Genômica comparativa de Francisella noatunensis subsp. orientalis

Detalhes bibliográficos
Autor(a) principal: Lucas Amorim Goncalves
Data de Publicação: 2015
Tipo de documento: Dissertação
Idioma: por
Título da fonte: Repositório Institucional da UFMG
Texto Completo: http://hdl.handle.net/1843/BUBD-9ZHHDE
Resumo: The Francisella species are intracellular facultative bacteria that cause a variety of infections in terrestrial and aquatic animals. In this genus, F. noatunensis subsp. orientalis (FNO) has a remarked importance as an emergent fish pathogen associated with outbreaks in Nile tilapia farms. Although the disease caused by FNO presents a high mortality rate during outbreaks and has been reported in several countries, the phylogenomic relationships among isolates from different countries, the evolutionary history of this pathogen and other aspects still are poorly characterized. In this context, comparative genomic analyzes were performed in order to assist in better understanding this species of great epidemiologic interest. Thus, 18 strains of F. noatunensis subsp. orientalis isolated from outbreaks in Brazilian Nile tilapia farms were sequenced, assembled and manually curated. Then, the Gegenes, Mauve, BRIG and Gipsy softwares, and the Genome Comparator module of the BIGsdb database were used to perform phylogeny, synteny, genomic plasticity and polymorphisms analyzes. Other Francisella subspecies and FNO strains available in the NCBI were included in all of these analyzes. Additionally, searches were made for genes possibly involved in the response to environmental stresses. Therefore, it was observed that the FNO strains are highly clonal and that the arrival of the disease in Brazil is probably due to the entrance of a single strain. Eight genomic islands were also predicted, six being considered pathogenicity islands. Finally, the search for genes potentially involved in the response to environmental stresses indicated a number of candidate genes for a more detailed study for the development of drugs.
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spelling Genômica comparativa de Francisella noatunensis subsp. orientalisGenômica comparativaFrancisella noatunensis subsp orientalisTilapia-do-nilo e franciseloseTilápia do NiloGenômicaBioinformáticaTilapia (Peixe) DoençasThe Francisella species are intracellular facultative bacteria that cause a variety of infections in terrestrial and aquatic animals. In this genus, F. noatunensis subsp. orientalis (FNO) has a remarked importance as an emergent fish pathogen associated with outbreaks in Nile tilapia farms. Although the disease caused by FNO presents a high mortality rate during outbreaks and has been reported in several countries, the phylogenomic relationships among isolates from different countries, the evolutionary history of this pathogen and other aspects still are poorly characterized. In this context, comparative genomic analyzes were performed in order to assist in better understanding this species of great epidemiologic interest. Thus, 18 strains of F. noatunensis subsp. orientalis isolated from outbreaks in Brazilian Nile tilapia farms were sequenced, assembled and manually curated. Then, the Gegenes, Mauve, BRIG and Gipsy softwares, and the Genome Comparator module of the BIGsdb database were used to perform phylogeny, synteny, genomic plasticity and polymorphisms analyzes. Other Francisella subspecies and FNO strains available in the NCBI were included in all of these analyzes. Additionally, searches were made for genes possibly involved in the response to environmental stresses. Therefore, it was observed that the FNO strains are highly clonal and that the arrival of the disease in Brazil is probably due to the entrance of a single strain. Eight genomic islands were also predicted, six being considered pathogenicity islands. Finally, the search for genes potentially involved in the response to environmental stresses indicated a number of candidate genes for a more detailed study for the development of drugs.As espécies de Francisella são caracterizadas por serem bactérias intracelulares facultativas que causam uma variedade de infecções em animais terrestres e aquáticos. Nesse gênero, Francisella noatunensis subsp. orientalis (FNO) apresenta uma grande importância por ser um patógeno emergente de peixes, associado a surtos em fazendas de cultura de tilápia-do-nilo. Apesar de a doença causada por FNO apresentar uma alta taxa de mortalidade durante os surtos e ter sido relatada em diversos países, as relações filogenômicas entre os isolados de diferentes países, a história evolucionária deste patógeno e diversos outros aspectos acerca da sua caracterização genômica ainda são pouco conhecidas. Neste contexto, análises de genômica comparativa foram realizadas afim de auxiliar no maior conhecimento dessa espécie de claro interesse epidemiológico. Para tanto, foram sequenciadas, montadas e curadas manualmente 18 linhagens de F. noatunensis subsp. orientalis isoladas de surtos em fazendas de cultivo de tilápia-do-nilo no Brasil. Em seguida, foram utilizados os softwares Gegenes, Mauve, BRIG, Gipsy e o módulo Genome Comparator do banco de dados BIGSdb para a realização de análises de filogenia, sintenia, plasticidade genômica e polimorfismo. Em todas essas análises foram incluídas outras subespécies de Francisella e linhagens de FNO disponíveis no NCBI. Além disso, foram feitas buscas por genes possivelmente envolvidos na resposta a estresses ambientais. Desse modo, foi observado que as linhagens de FNO são altamente clonais e que provavelmente a chegada da doença ao país se deu pela entrada de uma única linhagem. Foram também preditas oito ilhas genômicas, sendo seis consideradas ilhas de patogenicidade. Por fim, a busca por genes potencialmente envolvidos na resposta a estresses ambientais indicou uma série de genes candidatos a um estudo mais aprofundado para o desenvolvimento de drogas.Universidade Federal de Minas GeraisUFMGVasco Ariston de Carvalho AzevedoHenrique Cesar Pereira FigueiredoSiomar de Castro SoaresLucas Amorim Goncalves2019-08-12T09:12:23Z2019-08-12T09:12:23Z2015-03-26info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesisapplication/pdfhttp://hdl.handle.net/1843/BUBD-9ZHHDEinfo:eu-repo/semantics/openAccessporreponame:Repositório Institucional da UFMGinstname:Universidade Federal de Minas Gerais (UFMG)instacron:UFMG2019-11-14T18:46:54Zoai:repositorio.ufmg.br:1843/BUBD-9ZHHDERepositório InstitucionalPUBhttps://repositorio.ufmg.br/oairepositorio@ufmg.bropendoar:2019-11-14T18:46:54Repositório Institucional da UFMG - Universidade Federal de Minas Gerais (UFMG)false
dc.title.none.fl_str_mv Genômica comparativa de Francisella noatunensis subsp. orientalis
title Genômica comparativa de Francisella noatunensis subsp. orientalis
spellingShingle Genômica comparativa de Francisella noatunensis subsp. orientalis
Lucas Amorim Goncalves
Genômica comparativa
Francisella noatunensis subsp orientalis
Tilapia-do-nilo e franciselose
Tilápia do Nilo
Genômica
Bioinformática
Tilapia (Peixe) Doenças
title_short Genômica comparativa de Francisella noatunensis subsp. orientalis
title_full Genômica comparativa de Francisella noatunensis subsp. orientalis
title_fullStr Genômica comparativa de Francisella noatunensis subsp. orientalis
title_full_unstemmed Genômica comparativa de Francisella noatunensis subsp. orientalis
title_sort Genômica comparativa de Francisella noatunensis subsp. orientalis
author Lucas Amorim Goncalves
author_facet Lucas Amorim Goncalves
author_role author
dc.contributor.none.fl_str_mv Vasco Ariston de Carvalho Azevedo
Henrique Cesar Pereira Figueiredo
Siomar de Castro Soares
dc.contributor.author.fl_str_mv Lucas Amorim Goncalves
dc.subject.por.fl_str_mv Genômica comparativa
Francisella noatunensis subsp orientalis
Tilapia-do-nilo e franciselose
Tilápia do Nilo
Genômica
Bioinformática
Tilapia (Peixe) Doenças
topic Genômica comparativa
Francisella noatunensis subsp orientalis
Tilapia-do-nilo e franciselose
Tilápia do Nilo
Genômica
Bioinformática
Tilapia (Peixe) Doenças
description The Francisella species are intracellular facultative bacteria that cause a variety of infections in terrestrial and aquatic animals. In this genus, F. noatunensis subsp. orientalis (FNO) has a remarked importance as an emergent fish pathogen associated with outbreaks in Nile tilapia farms. Although the disease caused by FNO presents a high mortality rate during outbreaks and has been reported in several countries, the phylogenomic relationships among isolates from different countries, the evolutionary history of this pathogen and other aspects still are poorly characterized. In this context, comparative genomic analyzes were performed in order to assist in better understanding this species of great epidemiologic interest. Thus, 18 strains of F. noatunensis subsp. orientalis isolated from outbreaks in Brazilian Nile tilapia farms were sequenced, assembled and manually curated. Then, the Gegenes, Mauve, BRIG and Gipsy softwares, and the Genome Comparator module of the BIGsdb database were used to perform phylogeny, synteny, genomic plasticity and polymorphisms analyzes. Other Francisella subspecies and FNO strains available in the NCBI were included in all of these analyzes. Additionally, searches were made for genes possibly involved in the response to environmental stresses. Therefore, it was observed that the FNO strains are highly clonal and that the arrival of the disease in Brazil is probably due to the entrance of a single strain. Eight genomic islands were also predicted, six being considered pathogenicity islands. Finally, the search for genes potentially involved in the response to environmental stresses indicated a number of candidate genes for a more detailed study for the development of drugs.
publishDate 2015
dc.date.none.fl_str_mv 2015-03-26
2019-08-12T09:12:23Z
2019-08-12T09:12:23Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/masterThesis
format masterThesis
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/1843/BUBD-9ZHHDE
url http://hdl.handle.net/1843/BUBD-9ZHHDE
dc.language.iso.fl_str_mv por
language por
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Universidade Federal de Minas Gerais
UFMG
publisher.none.fl_str_mv Universidade Federal de Minas Gerais
UFMG
dc.source.none.fl_str_mv reponame:Repositório Institucional da UFMG
instname:Universidade Federal de Minas Gerais (UFMG)
instacron:UFMG
instname_str Universidade Federal de Minas Gerais (UFMG)
instacron_str UFMG
institution UFMG
reponame_str Repositório Institucional da UFMG
collection Repositório Institucional da UFMG
repository.name.fl_str_mv Repositório Institucional da UFMG - Universidade Federal de Minas Gerais (UFMG)
repository.mail.fl_str_mv repositorio@ufmg.br
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