Nucleotide diversity of genes related to chlorogenic acid biosynthesis of coffea
Autor(a) principal: | |
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Data de Publicação: | 2013 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng por |
Título da fonte: | Coffee Science (Online) |
Texto Completo: | https://coffeescience.ufla.br/index.php/Coffeescience/article/view/389 |
Resumo: | Chlorogenic acids (CGAs) are important chemical compounds of Coffea spp. related to beverage quality as they affect its astringency and can change its aroma and flavor. About 310,000 Coffea Expressed Sequence Tags (ESTs) are available and provide access to the nucleotide variability of the plant and to the development of molecular markers linked to beverage quality for the main enzymes involved in biosynthesis of the CGAs: PAL, C4H, 4CL, CQT and C3’H. In this study we identifiedSNP, INDELS and SSR polymorphisms within the nucleotide sequences available from the Brazilian Coffee Genome database and from the NCBI. The EST sequences for CGAs were trimmed and clustered by the program Codon Code Aligner, and polymorphisms and their validation detected (chromatogram quality). We identified six isoforms for PAL, one for C4H, six for 4CL, two for CQT and two for C3’H. The contigs formed exhibited a total of 248 polymorphisms (236 SNPs and 12 INDELs),with 201 in the coding region (127 non-synonymous and 74 synonymous). The frequency of polymorphisms was greater in the UTR regions (1pol/54pb) in relation to the coding region (1pol/81pb). The analysis of C. arabica sequences allowed identification of two different subgroups of sequences, related to their ancestral genomes (C. canephora and C. eugenioides). The presence of 67,4% of the polymorphisms between the ancestral groups and 32,6% within the groups were observed em C. arabica . The characterization of nucleotide diversity on those genes is essential for further studies on differential expression of their homeologs, as well as the use of CGAs as molecular markers related to genetic mapping. |
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Nucleotide diversity of genes related to chlorogenic acid biosynthesis of coffeaDiversidade nucleotídica de genes envolvidos na biossíntese de ácidos clorogênicos de cafeeirosPolymorphismsmolecular markersSNPsSSRsESTsCGAsCoffeaácidos clorogênicospolimorfismosdiversidade nucleotídicaChlorogenic acids (CGAs) are important chemical compounds of Coffea spp. related to beverage quality as they affect its astringency and can change its aroma and flavor. About 310,000 Coffea Expressed Sequence Tags (ESTs) are available and provide access to the nucleotide variability of the plant and to the development of molecular markers linked to beverage quality for the main enzymes involved in biosynthesis of the CGAs: PAL, C4H, 4CL, CQT and C3’H. In this study we identifiedSNP, INDELS and SSR polymorphisms within the nucleotide sequences available from the Brazilian Coffee Genome database and from the NCBI. The EST sequences for CGAs were trimmed and clustered by the program Codon Code Aligner, and polymorphisms and their validation detected (chromatogram quality). We identified six isoforms for PAL, one for C4H, six for 4CL, two for CQT and two for C3’H. The contigs formed exhibited a total of 248 polymorphisms (236 SNPs and 12 INDELs),with 201 in the coding region (127 non-synonymous and 74 synonymous). The frequency of polymorphisms was greater in the UTR regions (1pol/54pb) in relation to the coding region (1pol/81pb). The analysis of C. arabica sequences allowed identification of two different subgroups of sequences, related to their ancestral genomes (C. canephora and C. eugenioides). The presence of 67,4% of the polymorphisms between the ancestral groups and 32,6% within the groups were observed em C. arabica . The characterization of nucleotide diversity on those genes is essential for further studies on differential expression of their homeologs, as well as the use of CGAs as molecular markers related to genetic mapping.Os ácidos clorogênicos (CGAs) são compostos químicos importantes de Coffea spp. para a qualidade da bebida, pois eles interferem na adstringência e podem alterar o aroma e sabor da bebida. Aproximadamente 310.000 ESTs de Coffea estão disponíveis e possibilitam o acesso à variabilidade nucleotídica da planta e o desenvolvimento de marcadores moleculares ligados à qualidade da bebida para as principais enzimas da via de biossíntese dos CGAs: PAL, C4H, 4CL, CQT e C3’H. Neste trabalho foram detectados polimorfismos dos tipos SNP, INDEL ou SSR dentro das sequências nucleotídidicas disponíveis no Projeto Genoma Café e no NCBI. As sequências de ESTs de CGAs foram clusterizadas pelo programa Codon Code Aligner,assim como a detecção de polimorfismos e validação dos mesmos (qualidade de cromatograma). Foram identificadas seis isoformas para PAL, uma para C4H, seis para 4CL, duas para CQT e duas para C3’H. Os contigs formados apresentaram um total de 248 polimorfismos (236 SNPs e 12 INDELs), sendo 201 na região codante (127 não sinônimos e 74 sinônimos). A frequência dos polimorfismos foi maior nas regiões UTRs (1pol/54pb), em relação à codante (1pol/81pb). A análise dassequências de C. arabica permitiu a identificação de 2 subgrupos diferentes de sequências, referentes aos seus genomas ancestrais (C. canephora e C. eugenioides). Foi observada a presença de 67,4% dos polimorfismos entre os grupos ancestrais e 32,6% dentro dos grupos em C. arabica. Esses resultados vêm permitindo definir genes tanto para estudos de expressão de homeólogos de CGAs como para o desenvolvimento de marcadores moleculares para o mapeamento genético.Editora UFLA2013-12-24info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfimage/tiffimage/tiffhttps://coffeescience.ufla.br/index.php/Coffeescience/article/view/389Coffee Science - ISSN 1984-3909; Vol. 8 No. 2 (2013); 148-156Coffee Science; Vol. 8 Núm. 2 (2013); 148-156Coffee Science; v. 8 n. 2 (2013); 148-1561984-3909reponame:Coffee Science (Online)instname:Universidade Federal de Lavras (UFLA)instacron:UFLAengporhttps://coffeescience.ufla.br/index.php/Coffeescience/article/view/389/pdf_141https://coffeescience.ufla.br/index.php/Coffeescience/article/view/389/pdf_24https://coffeescience.ufla.br/index.php/Coffeescience/article/view/389/1087https://coffeescience.ufla.br/index.php/Coffeescience/article/view/389/1088Copyright (c) 2013 Coffee Science - ISSN 1984-3909https://creativecommons.org/info:eu-repo/semantics/openAccessIvamoto, Suzana TiemiPot, DavidLannes, Sergio DiasDomingues, Douglas SilvaVieira, Luiz Gonzaga EstevesPereira, Luiz Filipe Protasio2014-10-22T17:19:38Zoai:coffeescience.ufla.br:article/389Revistahttps://coffeescience.ufla.br/index.php/CoffeesciencePUBhttps://coffeescience.ufla.br/index.php/Coffeescience/oaicoffeescience@dag.ufla.br||coffeescience@dag.ufla.br|| alvaro-cozadi@hotmail.com1984-39091809-6875opendoar:2014-10-22T17:19:38Coffee Science (Online) - Universidade Federal de Lavras (UFLA)false |
dc.title.none.fl_str_mv |
Nucleotide diversity of genes related to chlorogenic acid biosynthesis of coffea Diversidade nucleotídica de genes envolvidos na biossíntese de ácidos clorogênicos de cafeeiros |
title |
Nucleotide diversity of genes related to chlorogenic acid biosynthesis of coffea |
spellingShingle |
Nucleotide diversity of genes related to chlorogenic acid biosynthesis of coffea Ivamoto, Suzana Tiemi Polymorphisms molecular markers SNPs SSRs ESTs CGAs Coffea ácidos clorogênicos polimorfismos diversidade nucleotídica |
title_short |
Nucleotide diversity of genes related to chlorogenic acid biosynthesis of coffea |
title_full |
Nucleotide diversity of genes related to chlorogenic acid biosynthesis of coffea |
title_fullStr |
Nucleotide diversity of genes related to chlorogenic acid biosynthesis of coffea |
title_full_unstemmed |
Nucleotide diversity of genes related to chlorogenic acid biosynthesis of coffea |
title_sort |
Nucleotide diversity of genes related to chlorogenic acid biosynthesis of coffea |
author |
Ivamoto, Suzana Tiemi |
author_facet |
Ivamoto, Suzana Tiemi Pot, David Lannes, Sergio Dias Domingues, Douglas Silva Vieira, Luiz Gonzaga Esteves Pereira, Luiz Filipe Protasio |
author_role |
author |
author2 |
Pot, David Lannes, Sergio Dias Domingues, Douglas Silva Vieira, Luiz Gonzaga Esteves Pereira, Luiz Filipe Protasio |
author2_role |
author author author author author |
dc.contributor.author.fl_str_mv |
Ivamoto, Suzana Tiemi Pot, David Lannes, Sergio Dias Domingues, Douglas Silva Vieira, Luiz Gonzaga Esteves Pereira, Luiz Filipe Protasio |
dc.subject.por.fl_str_mv |
Polymorphisms molecular markers SNPs SSRs ESTs CGAs Coffea ácidos clorogênicos polimorfismos diversidade nucleotídica |
topic |
Polymorphisms molecular markers SNPs SSRs ESTs CGAs Coffea ácidos clorogênicos polimorfismos diversidade nucleotídica |
description |
Chlorogenic acids (CGAs) are important chemical compounds of Coffea spp. related to beverage quality as they affect its astringency and can change its aroma and flavor. About 310,000 Coffea Expressed Sequence Tags (ESTs) are available and provide access to the nucleotide variability of the plant and to the development of molecular markers linked to beverage quality for the main enzymes involved in biosynthesis of the CGAs: PAL, C4H, 4CL, CQT and C3’H. In this study we identifiedSNP, INDELS and SSR polymorphisms within the nucleotide sequences available from the Brazilian Coffee Genome database and from the NCBI. The EST sequences for CGAs were trimmed and clustered by the program Codon Code Aligner, and polymorphisms and their validation detected (chromatogram quality). We identified six isoforms for PAL, one for C4H, six for 4CL, two for CQT and two for C3’H. The contigs formed exhibited a total of 248 polymorphisms (236 SNPs and 12 INDELs),with 201 in the coding region (127 non-synonymous and 74 synonymous). The frequency of polymorphisms was greater in the UTR regions (1pol/54pb) in relation to the coding region (1pol/81pb). The analysis of C. arabica sequences allowed identification of two different subgroups of sequences, related to their ancestral genomes (C. canephora and C. eugenioides). The presence of 67,4% of the polymorphisms between the ancestral groups and 32,6% within the groups were observed em C. arabica . The characterization of nucleotide diversity on those genes is essential for further studies on differential expression of their homeologs, as well as the use of CGAs as molecular markers related to genetic mapping. |
publishDate |
2013 |
dc.date.none.fl_str_mv |
2013-12-24 |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
https://coffeescience.ufla.br/index.php/Coffeescience/article/view/389 |
url |
https://coffeescience.ufla.br/index.php/Coffeescience/article/view/389 |
dc.language.iso.fl_str_mv |
eng por |
language |
eng por |
dc.relation.none.fl_str_mv |
https://coffeescience.ufla.br/index.php/Coffeescience/article/view/389/pdf_141 https://coffeescience.ufla.br/index.php/Coffeescience/article/view/389/pdf_24 https://coffeescience.ufla.br/index.php/Coffeescience/article/view/389/1087 https://coffeescience.ufla.br/index.php/Coffeescience/article/view/389/1088 |
dc.rights.driver.fl_str_mv |
Copyright (c) 2013 Coffee Science - ISSN 1984-3909 https://creativecommons.org/ info:eu-repo/semantics/openAccess |
rights_invalid_str_mv |
Copyright (c) 2013 Coffee Science - ISSN 1984-3909 https://creativecommons.org/ |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf application/pdf image/tiff image/tiff |
dc.publisher.none.fl_str_mv |
Editora UFLA |
publisher.none.fl_str_mv |
Editora UFLA |
dc.source.none.fl_str_mv |
Coffee Science - ISSN 1984-3909; Vol. 8 No. 2 (2013); 148-156 Coffee Science; Vol. 8 Núm. 2 (2013); 148-156 Coffee Science; v. 8 n. 2 (2013); 148-156 1984-3909 reponame:Coffee Science (Online) instname:Universidade Federal de Lavras (UFLA) instacron:UFLA |
instname_str |
Universidade Federal de Lavras (UFLA) |
instacron_str |
UFLA |
institution |
UFLA |
reponame_str |
Coffee Science (Online) |
collection |
Coffee Science (Online) |
repository.name.fl_str_mv |
Coffee Science (Online) - Universidade Federal de Lavras (UFLA) |
repository.mail.fl_str_mv |
coffeescience@dag.ufla.br||coffeescience@dag.ufla.br|| alvaro-cozadi@hotmail.com |
_version_ |
1789440320961773568 |