Characterization of the agent causing a new disease in leek (Allium ampeloprasum var-borrum) fields by RNA-Seq

A new disease, in this report called emergent disease in leeks (EDL), that affects leek (Allium ampeloprasum var. porrum) fields was discovered in the Segovia in 2011. This EDL is characterized by the development of abnormalities, which includes root geotropism and deformation, and leaves and bulb d...

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Detalhes bibliográficos
Autor: Ruiz Padilla, Ana
Formato: tesis de maestría
Fecha de publicación:2019
País:España
Recursos:Universitat Oberta de Catalunya (UOC)
Repositorio:O2, repositorio institucional de la UOC
OAI Identifier:oai:openaccess.uoc.edu:10609/88786
Acesso em linha:http://hdl.handle.net/10609/88786
Access Level:acceso abierto
Palavra-chave:porro
RNA-Seq
virus
leek
puerro
Bioinformatics -- TFM
Bioinformàtica -- TFM
Bioinformática -- TFM
id ES_46612fb0b239b3d4ce2e7d0aadcb9d41
oai_identifier_str oai:openaccess.uoc.edu:10609/88786
network_acronym_str ES
network_name_str España
repository_id_str
dc.title.none.fl_str_mv Characterization of the agent causing a new disease in leek (Allium ampeloprasum var-borrum) fields by RNA-Seq
title Characterization of the agent causing a new disease in leek (Allium ampeloprasum var-borrum) fields by RNA-Seq
spellingShingle Characterization of the agent causing a new disease in leek (Allium ampeloprasum var-borrum) fields by RNA-Seq
Ruiz Padilla, Ana
porro
RNA-Seq
virus
leek
RNA-Seq
virus
puerro
RNA-Seq
virus
Bioinformatics -- TFM
Bioinformàtica -- TFM
Bioinformática -- TFM
title_short Characterization of the agent causing a new disease in leek (Allium ampeloprasum var-borrum) fields by RNA-Seq
title_full Characterization of the agent causing a new disease in leek (Allium ampeloprasum var-borrum) fields by RNA-Seq
title_fullStr Characterization of the agent causing a new disease in leek (Allium ampeloprasum var-borrum) fields by RNA-Seq
title_full_unstemmed Characterization of the agent causing a new disease in leek (Allium ampeloprasum var-borrum) fields by RNA-Seq
title_sort Characterization of the agent causing a new disease in leek (Allium ampeloprasum var-borrum) fields by RNA-Seq
dc.creator.none.fl_str_mv Ruiz Padilla, Ana
author Ruiz Padilla, Ana
author_facet Ruiz Padilla, Ana
author_role author
dc.contributor.none.fl_str_mv Merino, David
Ylla Bou, Guillem
dc.subject.none.fl_str_mv porro
RNA-Seq
virus
leek
RNA-Seq
virus
puerro
RNA-Seq
virus
Bioinformatics -- TFM
Bioinformàtica -- TFM
Bioinformática -- TFM
topic porro
RNA-Seq
virus
leek
RNA-Seq
virus
puerro
RNA-Seq
virus
Bioinformatics -- TFM
Bioinformàtica -- TFM
Bioinformática -- TFM
description A new disease, in this report called emergent disease in leeks (EDL), that affects leek (Allium ampeloprasum var. porrum) fields was discovered in the Segovia in 2011. This EDL is characterized by the development of abnormalities, which includes root geotropism and deformation, and leaves and bulb discoloration. The etiology of the disease is currently unknown, but the symptoms are associated with the infection of systemic biotrophic pathogens like viruses and phytoplasmas. With the goal of identifying pathogens causing EDL, total RNA was extracted from leaves of healthy leek plants grown in a greenhouse facility and infected plants showing symptoms of the disease. Five pools were prepared by mixing total RNA: four from infected ones (Sick1, Sick2, Sick3, and Sick4) and one from control samples pool C- (Control) that were sent for sequencing. We analyzed the NGS data to identify the microorganisms associated with diseased leek plants. The most important steps of this analysis were: control of the quality of raw reads, trimming the adapter sequences and selection of the contigs present in the infected pools and not in the healthy ones. We took only a sample of 10 percent of the reads to avoid problems with lack of computational resources. Finally, the sequences of interest were analyzed to identify the possible pathogens present. The results showed the presence of phytoplasmas and other microorganisms as possible pathogens associated with the disease.
publishDate 2019
dc.date.none.fl_str_mv 2019
2019
2019
dc.type.none.fl_str_mv info:eu-repo/semantics/masterThesis
format masterThesis
dc.identifier.none.fl_str_mv http://hdl.handle.net/10609/88786
url http://hdl.handle.net/10609/88786
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.rights.none.fl_str_mv CC BY-NC-ND
http://creativecommons.org/licenses/by-nc-nd/3.0/es/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv CC BY-NC-ND
http://creativecommons.org/licenses/by-nc-nd/3.0/es/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Universitat Oberta de Catalunya (UOC)
publisher.none.fl_str_mv Universitat Oberta de Catalunya (UOC)
dc.source.none.fl_str_mv reponame:O2, repositorio institucional de la UOC
instname:Universitat Oberta de Catalunya (UOC)
instname_str Universitat Oberta de Catalunya (UOC)
reponame_str O2, repositorio institucional de la UOC
collection O2, repositorio institucional de la UOC
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869407224387862529
spelling Characterization of the agent causing a new disease in leek (Allium ampeloprasum var-borrum) fields by RNA-SeqRuiz Padilla, AnaporroRNA-SeqvirusleekRNA-SeqviruspuerroRNA-SeqvirusBioinformatics -- TFMBioinformàtica -- TFMBioinformática -- TFMA new disease, in this report called emergent disease in leeks (EDL), that affects leek (Allium ampeloprasum var. porrum) fields was discovered in the Segovia in 2011. This EDL is characterized by the development of abnormalities, which includes root geotropism and deformation, and leaves and bulb discoloration. The etiology of the disease is currently unknown, but the symptoms are associated with the infection of systemic biotrophic pathogens like viruses and phytoplasmas. With the goal of identifying pathogens causing EDL, total RNA was extracted from leaves of healthy leek plants grown in a greenhouse facility and infected plants showing symptoms of the disease. Five pools were prepared by mixing total RNA: four from infected ones (Sick1, Sick2, Sick3, and Sick4) and one from control samples pool C- (Control) that were sent for sequencing. We analyzed the NGS data to identify the microorganisms associated with diseased leek plants. The most important steps of this analysis were: control of the quality of raw reads, trimming the adapter sequences and selection of the contigs present in the infected pools and not in the healthy ones. We took only a sample of 10 percent of the reads to avoid problems with lack of computational resources. Finally, the sequences of interest were analyzed to identify the possible pathogens present. The results showed the presence of phytoplasmas and other microorganisms as possible pathogens associated with the disease.En 2011, se describió una nueva enfermedad, llamada en este informe enfermedad emergente en puerro (EEP), en campos de puerro de Segovia. La enfermedad estaba caracterizada por anormalidades en el desarrollo, como geotropismo y deformación de las raíces; y decoloración de bulbos y hojas. Se desconoce la etiología de la enfermedad, pero los síntomas podrían estar asociados a la infección por diferentes patógenos que se distribuyen de forma sistémica en las plantas como virus y fitoplasmas. Con el objetivo de identificar los patógenos causantes de la EEP, se tomaron muestras de hojas y se extrajo el ARN total de estas. A su vez, se realizó el mismo proceso con plantas sanas. A partir de estos extractos, se realizaron 4 mezclas con RNA de plantas enfermas (Sick1, Sick2, Sick3 and Sick4) y una mezcla con RNA de plantas sanas (Control2) que fueron enviadas a secuenciar. Los datos resultantes de la secuenciación fueron analizados con el objetivo de identificar los microorganismos patógenos causantes de la enfermedad. Este análisis bioinformático incluía distintos pasos. Los más relevantes fueron el control de calidad de las secuencias originales, la eliminación de adaptadores y la selección de lecturas presentes exclusivamente en las mezclas de plantas enfermas. Se seleccionaron aleatoriamente el 10% de las lecturas de cada pool para evitar problemas de falta de recursos computacionales. Finalmente, las secuencias de interés fueron analizadas para identificar los posibles patógenos presentes. Los resultados mostraron la presencia de fitoplasmas y otros microorganismos como posibles causantes de la enfermedad.L'any 2011, es va descriure una nova malaltia, en aquest informe anomenada malaltia emergent del porro o EDL (de l'anglès Emergent Disease in Leeks ), en camps de poerro de Segovia. La malaltia estava caracteritzada per anormalitats en el desenvolupament, com geotropisme i deformació de les arrels; i decoloració de bulbs i fulles. L'etiologia de la malaltia no es coneix, però els símptomes podrien estar associats a la infecció de diferents patògens que es distribueixen de forma sistèmica a les plantes com virus i fitoplasmes. Amb l'objectiu d'identificar els patògens causants de l'EDL, es van prendre mostres de fulles i es va extreure el ARN total d'aquestes. Al seu torn, es va realitzar el mateix procés amb plantes sanes. A partir d'aquests extractes, es van realitzar 4 mescles amb l'ARN de les plantes malaltes (Sick1, Sick2, Sick3 i Sick4) i una barreja amb l'ARN de les plantes sanes (Control2) i posteriorment van ser enviades a seqüenciar. Els dades resultants de la seqüenciació van ser analitzats amb l'objectiu d'identificar els microorganismes patògens causants de la malaltia. A partir d'aquí es van dur a terme uns anàlisi s bioinformàtics. Els anàlisis més rellevants van ser el control de qualitat de les seqüències originals, la eliminació d'adaptadors i la selecció de lectures presents exclusivament en les mescles de plantes malalties. Es van seleccionar aleatòriament el 10% dels "reads" de cada grup per evitar problemes de falta de recursos computacionals. Finalment, les seqüències d'interès van ser analitzades per identificar els possibles patògens presents. Els resultats van mostrar la presència de fitoplasmes i altres microorganismes com a possibles causants de la malaltia.Universitat Oberta de Catalunya (UOC)Merino, DavidYlla Bou, Guillem201920192019info:eu-repo/semantics/masterThesisapplication/pdfapplication/pdfhttp://hdl.handle.net/10609/88786reponame:O2, repositorio institucional de la UOCinstname:Universitat Oberta de Catalunya (UOC)InglésCC BY-NC-NDhttp://creativecommons.org/licenses/by-nc-nd/3.0/es/info:eu-repo/semantics/openAccessoai:openaccess.uoc.edu:10609/887862026-05-28T12:42:01Z
score 15.300719

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