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0000-0003-4389-9418
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Publisher: American Astronomical Society
Date: 11-09-2019
Publisher: Cold Spring Harbor Laboratory
Date: 11-08-2020
DOI: 10.1101/2020.08.10.235309
Abstract: The vascular wilt disease caused by the fungus Fusarium oxysporum f. sp. physali ( Foph ) is one of the most limiting factors for the production and export of cape gooseberry ( Physalis peruviana ) in Colombia. A previous study of the transcriptomic profile of a highly virulent strain of F. oxysporum in cape gooseberry plants, from a collection of 136 fungal isolates obtained from wilted cape gooseberry plants, revealed the presence of secreted in the xylem (SIX) effector genes, known to be involved in the pathogenicity of other F. oxysporum formae speciales (ff. spp.). This pathogenic strain was named Foph , due to its specificity for cape gooseberry hosts. Here, we sequenced the genome of Foph , using the Illumina MiSeq platform. We analyzed the assembled genome, focusing on the confirmation of the presence of homologues of SIX effectors and the identification of novel candidates of effector genes unique of Foph. By comparative and phylogenomic analyses based on single-copy orthologues, we identified that Foph is closely related to F. oxysporum ff. spp., associated with solanaceous hosts. We confirmed the presence of highly identical homologous genomic regions between Foph and Fol , that contain effector genes and identified seven new effector gene candidates, specific to Foph strains. We also conducted a molecular characterization of a panel of 29 F. oxysporum additional stains associated to cape gooseberry crops isolated from different regions of Colombia. These results suggest the polyphyletic origin of Foph and the putative independent acquisition of new candidate effectors in different clades of related strains. The novel effector candidates identified by sequencing and analyzing the genome of Foph , represent new sources involved in the interaction between Foph and cape gooseberry. These resources could be implemented to develop appropriate management strategies of the wilt disease caused by Foph in the cape gooseberry crop.
Publisher: Wiley
Date: 19-09-2016
DOI: 10.1111/MPP.12444
Publisher: Wiley
Date: 06-09-2018
DOI: 10.1111/MPP.12700
Publisher: Frontiers Media SA
Date: 18-01-2021
DOI: 10.3389/FMICB.2020.593915
Abstract: The vascular wilt disease caused by the fungus Fusarium oxysporum f. sp. physali ( Foph ) is one of the most limiting factors for the production and export of cape gooseberry ( Physalis peruviana ) in Colombia. A transcriptomic analysis of a highly virulent strain of F. oxysporum in cape gooseberry plants, revealed the presence of secreted in the xylem (SIX) effector genes, known to be involved in the pathogenicity of other formae speciales (ff. spp.) of F. oxysporum . This pathogenic strain was classified as a new f. sp. named Foph , due to its specificity for cape gooseberry hosts. Here, we sequenced and assembled the genome of five strains of F. oxysporum from a fungal collection associated to the cape gooseberry crop (including Foph ), focusing on the validation of the presence of SIX homologous and on the identification of putative effectors unique to Foph . By comparative and phylogenomic analyses based on single-copy orthologous, we found that Foph is closely related to F. oxysporum ff. spp., associated with solanaceous hosts. We confirmed the presence of highly identical homologous genomic regions between Foph and Fol that contain effector genes and identified six new putative effector genes, specific to Foph pathogenic strains. We also conducted a molecular characterization using this set of putative novel effectors in a panel of 36 additional stains of F. oxysporum including two of the four sequenced strains, from the fungal collection mentioned above. These results suggest the polyphyletic origin of Foph and the putative independent acquisition of new candidate effectors in different clades of related strains. The novel effector candidates identified in this genomic analysis, represent new sources involved in the interaction between Foph and cape gooseberry, that could be implemented to develop appropriate management strategies of the wilt disease caused by Foph in the cape gooseberry crop.
Publisher: American Physical Society (APS)
Date: 08-10-2024
Publisher: MDPI AG
Date: 20-01-2020
Abstract: In Colombia, tomato production under protected conditions represents an important economic contribution to the agricultural sector. Fusarium wilt diseases, caused by pathogenic formae speciales of the soil-borne fungus Fusarium oxysporum Schltdl., cause significant yield losses in tomatoes throughout the world. Investigation of the F. oxysporum–tomato pathosystem in Colombia is required to develop appropriate alternative disease management. In this study, 120 fungal isolates were obtained from four different departments in the Central Andean Region in Colombia from tomato crops with symptoms of wilt disease. A molecular characterization of the fungal isolates was performed using the SIX1, SIX3, and SIX4 effector genes of Fusarium oxysporum f. sp. lycopersici W.C. Snyder & H.N. Hansen (Fol). Additionally, we developed a new specific marker to distinguish between Fusarium oxysporum f. sp. radicis-lycopersici Jarvis & Shoemaker (Forl) and Fol isolates. Furthermore, a phylogenetic analysis using the Translation Elongation Factor 1-alpha (EF1a) gene was performed with the collected isolates. Two isolates (named Fol59 and Fol-UDC10) were identified as Fol race 2, four isolates were identified as Forl, six isolates were identified as F. solani, and most of the isolates were grouped within the F. oxysporum species complex. The phylogenetic tree of EF1a showed that most of the isolates could potentially correspond to nonpathogenic strains of F. oxysporum. Additional pathogenicity assays carried out with Fol59 and Fol-UDC10 confirmed that both isolates were highly virulent strains. This study represents a contribution to the understanding of the local interaction between tomatoes and F. oxysporum in Colombia.
Publisher: American Physical Society (APS)
Date: 11-07-2019
Publisher: American Physical Society (APS)
Date: 15-01-2019
Publisher: Public Library of Science (PLoS)
Date: 21-10-2011
Publisher: Cold Spring Harbor Laboratory
Date: 05-07-2023
DOI: 10.1101/2023.07.04.546705
Abstract: The plant species Cedrela odorata has been largely exploited in the timber industry due to the high demand of its wood. Therefore, C. odorata , has been considered as a vulnerable species since 1994, with the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). C. odorata is one of the key timber species included in the management and conservation plans in Colombia. These plans include the study of local populations by developing genetic resources for the species. In this study, two novel chloroplast (cp) genomes have been generated using the MinION long read sequencing technology. The new cp assemblies were compared with other cp genomes for the species, supporting previous hypothesis of intraspecific ersity associated to their place of origin. Furthermore, the cp genomes were screened for sequence variants (SV) and a total of 16 SNPs were identified, presumably unique to populations of the amazon region in Colombia. Here, the first cp genome sequences of C. odorata from Colombian in iduals represent novel and valuable genomic resources for the species suitable for DNA fingerprinting and DNA barcoding applications.
Location: Colombia
Location: Colombia
Location: Colombia
Start Date: 2018
End Date: 2019
Funder: Departamento Administrativo de Ciencia, Tecnología e Innovación (COLCIENCIAS)
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