Marcadores microssatélites para os genomas nuclear e organelar de amburana cearensis (Allemão) A.C. Smith
Autor(a) principal: | |
---|---|
Data de Publicação: | 2021 |
Tipo de documento: | Dissertação |
Idioma: | por |
Título da fonte: | Repositório Institucional da UFG |
dARK ID: | ark:/38995/0013000000zdw |
Texto Completo: | http://repositorio.bc.ufg.br/tede/handle/tede/11888 |
Resumo: | Amburana cearensis is a tree species, popularly known in Brazil as cerejeira, widely distributed in Brazil and also in Argentina, Bolivia, Paraguay and Peru. The species is distributed in a range of intense anthropic action and classified as endangered according to the International Union for the Conservation of Nature (IUCN). The economic demand for A. cearensis as a wood source and medicinal source has boosted its predatory exploitation, representing a threat to the survival of the species. In this scenario, conservation genetics is essential for generating knowledge about the genetic diversity of the species and defining appropriate strategies for its conservation and management. The general objective of this work was to design primer pairs with high potential for the development of robust and informative microsatellite markers for the nuclear, chloroplast and mitochondrial genomes of A. cearensis. Moreover, for quickness and cost savings, nuclear microsatellite primer pairs were designed for amplification in multiplex PCR. To achieve the proposed objectives, the genome of A. cearensis was partially sequenced, using the Illumina MiSeq platform. The assembly of the genomic library was performed from the DNA of an individual of the species and the genomic sequences obtained were analyzed using FastQC, Trimmomatic and DipSPAdes software. The search for microsatellite regions was performed using the QDD program. Thirty pairs of primers for nuclear microsatellite regions were designed, organized into five sets for amplification in multiplex PCR. The primer pairs designed in this study have the potential to generate new microsatellite markers with high individual discrimination capacity and transferability to other species of the genus Amburana. These markers can be applied quickly and efficiently for different types of genetic diversity studies of A. cearensis and Amburana genus. |
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Soares, Thannya Nascimentohttp://lattes.cnpq.br/5590256762396056Mansano, Vidal de Freitashttp://lattes.cnpq.br/5618078551561118Soares, Thannya NascimentoTelles, Mariana Pires de CamposVianello, Rosana Pereirahttp://lattes.cnpq.br/9501670056221505Santos, Laís Souza2022-02-16T10:04:26Z2022-02-16T10:04:26Z2021-08-30SANTOS, L. S. Marcadores microssatélites para os genomas nuclear e organelar de amburana cearensis (Allemão) A.C. Smith. 2021. 73 f. Dissertação (Mestrado em Genética e Biologia Molecular) - Universidade Federal de Goiás, Goiânia, 2021.http://repositorio.bc.ufg.br/tede/handle/tede/11888ark:/38995/0013000000zdwAmburana cearensis is a tree species, popularly known in Brazil as cerejeira, widely distributed in Brazil and also in Argentina, Bolivia, Paraguay and Peru. The species is distributed in a range of intense anthropic action and classified as endangered according to the International Union for the Conservation of Nature (IUCN). The economic demand for A. cearensis as a wood source and medicinal source has boosted its predatory exploitation, representing a threat to the survival of the species. In this scenario, conservation genetics is essential for generating knowledge about the genetic diversity of the species and defining appropriate strategies for its conservation and management. The general objective of this work was to design primer pairs with high potential for the development of robust and informative microsatellite markers for the nuclear, chloroplast and mitochondrial genomes of A. cearensis. Moreover, for quickness and cost savings, nuclear microsatellite primer pairs were designed for amplification in multiplex PCR. To achieve the proposed objectives, the genome of A. cearensis was partially sequenced, using the Illumina MiSeq platform. The assembly of the genomic library was performed from the DNA of an individual of the species and the genomic sequences obtained were analyzed using FastQC, Trimmomatic and DipSPAdes software. The search for microsatellite regions was performed using the QDD program. Thirty pairs of primers for nuclear microsatellite regions were designed, organized into five sets for amplification in multiplex PCR. The primer pairs designed in this study have the potential to generate new microsatellite markers with high individual discrimination capacity and transferability to other species of the genus Amburana. These markers can be applied quickly and efficiently for different types of genetic diversity studies of A. cearensis and Amburana genus.Amburana cearensis é uma espécie arbórea, conhecida popularmente como cerejeira, amplamente distribuída no Brasil e na Argentina, Bolívia, Paraguai e Peru. A espécie está distribuída em uma faixa de intensa ação antrópica e classificada como quase ameaçada de extinção de acordo com a União Internacional para a Conservação da Natureza (IUCN). A demanda econômica de A. cearensis como fonte madeireira e fonte medicinal impulsionou a sua exploração predatória, representando uma ameaça à sobrevivência da espécie. Nesse cenário, a genética de conservação é fundamental para a geração de conhecimentos sobre diversidade genética da espécie e definição de estratégias adequadas para a sua conservação e manejo. O objetivo geral deste trabalho foi desenhar pares de primers com alto potencial para o desenvolvimento de marcadores microssatélites robustos e informativos para os genomas nuclear, cloroplastidial e mitocondrial de A. cearensis. Além disso, visando a rapidez e a diminuição dos custos, os pares de primers de microssatélites nucleares foram desenhados para a amplificação em PCR multiplex. Para atingir os objetivos propostos, o genoma de A. cearensis foi parcialmente sequenciado, com o uso da plataforma Illumina MiSeq. A montagem da biblioteca genômica foi realizada a partir do DNA de um indivíduo da espécie e as sequências genômicas obtidas foram analisadas utilizando os softwares FastQC, Trimmomatic e DipSPAdes. A busca de regiões microssatélites foi realizada com o uso do programa QDD. Foram desenhados trinta pares de primers para regiões microssatélites nucleares, organizados em cinco conjuntos para a amplificação em PCR multiplex. Além disso, foram desenhados três pares de primers microssatélites cloroplastidiais e sete mitocondriais. Os pares de primers desenhados no presente estudo apresentam potencial de geração de novos marcadores microssatélites com alta capacidade de discriminação individual e transferibilidade para as outras espécies do gênero Amburana. Estes marcadores poderão ser aplicados de forma rápida e eficiente para os diversos tipos de estudos de diversidade genética de A. cearensis e do gênero Amburana.Submitted by Marlene Santos (marlene.bc.ufg@gmail.com) on 2022-02-05T18:09:58Z No. of bitstreams: 2 Dissertação - Laís Souza Santos - 2021.pdf: 1575011 bytes, checksum: 27b01a606d5f45ad71e4289a51b12cce (MD5) license_rdf: 805 bytes, checksum: 4460e5956bc1d1639be9ae6146a50347 (MD5)Approved for entry into archive by Liliane Ferreira (ljuvencia30@gmail.com) on 2022-02-16T10:04:26Z (GMT) No. of bitstreams: 2 Dissertação - Laís Souza Santos - 2021.pdf: 1575011 bytes, checksum: 27b01a606d5f45ad71e4289a51b12cce (MD5) license_rdf: 805 bytes, checksum: 4460e5956bc1d1639be9ae6146a50347 (MD5)Made available in DSpace on 2022-02-16T10:04:26Z (GMT). No. of bitstreams: 2 Dissertação - Laís Souza Santos - 2021.pdf: 1575011 bytes, checksum: 27b01a606d5f45ad71e4289a51b12cce (MD5) license_rdf: 805 bytes, checksum: 4460e5956bc1d1639be9ae6146a50347 (MD5) Previous issue date: 2021-08-30Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPESporUniversidade Federal de GoiásPrograma de Pós-graduação em Genética e Biologia Molecular (ICB)UFGBrasilInstituto de Ciências Biológicas - ICB (RG)Attribution-NonCommercial-NoDerivatives 4.0 Internationalhttp://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccessAmburana cearensisMarcadores microssatélitesNGSMicrosatellite markersCIENCIAS BIOLOGICAS::GENETICA::GENETICA MOLECULAR E DE MICROORGANISMOSMarcadores microssatélites para os genomas nuclear e organelar de amburana cearensis (Allemão) A.C. SmithMicrosatellite markers for the nuclear and organellar genomes of amburana cearensis (Allemão) A.C. 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dc.title.pt_BR.fl_str_mv |
Marcadores microssatélites para os genomas nuclear e organelar de amburana cearensis (Allemão) A.C. Smith |
dc.title.alternative.eng.fl_str_mv |
Microsatellite markers for the nuclear and organellar genomes of amburana cearensis (Allemão) A.C. Smith |
title |
Marcadores microssatélites para os genomas nuclear e organelar de amburana cearensis (Allemão) A.C. Smith |
spellingShingle |
Marcadores microssatélites para os genomas nuclear e organelar de amburana cearensis (Allemão) A.C. Smith Santos, Laís Souza Amburana cearensis Marcadores microssatélites NGS Microsatellite markers CIENCIAS BIOLOGICAS::GENETICA::GENETICA MOLECULAR E DE MICROORGANISMOS |
title_short |
Marcadores microssatélites para os genomas nuclear e organelar de amburana cearensis (Allemão) A.C. Smith |
title_full |
Marcadores microssatélites para os genomas nuclear e organelar de amburana cearensis (Allemão) A.C. Smith |
title_fullStr |
Marcadores microssatélites para os genomas nuclear e organelar de amburana cearensis (Allemão) A.C. Smith |
title_full_unstemmed |
Marcadores microssatélites para os genomas nuclear e organelar de amburana cearensis (Allemão) A.C. Smith |
title_sort |
Marcadores microssatélites para os genomas nuclear e organelar de amburana cearensis (Allemão) A.C. Smith |
author |
Santos, Laís Souza |
author_facet |
Santos, Laís Souza |
author_role |
author |
dc.contributor.advisor1.fl_str_mv |
Soares, Thannya Nascimento |
dc.contributor.advisor1Lattes.fl_str_mv |
http://lattes.cnpq.br/5590256762396056 |
dc.contributor.advisor-co1.fl_str_mv |
Mansano, Vidal de Freitas |
dc.contributor.advisor-co1Lattes.fl_str_mv |
http://lattes.cnpq.br/5618078551561118 |
dc.contributor.referee1.fl_str_mv |
Soares, Thannya Nascimento |
dc.contributor.referee2.fl_str_mv |
Telles, Mariana Pires de Campos |
dc.contributor.referee3.fl_str_mv |
Vianello, Rosana Pereira |
dc.contributor.authorLattes.fl_str_mv |
http://lattes.cnpq.br/9501670056221505 |
dc.contributor.author.fl_str_mv |
Santos, Laís Souza |
contributor_str_mv |
Soares, Thannya Nascimento Mansano, Vidal de Freitas Soares, Thannya Nascimento Telles, Mariana Pires de Campos Vianello, Rosana Pereira |
dc.subject.por.fl_str_mv |
Amburana cearensis Marcadores microssatélites NGS |
topic |
Amburana cearensis Marcadores microssatélites NGS Microsatellite markers CIENCIAS BIOLOGICAS::GENETICA::GENETICA MOLECULAR E DE MICROORGANISMOS |
dc.subject.eng.fl_str_mv |
Microsatellite markers |
dc.subject.cnpq.fl_str_mv |
CIENCIAS BIOLOGICAS::GENETICA::GENETICA MOLECULAR E DE MICROORGANISMOS |
description |
Amburana cearensis is a tree species, popularly known in Brazil as cerejeira, widely distributed in Brazil and also in Argentina, Bolivia, Paraguay and Peru. The species is distributed in a range of intense anthropic action and classified as endangered according to the International Union for the Conservation of Nature (IUCN). The economic demand for A. cearensis as a wood source and medicinal source has boosted its predatory exploitation, representing a threat to the survival of the species. In this scenario, conservation genetics is essential for generating knowledge about the genetic diversity of the species and defining appropriate strategies for its conservation and management. The general objective of this work was to design primer pairs with high potential for the development of robust and informative microsatellite markers for the nuclear, chloroplast and mitochondrial genomes of A. cearensis. Moreover, for quickness and cost savings, nuclear microsatellite primer pairs were designed for amplification in multiplex PCR. To achieve the proposed objectives, the genome of A. cearensis was partially sequenced, using the Illumina MiSeq platform. The assembly of the genomic library was performed from the DNA of an individual of the species and the genomic sequences obtained were analyzed using FastQC, Trimmomatic and DipSPAdes software. The search for microsatellite regions was performed using the QDD program. Thirty pairs of primers for nuclear microsatellite regions were designed, organized into five sets for amplification in multiplex PCR. The primer pairs designed in this study have the potential to generate new microsatellite markers with high individual discrimination capacity and transferability to other species of the genus Amburana. These markers can be applied quickly and efficiently for different types of genetic diversity studies of A. cearensis and Amburana genus. |
publishDate |
2021 |
dc.date.issued.fl_str_mv |
2021-08-30 |
dc.date.accessioned.fl_str_mv |
2022-02-16T10:04:26Z |
dc.date.available.fl_str_mv |
2022-02-16T10:04:26Z |
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info:eu-repo/semantics/publishedVersion |
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info:eu-repo/semantics/masterThesis |
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masterThesis |
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publishedVersion |
dc.identifier.citation.fl_str_mv |
SANTOS, L. S. Marcadores microssatélites para os genomas nuclear e organelar de amburana cearensis (Allemão) A.C. Smith. 2021. 73 f. Dissertação (Mestrado em Genética e Biologia Molecular) - Universidade Federal de Goiás, Goiânia, 2021. |
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http://repositorio.bc.ufg.br/tede/handle/tede/11888 |
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ark:/38995/0013000000zdw |
identifier_str_mv |
SANTOS, L. S. Marcadores microssatélites para os genomas nuclear e organelar de amburana cearensis (Allemão) A.C. Smith. 2021. 73 f. Dissertação (Mestrado em Genética e Biologia Molecular) - Universidade Federal de Goiás, Goiânia, 2021. ark:/38995/0013000000zdw |
url |
http://repositorio.bc.ufg.br/tede/handle/tede/11888 |
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por |
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por |
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23 |
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1 |
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Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/ info:eu-repo/semantics/openAccess |
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Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/ |
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openAccess |
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Universidade Federal de Goiás |
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Programa de Pós-graduação em Genética e Biologia Molecular (ICB) |
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UFG |
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Brasil |
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Instituto de Ciências Biológicas - ICB (RG) |
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Universidade Federal de Goiás |
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