scholarly journals Understanding the Molecular Bases of the Endophytic/Pathogenic Behavior of Fusarium Oxysporum Interacting With Vanilla Planifolia

2021 ◽  
Author(s):  
Marco Tulio Solano De la Cruz ◽  
Esteban Elías Elías Escobar – Hernández ◽  
Jorge Arturo Arciniega – González ◽  
Rocío del Pilar Rueda – Zozaya ◽  
Jacel Adame – García ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Fusarium Oxysporum ◽  
Fusaric Acid ◽  
Genetic Determinants ◽  
Formae Speciales ◽  
Rot Disease ◽  
Genomic Regions ◽  
Molecular Bases ◽  
Fusarium Oxysporum Species Complex

Members of the Fusarium oxysporum species complex (FOSC) has the capacity to specialize into host-specific pathogens known as formae speciales through horizontal gene transfer between pathogenic and endophytic individuals. To this day, the origin of these formae speciales and the genetic determinants dictating the switch from endophytic to pathogenic Fusarium oxysporum (Fox) are still unknown. F. oxysporum f. sp. vanillae (Fov), member of FOSC, is the causal agent of root and stem rot disease, representing the main phytosanitary problem in vanilla plantations worldwide. Here we analyzed the RNA-seq libraries resulting from the interaction vanilla-Fov at early and late stages of the infection, and what we initially identified as control in a previous study, detecting the presence of Fox endophytes. We identified virulence, hypervirulence, sporulation, conidiation, necrosis, and production of fusaric acid as key processes taking place during Fov-vanilla interaction. Through comparison with endophytic Fox, we found that Fov can infect vanilla thanks to the presence of pathogenicity islands and genomic regions associated with supernumerary chromosomes. These play a central role as carriers of genes involved with pathogenic activity and could have being obtained by Fov through horizontal gene transfer. We also found that, unlike other pathogenic members of FOSC, Fov do not use Secreted in Xylem proteins (SIX) to infect vanilla.

scholarly journals panRGP: a pangenome-based method to predict genomic islands and explore their diversity

2020 ◽  
Vol 36 (Supplement_2) ◽  
pp. i651-i658 ◽  
Author(s):  
Adelme Bazin ◽  
Guillaume Gautreau ◽  
Claudine Médigue ◽  
David Vallenet ◽  
Alexandra Calteau
Keyword(s):  
Escherichia Coli ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Species Level ◽  
Genomic Islands ◽  
Genome Plasticity ◽  
Reference Dataset ◽  
Prokaryotic Genomes ◽  
Ideal Approach ◽  
Genomic Regions

Abstract Motivation Horizontal gene transfer (HGT) is a major source of variability in prokaryotic genomes. Regions of genome plasticity (RGPs) are clusters of genes located in highly variable genomic regions. Most of them arise from HGT and correspond to genomic islands (GIs). The study of those regions at the species level has become increasingly difficult with the data deluge of genomes. To date, no methods are available to identify GIs using hundreds of genomes to explore their diversity. Results We present here the panRGP method that predicts RGPs using pangenome graphs made of all available genomes for a given species. It allows the study of thousands of genomes in order to access the diversity of RGPs and to predict spots of insertions. It gave the best predictions when benchmarked along other GI detection tools against a reference dataset. In addition, we illustrated its use on metagenome assembled genomes by redefining the borders of the leuX tRNA hotspot, a well-studied spot of insertion in Escherichia coli. panRPG is a scalable and reliable tool to predict GIs and spots making it an ideal approach for large comparative studies. Availability and implementation The methods presented in the current work are available through the following software: https://github.com/labgem/PPanGGOLiN. Detailed results and scripts to compute the benchmark metrics are available at https://github.com/axbazin/panrgp_supdata.

scholarly journals Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria

2016 ◽  
Author(s):  
Kevin S. Bonham ◽  
Benjamin E. Wolfe ◽  
Rachel J. Dutton
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Molecular Mechanisms ◽  
Protein Coding ◽  
Associated Bacteria ◽  
The Us ◽  
Selective Forces ◽  
Genomic Regions ◽  
Microbiome Assembly ◽  
Insight Into

AbstractAcquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly-sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4,733 protein coding genes. The largest of these regions are enriched for genes involved in siderophore acquisition, and are widely distributed in cheese rinds in both Europe and the US. These results suggest that horizontal gene transfer (HGT) is prevalent in cheese rind microbiomes, and the identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities.

scholarly journals Investigation of the diversity of effector genes in the banana pathogen, Fusarium oxysporum f. sp. cubense , reveals evidence of horizontal gene transfer

2017 ◽  
Vol 19 (5) ◽  
pp. 1155-1171 ◽  
Author(s):  
Elizabeth Czislowski ◽  
Sam Fraser-Smith ◽  
Manuel Zander ◽  
Wayne T. O'Neill ◽  
Rachel A. Meldrum ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Fusarium Oxysporum ◽  
Effector Genes

scholarly journals Gene Genealogies and AFLP Analyses in the Fusarium oxysporum Complex Identify Monophyletic and Nonmonophyletic Formae Speciales Causing Wilt and Rot Disease

2000 ◽  
Vol 90 (8) ◽  
pp. 891-900 ◽  
Author(s):  
Robert P. Baayen ◽  
Kerry O'Donnell ◽  
Peter J. M. Bonants ◽  
Elizabeth Cigelnik ◽  
Laurens P. N. M. Kroon ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Dna Sequences ◽  
Mitochondrial Gene ◽  
Elongation Factor ◽  
Small Subunit ◽  
Vegetative Compatibility Groups ◽  
Formae Speciales ◽  
Evolutionary Origins ◽  
Bulb Rot ◽  
Rot Disease

The monophyletic origin of host-specific taxa in the plant-pathogenic Fusarium oxysporum complex was tested by constructing nuclear and mitochondrial gene genealogies and amplified fragment length polymorphism (AFLP)-based phylogenies for 89 strains representing the known genetic and pathogenic diversity in 8 formae speciales associated with wilt diseases and root and bulb rot. We included strains from clonal lineages of F. oxysporum f. spp. asparagi, dianthi, gladioli, lilii, lini, opuntiarum, spinaciae, and tulipae. Putatively nonpathogenic strains from carnation and lily were included and a reference strain from each of the three main clades identified previously in the F. oxysporum complex; sequences from related species were used as outgroups. DNA sequences from the nuclear translation elongation factor 1α and the mitochondrial small subunit (mtSSU) ribosomal RNA genes were combined for phylogenetic analysis. Strains in vegetative compatibility groups (VCGs) shared identical sequences and AFLP profiles, supporting the monophyly of the two single-VCG formae speciales, lilii and tulipae. Identical genotypes were also found for the three VCGs in F. oxysporum f. sp. spinaciae. In contrast, multiple evolutionary origins were apparent for F. oxysporum f. spp. asparagi, dianthi, gladioli, lini, and opuntiarum, although different VCGs within each of these formae speciales often clustered close together or shared identical EF-1α and mtSSU rDNA haplotypes. Kishino-Hasegawa analyses of constraints forcing the monophyly of these formae speciales supported the exclusive origin of F. oxysporum f. sp. opuntiarum but not the monophyly of F. oxysporum f. spp. asparagi, dianthi, gladioli, and lini. Most of the putatively nonpathogenic strains from carnation and lily, representing unique VCGs, were unrelated to F. oxysporum f. spp. dianthi and lilii, respectively. Putatively nonpathogenic or rot-inducing strains did not form exclusive groups within the molecular phylogeny. Parsimony analyses of AFLP fingerprint data supported the gene genealogy-based phylogram; however, AFLP-based phylogenies were considerably more homoplasious than the gene genealogies. The predictive value of the forma specialis naming system within the F. oxysporum complex is questioned.

scholarly journals PENEKANAN PERKEMBANGAN PENYAKIT BUSUK BATANG VANILI (FUSARIUM OXYSPORUM F.SP. VANILLAE) MELALUI SELEKSI ASAM FUSARAT SECARA IN VITRO

2012 ◽  
Vol 12 (1) ◽  
pp. 12-22
Author(s):  
Endang Nurcahyani ◽  
Issirep Sumardi ◽  
Bambang Hadisutrisno ◽  
E. Suharyanto
Keyword(s):  
Fusarium Oxysporum ◽  
In Vitro Selection ◽  
Protein Profile ◽  
Fusaric Acid ◽  
Total Phenol Content ◽  
Vanilla Planifolia ◽  
Rot Disease ◽  
Set Up ◽  
Important Disease

The most biological constrain on Vanilla planifolia plantation recently was caused by epidemical disease that laterdecrease vanilla production. The most important disease on vanilla is foot rot disease caused by Fusarium oxysporum f. sp.vanillae. So far, the disease has not been successfully controlled although some experiments had been conducted. Onealternative method has been introduced by using a new cultivar which was resistance to Fusarium). A mutant vanilla to thefungus has been initiated by in vitro selection on medium containing fusaric acid. The aims of this research were: (1) to investigate effective concentration of fusaric acid used for in vitro selection, (2) to characterize mutants which have been set up and also to test those mutants for their resistance to the fungus. The results showed that: (1) fusaric acid at the concentration of 110 ppm effectively suppressed the disease intensity up to 25% compared to the concentration of 90 ppm and 100 ppm. In other words, 110 ppm of fusaric acid has increased the category criterion from moderate to resistant, (2) there was an increase of the total phenol content and thickness of lignin in vanilla stem, and (3) the protein profile of vanilla plantlet was different from the control. There was an initiation of a new band of about 18 kD in a mutant predicted as a protein which is responsible for vanilla resistance to Fusarium.

scholarly journals Current Status of Fusarium oxysporum Formae Speciales and Races

2019 ◽  
Vol 109 (4) ◽  
pp. 512-530 ◽  
Author(s):  
V. Edel-Hermann ◽  
C. Lecomte
Keyword(s):  
Fusarium Oxysporum ◽  
Host Range ◽  
Plant Species ◽  
Current Status ◽  
Economic Losses ◽  
Broad Host Range ◽  
Formae Speciales ◽  
Forma Specialis ◽  
Comprehensive Search ◽  
Fusarium Oxysporum Species Complex

The Fusarium oxysporum species complex includes both plant pathogenic and nonpathogenic strains, which are commonly found in soils. F. oxysporum has received considerable attention from plant pathologists for more than a century owing to its broad host range and the economic losses it causes. The narrow host specificity of pathogenic strains has led to the concept of formae speciales, each forma specialis grouping strains with the same host range. Initially restricted to one plant species, this host range was later found to be broader for many formae speciales. In addition, races were identified in some formae speciales, generally with cultivar-level specialization. In 1981, Armstrong and Armstrong listed 79 F. oxysporum formae speciales and mentioned races in 16 of them. Since then, the known host range of F. oxysporum has considerably increased, and many new formae speciales and races have been identified. We carried out a comprehensive search of the literature to propose this review of F. oxysporum formae speciales and races. We recorded 106 well-characterized formae speciales, together with 37 insufficiently documented ones, and updated knowledge on races and host ranges. We also recorded 58 plant species/genera susceptible to F. oxysporum but for which a forma specialis has not been characterized yet. This review raises issues regarding the nomenclature and the description of F. oxysporum formae speciales and races.

scholarly journals Environmental and genetic determinants of plasmid mobility in pathogenic Escherichia coli

2020 ◽  
Vol 6 (4) ◽  
pp. eaax3173 ◽  
Author(s):  
Jonathan H. Bethke ◽  
Adam Davidovich ◽  
Li Cheng ◽  
Allison J. Lopatkin ◽  
Wenchen Song ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Quantitative Analysis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genomic Analysis ◽  
Genetic Determinants ◽  
Incompatibility Group ◽  
Bacterial Populations ◽  
Pathogenic Escherichia Coli

Plasmids are key vehicles of horizontal gene transfer (HGT), mobilizing antibiotic resistance, virulence, and other traits among bacterial populations. The environmental and genetic forces that drive plasmid transfer are poorly understood, however, due to the lack of definitive quantification coupled with genomic analysis. Here, we integrate conjugative phenotype with plasmid genotype to provide quantitative analysis of HGT in clinical Escherichia coli pathogens. We find a substantial proportion of these pathogens (>25%) able to readily spread resistance to the most common classes of antibiotics. Antibiotics of varied modes of action had less than a 5-fold effect on conjugation efficiency in general, with one exception displaying 31-fold promotion upon exposure to macrolides and chloramphenicol. In contrast, genome sequencing reveals plasmid incompatibility group strongly correlates with transfer efficiency. Our findings offer new insights into the determinants of plasmid mobility and have implications for the development of treatments that target HGT.

scholarly journals Gut Fungi Possess a Conserved Toxin Immunity Gene of Bacterial Origin

2020 ◽  
Author(s):  
Syed M. Rizvi ◽  
Chengxin Zhang ◽  
Peter L. Freddolino ◽  
Yang Zhang
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Bacterial Toxin ◽  
Specific Gene ◽  
Chromosomal Dna ◽  
Immunity Gene ◽  
Definitive Evidence ◽  
Putative Toxin ◽  
Bona Fide ◽  
Genomic Regions

AbstractProkaryotes and some unicellular eukaryotes routinely overcome evolutionary pressures with the help of horizontally acquired genes. In contrast, it is unusual for multicellular eukaryotes to adapt through horizontal gene transfer (HGT). Recent studies identified several cases of adaptive acquisition in the gut-dwelling multicellular fungal phylum Neocallimastigomycota. Here, we add to these cases the acquisition of a putative bacterial toxin immunity gene, PoNi, by an ancient common ancestor of four extant Neocallimastigomycota genera through HGT from an extracellular Ruminococcus bacterium. The PoNi homologs in these fungal genera share extraordinarily high (>70%) amino acid sequence identity with their bacterial donor xenolog, providing definitive evidence of HGT as opposed to lineage-specific gene retention. Furthermore, PoNi genes are nested on native sections of chromosomal DNA in multiple fungal genomes and are also found in polyadenylated fungal transcriptomes, confirming that these genes are authentic fungal genomic regions rather than sequencing artifacts from bacterial contamination. The HGT event, which is estimated to have occurred at least 66 (±10) million years ago in the gut of a Cretaceous mammal, gave the fungi a putative toxin immunity protein (PoNi) which likely helps them survive toxin-mediated attacks by bacterial competitors in the mammalian gut microbiome.SignificanceAdaptation via horizontal gene transfer (HGT) is uncommon in multicellular eukaryotes. Here, we report another bona fide case of adaptive evolution involving the horizontal transfer of a bacterial toxin immunity gene from extracellular Ruminococcus bacteria to gut-dwelling multicellular fungi. The acquired gene may help the fungi compete against bacterial neighbors in the gut.

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