s D (measures the fraction of allelic variations) and physical distances provided evidence of linkage throughout the entire genome, consistent with the hypothesis of non-random association of alleles among loci. Our findings provide new insights into the understanding of clonal populations on a genome-wide scale and microevolutionary factors that might play an important role in population structure. Although we found limited genetic diversity, the three Alternaria spp. studied here are genetically distinct and each species is preferentially associated with one host.

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