Analysis of Carbohydrate Metabolism Genes of Spongospora subterranea Using 454 Pyrosequencing
ABSTRACT: Spongospora subterranea, the causal agent of Potato powdery scab, is an important soil-borne obligate protozoan commonly found in Andean soils. This is a serious problem that causes cosmetic damage on the skin of tubers and induces root gall formation, diminishing the yield and commercial...
- Autores:
-
Gutiérrez Sánchez, Pablo Andrés
Alzate Restrepo, Juan Fernando
Marín Montoya, Mauricio
- Tipo de recurso:
- Article of investigation
- Fecha de publicación:
- 2014
- Institución:
- Universidad de Antioquia
- Repositorio:
- Repositorio UdeA
- Idioma:
- eng
- OAI Identifier:
- oai:bibliotecadigital.udea.edu.co:10495/26091
- Acceso en línea:
- http://hdl.handle.net/10495/26091
- Palabra clave:
- Genómica
Genomics
Plasmodióphora
Plasmodiophora
Solanum tuberosum
http://aims.fao.org/aos/agrovoc/c_5994
http://aims.fao.org/aos/agrovoc/c_7221
- Rights
- openAccess
- License
- https://creativecommons.org/licenses/by-nc-sa/4.0/
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| dc.title.spa.fl_str_mv |
Analysis of Carbohydrate Metabolism Genes of Spongospora subterranea Using 454 Pyrosequencing |
| dc.title.translated.spa.fl_str_mv |
Análisis de genes del metabolismo de carbohidratos de Spongospora subterranea utilizando pirosecuenciación 454 |
| title |
Analysis of Carbohydrate Metabolism Genes of Spongospora subterranea Using 454 Pyrosequencing |
| spellingShingle |
Analysis of Carbohydrate Metabolism Genes of Spongospora subterranea Using 454 Pyrosequencing Genómica Genomics Plasmodióphora Plasmodiophora Solanum tuberosum http://aims.fao.org/aos/agrovoc/c_5994 http://aims.fao.org/aos/agrovoc/c_7221 |
| title_short |
Analysis of Carbohydrate Metabolism Genes of Spongospora subterranea Using 454 Pyrosequencing |
| title_full |
Analysis of Carbohydrate Metabolism Genes of Spongospora subterranea Using 454 Pyrosequencing |
| title_fullStr |
Analysis of Carbohydrate Metabolism Genes of Spongospora subterranea Using 454 Pyrosequencing |
| title_full_unstemmed |
Analysis of Carbohydrate Metabolism Genes of Spongospora subterranea Using 454 Pyrosequencing |
| title_sort |
Analysis of Carbohydrate Metabolism Genes of Spongospora subterranea Using 454 Pyrosequencing |
| dc.creator.fl_str_mv |
Gutiérrez Sánchez, Pablo Andrés Alzate Restrepo, Juan Fernando Marín Montoya, Mauricio |
| dc.contributor.author.none.fl_str_mv |
Gutiérrez Sánchez, Pablo Andrés Alzate Restrepo, Juan Fernando Marín Montoya, Mauricio |
| dc.contributor.researchgroup.spa.fl_str_mv |
Grupo de Parasitología Universidad de Antioquia |
| dc.subject.lemb.none.fl_str_mv |
Genómica Genomics |
| topic |
Genómica Genomics Plasmodióphora Plasmodiophora Solanum tuberosum http://aims.fao.org/aos/agrovoc/c_5994 http://aims.fao.org/aos/agrovoc/c_7221 |
| dc.subject.agrovoc.none.fl_str_mv |
Plasmodióphora Plasmodiophora Solanum tuberosum |
| dc.subject.agrovocuri.none.fl_str_mv |
http://aims.fao.org/aos/agrovoc/c_5994 http://aims.fao.org/aos/agrovoc/c_7221 |
| description |
ABSTRACT: Spongospora subterranea, the causal agent of Potato powdery scab, is an important soil-borne obligate protozoan commonly found in Andean soils. This is a serious problem that causes cosmetic damage on the skin of tubers and induces root gall formation, diminishing the yield and commercial value of the potato. Genetic studies on S. subterranea are difficult due to its obligate parasitism, which explains the lack of available knowledge on its basic biology. S. subterranea is a member of the Plasmodiophorida order, a protist taxa that includes other important plant pathogens such as Plasmodiophora brassicae and Spongospora nasturtii. Little is known about the genomes of Plasmodiophorida; however, with the use of Next-Generation Sequencing technologies combined with appropriate bioinformatic techniques, it is possible to obtain genomic sequences from obligate pathogens such as S. subterranea. To gain a better understanding of the biology of this pathogen and Plasmodiophorida in general, DNA sequences from a cystosori-enriched sample of S. subterranea were obtained using 454 pyrosequencing technology. As a first step in understanding the nutritional requirements of S. subterranea as well as its infective and resistance structures, we present a bioinformatic analysis of 24 contigs related to genes involved in the glycolysis, starch, celullose and chitin metabolism. Intron structure and codon usage is also discussed. The genes analyzed in this study are a good source of information for studies aimed at characterizing these enzymes in vitro, as well as the generation of new methods for the molecular detection of S. subterranea in either soils or infected plants. |
| publishDate |
2014 |
| dc.date.issued.none.fl_str_mv |
2014 |
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2022-02-17T16:00:02Z |
| dc.date.available.none.fl_str_mv |
2022-02-17T16:00:02Z |
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Artículo de investigación |
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Gutiérrez Sánchez, P. A., Alzate, J. F., & Montoya, M. M. (2014). Analysis of Carbohydrate Metabolism Genes of Spongospora subterranea Using 454 Pyrosequencing. Revista Facultad Nacional de Agronomía Medellín, 67(2), 7247-7260. https://doi.org/10.15446/rfnam.v67n2.44166 |
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0304-2847 |
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http://hdl.handle.net/10495/26091 |
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10.15446/rfnam.v67n2.44166 |
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2248-7026 |
| identifier_str_mv |
Gutiérrez Sánchez, P. A., Alzate, J. F., & Montoya, M. M. (2014). Analysis of Carbohydrate Metabolism Genes of Spongospora subterranea Using 454 Pyrosequencing. Revista Facultad Nacional de Agronomía Medellín, 67(2), 7247-7260. https://doi.org/10.15446/rfnam.v67n2.44166 0304-2847 10.15446/rfnam.v67n2.44166 2248-7026 |
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eng |
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eng |
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Rev. Fac. Nac. Agron. Medellín |
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7260 |
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2 |
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7247 |
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67 |
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Revista Facultad Nacional de Agronomía Medellín |
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Medellín, Colombia |
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Gutiérrez Sánchez, Pablo AndrésAlzate Restrepo, Juan FernandoMarín Montoya, MauricioGrupo de Parasitología Universidad de Antioquia2022-02-17T16:00:02Z2022-02-17T16:00:02Z2014Gutiérrez Sánchez, P. A., Alzate, J. F., & Montoya, M. M. (2014). Analysis of Carbohydrate Metabolism Genes of Spongospora subterranea Using 454 Pyrosequencing. Revista Facultad Nacional de Agronomía Medellín, 67(2), 7247-7260. https://doi.org/10.15446/rfnam.v67n2.441660304-2847http://hdl.handle.net/10495/2609110.15446/rfnam.v67n2.441662248-7026ABSTRACT: Spongospora subterranea, the causal agent of Potato powdery scab, is an important soil-borne obligate protozoan commonly found in Andean soils. This is a serious problem that causes cosmetic damage on the skin of tubers and induces root gall formation, diminishing the yield and commercial value of the potato. Genetic studies on S. subterranea are difficult due to its obligate parasitism, which explains the lack of available knowledge on its basic biology. S. subterranea is a member of the Plasmodiophorida order, a protist taxa that includes other important plant pathogens such as Plasmodiophora brassicae and Spongospora nasturtii. Little is known about the genomes of Plasmodiophorida; however, with the use of Next-Generation Sequencing technologies combined with appropriate bioinformatic techniques, it is possible to obtain genomic sequences from obligate pathogens such as S. subterranea. To gain a better understanding of the biology of this pathogen and Plasmodiophorida in general, DNA sequences from a cystosori-enriched sample of S. subterranea were obtained using 454 pyrosequencing technology. As a first step in understanding the nutritional requirements of S. subterranea as well as its infective and resistance structures, we present a bioinformatic analysis of 24 contigs related to genes involved in the glycolysis, starch, celullose and chitin metabolism. Intron structure and codon usage is also discussed. The genes analyzed in this study are a good source of information for studies aimed at characterizing these enzymes in vitro, as well as the generation of new methods for the molecular detection of S. subterranea in either soils or infected plants.RESUMEN: Spongospora subterranea, el agente causal de la sarna polvosa de la papa, es un protozoo y patógeno obligado presente en los suelos andinos. Esta enfermedad es un serio problema para el cultivo de papa, al causar lesiones cosméticas en la piel de los tubérculos, así como agallas en las raíces, limitando sus rendimientos y valor comercial. Debido al caracter de parásito obligado de S. subterranea, es muy poco lo que se conoce sobre su biología básica. Este patógeno es un miembro del orden Plasmodiophorida, un taxón que incluye otros microorganismos de importancia como Plasmodiophora brassicae y Spongospora nasturtii. Sin embargo, con el uso combinado de métodos de secuenciación de nueva generación y herramientas bioinformáticas apropiadas, es posible obtener información genómica sobre microorganismos no cultivables. Con el fin de profundizar en la comprensión de la biología de S. subterranea y del orden Plasmidiophora en general, se llevó a cabo la secuenciación mediante la metodología 454 de una muestra enriquecida con quistorosoros del patógeno. En este trabajo se identificaron 24 ensamblajes (contigs) de secuencias relacionadas con la glicólisis y el metabolismo del almidón, celulosa y quitina. Tambien se discute la estructura de los intrones y el uso de codones. Los genes analizados en este estudio son una buena fuente de información para estudios futuros enfocados en la caracterización de estas enzimas, así como para la generación de nuevos métodos de detección molecular de S. subterranea en suelos y plantas infectadas.COL000750614application/pdfengUniversidad Nacional de Colombia, Facultad de Ciencias AgrariasMedellín, Colombiahttps://creativecommons.org/licenses/by-nc-sa/4.0/http://creativecommons.org/licenses/by-nc-sa/2.5/co/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Analysis of Carbohydrate Metabolism Genes of Spongospora subterranea Using 454 PyrosequencingAnálisis de genes del metabolismo de carbohidratos de Spongospora subterranea utilizando pirosecuenciación 454Artículo de investigaciónhttp://purl.org/coar/resource_type/c_2df8fbb1https://purl.org/redcol/resource_type/ARThttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionGenómicaGenomicsPlasmodióphoraPlasmodiophoraSolanum tuberosumhttp://aims.fao.org/aos/agrovoc/c_5994http://aims.fao.org/aos/agrovoc/c_7221Rev. Fac. Nac. Agron. Medellín72602724767Revista Facultad Nacional de Agronomía MedellínPublicationLICENSElicense.txtlicense.txttext/plain; charset=utf-81748https://bibliotecadigital.udea.edu.co/bitstreams/fe3977b2-56e8-4a8a-9363-b3f3a3288705/download8a4605be74aa9ea9d79846c1fba20a33MD53falseAnonymousREADORIGINALGutierrezPablo_2014_GenomicsPlasmodiophoraPowderyscab.pdfGutierrezPablo_2014_GenomicsPlasmodiophoraPowderyscab.pdfArtículo de investigaciónapplication/pdf1024075https://bibliotecadigital.udea.edu.co/bitstreams/4b68f11c-4d5e-4054-9ef9-bdb250828c7e/download9b40454fe0e97b7de609cd7d7f3f859eMD51trueAnonymousREADCC-LICENSElicense_rdflicense_rdfapplication/rdf+xml; charset=utf-81051https://bibliotecadigital.udea.edu.co/bitstreams/39fc1455-5b46-45ec-95ba-4012de10fa61/downloade2060682c9c70d4d30c83c51448f4eedMD52falseAnonymousREADTEXTGutierrezPablo_2014_GenomicsPlasmodiophoraPowderyscab.pdf.txtGutierrezPablo_2014_GenomicsPlasmodiophoraPowderyscab.pdf.txtExtracted texttext/plain50083https://bibliotecadigital.udea.edu.co/bitstreams/ebb21847-f143-4e19-9ae4-3440dd399cca/downloadeca5ee88a0360714fbb87efe09ae8563MD54falseAnonymousREADTHUMBNAILGutierrezPablo_2014_GenomicsPlasmodiophoraPowderyscab.pdf.jpgGutierrezPablo_2014_GenomicsPlasmodiophoraPowderyscab.pdf.jpgGenerated Thumbnailimage/jpeg15410https://bibliotecadigital.udea.edu.co/bitstreams/31be318f-9a91-4fd9-8b66-4f00b7a4e47f/download810722f6b9a2ce55dbc42330df5fcf18MD55falseAnonymousREAD10495/26091oai:bibliotecadigital.udea.edu.co:10495/260912025-03-27 01:08:47.704https://creativecommons.org/licenses/by-nc-sa/4.0/open.accesshttps://bibliotecadigital.udea.edu.coRepositorio Institucional de la Universidad de Antioquiaaplicacionbibliotecadigitalbiblioteca@udea.edu.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 |