Análise de sequências de genes de limoneno sintases em genomas de citros
Autor(a) principal: | |
---|---|
Data de Publicação: | 2020 |
Tipo de documento: | Dissertação |
Idioma: | por |
Título da fonte: | Repositório Institucional da UFSCAR |
Texto Completo: | https://repositorio.ufscar.br/handle/ufscar/13386 |
Resumo: | Limonene, a terpene found in essential oil extracted from citrus peel, has great applicability on industry. Is it known that there are great limonene concentration differences among citrus varieties, however, limonene remains the principal component of essential oils from this group. In this study, it was hypothesized that genomic differences could be related to the variations of limonene observed between different species. In order to prove this, an in silico analysis was performed and limonene synthase sequences were searched on Citrus sinensis variety “Valencia” genome, available on “Citrus Genome Database”. Those results were used to obtain highly similar sequences from species such as C. sinensis (sweet orange “Ridge Pineapple”), C. reticulata (tangerine), C. ichangensis (papeda), C. maxima (pomelo) and C. medica (cider). Results indicate that there are thirteen gene sequences coding for limonene synthases in Valencia. Those thirteen sequences were aligned. The results of the alignments served to have an initial idea ofthe real similarity between the sequences, we see that there are conserved regions in several of the alignments performed, which implies that the varieties have phylogenetic relationships, which is expected since they all belong to the same genus. At no time, the sequences were 100% identical, which shows an interesting result, after all, studies have proven that different varieties/species have different amounts of limonene in their essential oils. There is high sequence similarity among the sweet oranges, C. maxima and C. reticulate, which confirms the ancestral origin of those varieties, since C. sinensis is a hybrid among C. maxima, C. reticulata and another unknown citrus species. Another analysis that was performed was a sequence similarity search using the translated sequence from the thirteen limonene synthase proteins from Valencia against the same varieties used on genomic similarity search. This analysis resulted the same pattern of similarity among C. sinensis, C. maxima and C. reticulate found on genomic similarity results, and the phylogenetic analysis confirmed those results. The analysis of the promoter region did not show the similarities found in the analysis of gene and protein sequences, which may be the expected result, these differences between promoters may be related to the regulation of genes and thereby explain the difference in limonene synthases between species and variety of citrus. Although eukaryotic promoter analysis is one of the most difficult computation problems, an in-depth study of the referred promoter regions is needed to elucidate our interpretation of genomic and proteomic comparisons. |
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Ferreira, Francisco Inacio PaivaTakita, Marco Auréliohttp://lattes.cnpq.br/0578612884434541Medeiros, Ane Hackbart dehttp://lattes.cnpq.br/6315858319851377http://lattes.cnpq.br/6675777553887685d377f229-0e63-40a1-90f0-68f6af00fef22020-10-27T20:49:29Z2020-10-27T20:49:29Z2020-08-31FERREIRA, Francisco Inacio Paiva. Análise de sequências de genes de limoneno sintases em genomas de citros. 2020. Dissertação (Mestrado em Produção Vegetal e Bioprocessos Associados) – Universidade Federal de São Carlos, Araras, 2020. Disponível em: https://repositorio.ufscar.br/handle/ufscar/13386.https://repositorio.ufscar.br/handle/ufscar/13386Limonene, a terpene found in essential oil extracted from citrus peel, has great applicability on industry. Is it known that there are great limonene concentration differences among citrus varieties, however, limonene remains the principal component of essential oils from this group. In this study, it was hypothesized that genomic differences could be related to the variations of limonene observed between different species. In order to prove this, an in silico analysis was performed and limonene synthase sequences were searched on Citrus sinensis variety “Valencia” genome, available on “Citrus Genome Database”. Those results were used to obtain highly similar sequences from species such as C. sinensis (sweet orange “Ridge Pineapple”), C. reticulata (tangerine), C. ichangensis (papeda), C. maxima (pomelo) and C. medica (cider). Results indicate that there are thirteen gene sequences coding for limonene synthases in Valencia. Those thirteen sequences were aligned. The results of the alignments served to have an initial idea ofthe real similarity between the sequences, we see that there are conserved regions in several of the alignments performed, which implies that the varieties have phylogenetic relationships, which is expected since they all belong to the same genus. At no time, the sequences were 100% identical, which shows an interesting result, after all, studies have proven that different varieties/species have different amounts of limonene in their essential oils. There is high sequence similarity among the sweet oranges, C. maxima and C. reticulate, which confirms the ancestral origin of those varieties, since C. sinensis is a hybrid among C. maxima, C. reticulata and another unknown citrus species. Another analysis that was performed was a sequence similarity search using the translated sequence from the thirteen limonene synthase proteins from Valencia against the same varieties used on genomic similarity search. This analysis resulted the same pattern of similarity among C. sinensis, C. maxima and C. reticulate found on genomic similarity results, and the phylogenetic analysis confirmed those results. The analysis of the promoter region did not show the similarities found in the analysis of gene and protein sequences, which may be the expected result, these differences between promoters may be related to the regulation of genes and thereby explain the difference in limonene synthases between species and variety of citrus. Although eukaryotic promoter analysis is one of the most difficult computation problems, an in-depth study of the referred promoter regions is needed to elucidate our interpretation of genomic and proteomic comparisons.O limoneno, um terpeno encontrado em óleos essenciais extraído da casca de citros, tem grande aplicabilidade na indústria. Sabe-se que existe grande diferença de concentração de limoneno entre as variedades de citros, sendo, o principal componente dos óleos essenciais do grupo. Nesse estudo, hipotetizou-se que diferenças genômicas poderiam estar relacionadas às variações de limoneno observadas entre as diferentes espécies. Para isso, fez-se uma análise in silico, onde buscou-se sequências de genes codificando limoneno sintase no genoma de Citrus sinensis variedade “Valência”, disponíveis no banco de dados de citros “Citrus Genome Database”, que foram usadas para obtenção de sequências com alta similaridade das espécies: C. sinensis (laranja doce “Ridge Pineapple”), C. reticulata (tangerina), C. ichangensis (papeda), C. maxima (toranja) e C. medica (cidra). Os resultados indicam que existem treze sequências de genes codificando limoneno sintases em Valência. As treze sequências foram alinhadas. Os resultados dos alinhamentos serviram para se ter uma ideia inicial da semelhança real entre as sequências, vemos que há regiões conservadas em diversos dos alinhamentos realizados, que implica que as variedades possuem relações filogenéticas, o que é esperado já que todas pertencem ao mesmo gênero. Em nenhum momento, as sequências foram 100% idênticas, o que se mostra um resultado interessante, afinal estudos já comprovaram que variedades/espécies diferentes possuem quantidades diferentes de limoneno em seus óleos essenciais. Há alta similaridade de sequência entre laranjas doce, C. maxima e C. reticulata, o que na realidade, confirma a origem dessas variedades pois C. sinensis é um híbrido entre C. maxima, C. reticulata e uma espécie desconhecida de citros. Também foi feita uma busca por similaridade usando a sequência traduzida das treze proteínas de limoneno sintase de “Valência” com as mesmas variedades. Esta análise de proteínas mostrou o mesmo padrão de similaridade entre C. sinensis, C. maxima, e C. reticulata, e a análise de filogenia confirma esses resultados. A análise da região promotora não mostrou as semelhanças encontradas na análise de sequências gênicas e protéicas, o que pode ser o resultado esperado, essas diferenças entre os promotores podem estar relacionadas com a regulação dos genes e com isso explicar a diferença de limoneno sintases entre espécies e variedade de citros. Porém, o ideal neste caso seria um estudo mais aprofundado com tais regiões promotoras, para resultados com melhor clareza, afinal a análise de promotores eucarióticos é um dos problemas mais difíceis na genômica computacional.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)CAPES: 001porUniversidade Federal de São CarlosCâmpus ArarasPrograma de Pós-Graduação em Produção Vegetal e Bioprocessos Associados - PPGPVBA-ArUFSCarAttribution-NonCommercial-NoDerivs 3.0 Brazilhttp://creativecommons.org/licenses/by-nc-nd/3.0/br/info:eu-repo/semantics/openAccessCitrosGenomaLimonenoCitrusGenomeLimoneneCIENCIAS AGRARIASAnálise de sequências de genes de limoneno sintases em genomas de citrosSequence analysis of limonene synthases genes in citrus genomesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesis60060006e29331-03d2-4150-b6de-99599961ecd3reponame:Repositório Institucional da UFSCARinstname:Universidade Federal de São Carlos (UFSCAR)instacron:UFSCARORIGINALFERREIRA_Francisco_2020.pdfFERREIRA_Francisco_2020.pdfapplication/pdf7791992https://repositorio.ufscar.br/bitstream/ufscar/13386/8/FERREIRA_Francisco_2020.pdf02c5b1f1f29cb2a66a250a7df2de8403MD58CC-LICENSElicense_rdflicense_rdfapplication/rdf+xml; charset=utf-8811https://repositorio.ufscar.br/bitstream/ufscar/13386/3/license_rdfe39d27027a6cc9cb039ad269a5db8e34MD53TEXTDISSERTAÇÃO FRANCISCO INACIO PAIVA FERREIRA.pdf.txtDISSERTAÇÃO FRANCISCO INACIO PAIVA FERREIRA.pdf.txtExtracted texttext/plain113621https://repositorio.ufscar.br/bitstream/ufscar/13386/4/DISSERTA%c3%87%c3%83O%20FRANCISCO%20INACIO%20PAIVA%20FERREIRA.pdf.txtea644b80f14fa60380cb22c90a820083MD54Carta de Encaminhamento de Versão Definitiva de Dissertação.pdf.txtCarta de Encaminhamento de Versão Definitiva de Dissertação.pdf.txtExtracted texttext/plain1299https://repositorio.ufscar.br/bitstream/ufscar/13386/6/Carta%20de%20Encaminhamento%20de%20Vers%c3%a3o%20Definitiva%20de%20Disserta%c3%a7%c3%a3o.pdf.txtfc381f9a6344ba2815321466f251e615MD56FERREIRA_Francisco_2020.pdf.txtFERREIRA_Francisco_2020.pdf.txtExtracted texttext/plain113621https://repositorio.ufscar.br/bitstream/ufscar/13386/9/FERREIRA_Francisco_2020.pdf.txtea644b80f14fa60380cb22c90a820083MD59THUMBNAILDISSERTAÇÃO FRANCISCO INACIO PAIVA FERREIRA.pdf.jpgDISSERTAÇÃO FRANCISCO INACIO PAIVA FERREIRA.pdf.jpgIM Thumbnailimage/jpeg7153https://repositorio.ufscar.br/bitstream/ufscar/13386/5/DISSERTA%c3%87%c3%83O%20FRANCISCO%20INACIO%20PAIVA%20FERREIRA.pdf.jpg283fc5f4c59caaee4dd95ea51cac0a8bMD55Carta de Encaminhamento de Versão Definitiva de Dissertação.pdf.jpgCarta de Encaminhamento de Versão Definitiva de Dissertação.pdf.jpgIM Thumbnailimage/jpeg6383https://repositorio.ufscar.br/bitstream/ufscar/13386/7/Carta%20de%20Encaminhamento%20de%20Vers%c3%a3o%20Definitiva%20de%20Disserta%c3%a7%c3%a3o.pdf.jpg338028df776c55a096ccff9b76422ee8MD57FERREIRA_Francisco_2020.pdf.jpgFERREIRA_Francisco_2020.pdf.jpgIM Thumbnailimage/jpeg7153https://repositorio.ufscar.br/bitstream/ufscar/13386/10/FERREIRA_Francisco_2020.pdf.jpg283fc5f4c59caaee4dd95ea51cac0a8bMD510ufscar/133862023-09-18 18:32:03.264oai:repositorio.ufscar.br:ufscar/13386Repositório InstitucionalPUBhttps://repositorio.ufscar.br/oai/requestopendoar:43222023-09-18T18:32:03Repositório Institucional da UFSCAR - Universidade Federal de São Carlos (UFSCAR)false |
dc.title.por.fl_str_mv |
Análise de sequências de genes de limoneno sintases em genomas de citros |
dc.title.alternative.eng.fl_str_mv |
Sequence analysis of limonene synthases genes in citrus genomes |
title |
Análise de sequências de genes de limoneno sintases em genomas de citros |
spellingShingle |
Análise de sequências de genes de limoneno sintases em genomas de citros Ferreira, Francisco Inacio Paiva Citros Genoma Limoneno Citrus Genome Limonene CIENCIAS AGRARIAS |
title_short |
Análise de sequências de genes de limoneno sintases em genomas de citros |
title_full |
Análise de sequências de genes de limoneno sintases em genomas de citros |
title_fullStr |
Análise de sequências de genes de limoneno sintases em genomas de citros |
title_full_unstemmed |
Análise de sequências de genes de limoneno sintases em genomas de citros |
title_sort |
Análise de sequências de genes de limoneno sintases em genomas de citros |
author |
Ferreira, Francisco Inacio Paiva |
author_facet |
Ferreira, Francisco Inacio Paiva |
author_role |
author |
dc.contributor.authorlattes.por.fl_str_mv |
http://lattes.cnpq.br/6675777553887685 |
dc.contributor.author.fl_str_mv |
Ferreira, Francisco Inacio Paiva |
dc.contributor.advisor1.fl_str_mv |
Takita, Marco Aurélio |
dc.contributor.advisor1Lattes.fl_str_mv |
http://lattes.cnpq.br/0578612884434541 |
dc.contributor.advisor-co1.fl_str_mv |
Medeiros, Ane Hackbart de |
dc.contributor.advisor-co1Lattes.fl_str_mv |
http://lattes.cnpq.br/6315858319851377 |
dc.contributor.authorID.fl_str_mv |
d377f229-0e63-40a1-90f0-68f6af00fef2 |
contributor_str_mv |
Takita, Marco Aurélio Medeiros, Ane Hackbart de |
dc.subject.por.fl_str_mv |
Citros Genoma Limoneno |
topic |
Citros Genoma Limoneno Citrus Genome Limonene CIENCIAS AGRARIAS |
dc.subject.eng.fl_str_mv |
Citrus Genome Limonene |
dc.subject.cnpq.fl_str_mv |
CIENCIAS AGRARIAS |
description |
Limonene, a terpene found in essential oil extracted from citrus peel, has great applicability on industry. Is it known that there are great limonene concentration differences among citrus varieties, however, limonene remains the principal component of essential oils from this group. In this study, it was hypothesized that genomic differences could be related to the variations of limonene observed between different species. In order to prove this, an in silico analysis was performed and limonene synthase sequences were searched on Citrus sinensis variety “Valencia” genome, available on “Citrus Genome Database”. Those results were used to obtain highly similar sequences from species such as C. sinensis (sweet orange “Ridge Pineapple”), C. reticulata (tangerine), C. ichangensis (papeda), C. maxima (pomelo) and C. medica (cider). Results indicate that there are thirteen gene sequences coding for limonene synthases in Valencia. Those thirteen sequences were aligned. The results of the alignments served to have an initial idea ofthe real similarity between the sequences, we see that there are conserved regions in several of the alignments performed, which implies that the varieties have phylogenetic relationships, which is expected since they all belong to the same genus. At no time, the sequences were 100% identical, which shows an interesting result, after all, studies have proven that different varieties/species have different amounts of limonene in their essential oils. There is high sequence similarity among the sweet oranges, C. maxima and C. reticulate, which confirms the ancestral origin of those varieties, since C. sinensis is a hybrid among C. maxima, C. reticulata and another unknown citrus species. Another analysis that was performed was a sequence similarity search using the translated sequence from the thirteen limonene synthase proteins from Valencia against the same varieties used on genomic similarity search. This analysis resulted the same pattern of similarity among C. sinensis, C. maxima and C. reticulate found on genomic similarity results, and the phylogenetic analysis confirmed those results. The analysis of the promoter region did not show the similarities found in the analysis of gene and protein sequences, which may be the expected result, these differences between promoters may be related to the regulation of genes and thereby explain the difference in limonene synthases between species and variety of citrus. Although eukaryotic promoter analysis is one of the most difficult computation problems, an in-depth study of the referred promoter regions is needed to elucidate our interpretation of genomic and proteomic comparisons. |
publishDate |
2020 |
dc.date.accessioned.fl_str_mv |
2020-10-27T20:49:29Z |
dc.date.available.fl_str_mv |
2020-10-27T20:49:29Z |
dc.date.issued.fl_str_mv |
2020-08-31 |
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info:eu-repo/semantics/masterThesis |
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FERREIRA, Francisco Inacio Paiva. Análise de sequências de genes de limoneno sintases em genomas de citros. 2020. Dissertação (Mestrado em Produção Vegetal e Bioprocessos Associados) – Universidade Federal de São Carlos, Araras, 2020. Disponível em: https://repositorio.ufscar.br/handle/ufscar/13386. |
dc.identifier.uri.fl_str_mv |
https://repositorio.ufscar.br/handle/ufscar/13386 |
identifier_str_mv |
FERREIRA, Francisco Inacio Paiva. Análise de sequências de genes de limoneno sintases em genomas de citros. 2020. Dissertação (Mestrado em Produção Vegetal e Bioprocessos Associados) – Universidade Federal de São Carlos, Araras, 2020. Disponível em: https://repositorio.ufscar.br/handle/ufscar/13386. |
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https://repositorio.ufscar.br/handle/ufscar/13386 |
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Universidade Federal de São Carlos Câmpus Araras |
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