A high-throughput data mining of single nucleotide polymorphisms in Coffea species expressed sequence tags suggests differential homeologous gene expression in the allotetraploid Coffea arabica 1[W]
Polyploidization constitutes a common mode of evolution in flowering plants. This event provides the raw material for the divergence of function in homeologous genes, leading to phenotypic novelty that can contribute to the success of polyploids in nature or their selection for use in agriculture. Mounting evidence underlined the existence of homeologous expression biases in polyploid genomes; however, strategies to analyze such transcriptome regulation remained scarce. Important factors regarding homeologous expression biases remain to be explored, such as whether this phenomenon influences specific genes, how paralogs are affected by genome doubling, and what is the importance of the variability of homeologous expression bias to genotype differences. This study reports the expressed sequence tag assembly of the allopolyploid Coffea arabica and one of its direct ancestors, Coffea canephora. The assembly was used for the discovery of single nucleotide polymorphisms through the identification of high-quality discrepancies in overlapped expressed sequence tags and for gene expression information indirectly estimated by the transcript redundancy. Sequence diversity profiles were evaluated within C. arabica (Ca) and C. canephora (Cc) and used to deduce the transcript contribution of the Coffea eugenioides (Ce) ancestor. The assignment of the C. arabica haplotypes to the C. canephora (CaCc) or C. eugenioides (CaCe) ancestral genomes allowed us to analyze gene expression contributions of each subgenome in C. arabica. In silico data were validated by the quantitative polymerase chain reaction and allele-specific combination TaqMAMA-based method. The presence of differential expression of C. arabica homeologous genes and its implications in coffee gene expression, ontology, and physiology are discussed.
Main Authors: | , , , , , , , , , |
---|---|
Format: | article biblioteca |
Language: | eng |
Subjects: | F30 - Génétique et amélioration des plantes, U30 - Méthodes de recherche, Coffea, Coffea arabica, Coffea canephora, Coffea eugenioides, expression des gènes, polymorphisme génétique, variation génétique, séquence nucléotidique, gène, génome, PCR, http://aims.fao.org/aos/agrovoc/c_1720, http://aims.fao.org/aos/agrovoc/c_1721, http://aims.fao.org/aos/agrovoc/c_1723, http://aims.fao.org/aos/agrovoc/c_1725, http://aims.fao.org/aos/agrovoc/c_27527, http://aims.fao.org/aos/agrovoc/c_24031, http://aims.fao.org/aos/agrovoc/c_15975, http://aims.fao.org/aos/agrovoc/c_27583, http://aims.fao.org/aos/agrovoc/c_3214, http://aims.fao.org/aos/agrovoc/c_3224, http://aims.fao.org/aos/agrovoc/c_34079, http://aims.fao.org/aos/agrovoc/c_1070, |
Online Access: | http://agritrop.cirad.fr/557117/ http://agritrop.cirad.fr/557117/1/document_557117.pdf |
Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
id |
dig-cirad-fr-557117 |
---|---|
record_format |
koha |
institution |
CIRAD FR |
collection |
DSpace |
country |
Francia |
countrycode |
FR |
component |
Bibliográfico |
access |
En linea |
databasecode |
dig-cirad-fr |
tag |
biblioteca |
region |
Europa del Oeste |
libraryname |
Biblioteca del CIRAD Francia |
language |
eng |
topic |
F30 - Génétique et amélioration des plantes U30 - Méthodes de recherche Coffea Coffea arabica Coffea canephora Coffea eugenioides expression des gènes polymorphisme génétique variation génétique séquence nucléotidique gène génome PCR http://aims.fao.org/aos/agrovoc/c_1720 http://aims.fao.org/aos/agrovoc/c_1721 http://aims.fao.org/aos/agrovoc/c_1723 http://aims.fao.org/aos/agrovoc/c_1725 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_24031 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_3214 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_34079 http://aims.fao.org/aos/agrovoc/c_1070 F30 - Génétique et amélioration des plantes U30 - Méthodes de recherche Coffea Coffea arabica Coffea canephora Coffea eugenioides expression des gènes polymorphisme génétique variation génétique séquence nucléotidique gène génome PCR http://aims.fao.org/aos/agrovoc/c_1720 http://aims.fao.org/aos/agrovoc/c_1721 http://aims.fao.org/aos/agrovoc/c_1723 http://aims.fao.org/aos/agrovoc/c_1725 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_24031 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_3214 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_34079 http://aims.fao.org/aos/agrovoc/c_1070 |
spellingShingle |
F30 - Génétique et amélioration des plantes U30 - Méthodes de recherche Coffea Coffea arabica Coffea canephora Coffea eugenioides expression des gènes polymorphisme génétique variation génétique séquence nucléotidique gène génome PCR http://aims.fao.org/aos/agrovoc/c_1720 http://aims.fao.org/aos/agrovoc/c_1721 http://aims.fao.org/aos/agrovoc/c_1723 http://aims.fao.org/aos/agrovoc/c_1725 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_24031 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_3214 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_34079 http://aims.fao.org/aos/agrovoc/c_1070 F30 - Génétique et amélioration des plantes U30 - Méthodes de recherche Coffea Coffea arabica Coffea canephora Coffea eugenioides expression des gènes polymorphisme génétique variation génétique séquence nucléotidique gène génome PCR http://aims.fao.org/aos/agrovoc/c_1720 http://aims.fao.org/aos/agrovoc/c_1721 http://aims.fao.org/aos/agrovoc/c_1723 http://aims.fao.org/aos/agrovoc/c_1725 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_24031 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_3214 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_34079 http://aims.fao.org/aos/agrovoc/c_1070 Vidal, Ramon Oliveira Mondego, Jorge M.C. Pot, David Batista Ambrosio, Alinne Carvalho Andrade, Alan Protasio Pereira, Luiz Filipe Colombo, Carlos Augusto Vieira, Luiz Gonzaga Esteves Carazzolle, Marcelo Falsarella Guimarães Pereira, Gonçalo Amarante A high-throughput data mining of single nucleotide polymorphisms in Coffea species expressed sequence tags suggests differential homeologous gene expression in the allotetraploid Coffea arabica 1[W] |
description |
Polyploidization constitutes a common mode of evolution in flowering plants. This event provides the raw material for the divergence of function in homeologous genes, leading to phenotypic novelty that can contribute to the success of polyploids in nature or their selection for use in agriculture. Mounting evidence underlined the existence of homeologous expression biases in polyploid genomes; however, strategies to analyze such transcriptome regulation remained scarce. Important factors regarding homeologous expression biases remain to be explored, such as whether this phenomenon influences specific genes, how paralogs are affected by genome doubling, and what is the importance of the variability of homeologous expression bias to genotype differences. This study reports the expressed sequence tag assembly of the allopolyploid Coffea arabica and one of its direct ancestors, Coffea canephora. The assembly was used for the discovery of single nucleotide polymorphisms through the identification of high-quality discrepancies in overlapped expressed sequence tags and for gene expression information indirectly estimated by the transcript redundancy. Sequence diversity profiles were evaluated within C. arabica (Ca) and C. canephora (Cc) and used to deduce the transcript contribution of the Coffea eugenioides (Ce) ancestor. The assignment of the C. arabica haplotypes to the C. canephora (CaCc) or C. eugenioides (CaCe) ancestral genomes allowed us to analyze gene expression contributions of each subgenome in C. arabica. In silico data were validated by the quantitative polymerase chain reaction and allele-specific combination TaqMAMA-based method. The presence of differential expression of C. arabica homeologous genes and its implications in coffee gene expression, ontology, and physiology are discussed. |
format |
article |
topic_facet |
F30 - Génétique et amélioration des plantes U30 - Méthodes de recherche Coffea Coffea arabica Coffea canephora Coffea eugenioides expression des gènes polymorphisme génétique variation génétique séquence nucléotidique gène génome PCR http://aims.fao.org/aos/agrovoc/c_1720 http://aims.fao.org/aos/agrovoc/c_1721 http://aims.fao.org/aos/agrovoc/c_1723 http://aims.fao.org/aos/agrovoc/c_1725 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_24031 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_3214 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_34079 http://aims.fao.org/aos/agrovoc/c_1070 |
author |
Vidal, Ramon Oliveira Mondego, Jorge M.C. Pot, David Batista Ambrosio, Alinne Carvalho Andrade, Alan Protasio Pereira, Luiz Filipe Colombo, Carlos Augusto Vieira, Luiz Gonzaga Esteves Carazzolle, Marcelo Falsarella Guimarães Pereira, Gonçalo Amarante |
author_facet |
Vidal, Ramon Oliveira Mondego, Jorge M.C. Pot, David Batista Ambrosio, Alinne Carvalho Andrade, Alan Protasio Pereira, Luiz Filipe Colombo, Carlos Augusto Vieira, Luiz Gonzaga Esteves Carazzolle, Marcelo Falsarella Guimarães Pereira, Gonçalo Amarante |
author_sort |
Vidal, Ramon Oliveira |
title |
A high-throughput data mining of single nucleotide polymorphisms in Coffea species expressed sequence tags suggests differential homeologous gene expression in the allotetraploid Coffea arabica 1[W] |
title_short |
A high-throughput data mining of single nucleotide polymorphisms in Coffea species expressed sequence tags suggests differential homeologous gene expression in the allotetraploid Coffea arabica 1[W] |
title_full |
A high-throughput data mining of single nucleotide polymorphisms in Coffea species expressed sequence tags suggests differential homeologous gene expression in the allotetraploid Coffea arabica 1[W] |
title_fullStr |
A high-throughput data mining of single nucleotide polymorphisms in Coffea species expressed sequence tags suggests differential homeologous gene expression in the allotetraploid Coffea arabica 1[W] |
title_full_unstemmed |
A high-throughput data mining of single nucleotide polymorphisms in Coffea species expressed sequence tags suggests differential homeologous gene expression in the allotetraploid Coffea arabica 1[W] |
title_sort |
high-throughput data mining of single nucleotide polymorphisms in coffea species expressed sequence tags suggests differential homeologous gene expression in the allotetraploid coffea arabica 1[w] |
url |
http://agritrop.cirad.fr/557117/ http://agritrop.cirad.fr/557117/1/document_557117.pdf |
work_keys_str_mv |
AT vidalramonoliveira ahighthroughputdataminingofsinglenucleotidepolymorphismsincoffeaspeciesexpressedsequencetagssuggestsdifferentialhomeologousgeneexpressionintheallotetraploidcoffeaarabica1w AT mondegojorgemc ahighthroughputdataminingofsinglenucleotidepolymorphismsincoffeaspeciesexpressedsequencetagssuggestsdifferentialhomeologousgeneexpressionintheallotetraploidcoffeaarabica1w AT potdavid ahighthroughputdataminingofsinglenucleotidepolymorphismsincoffeaspeciesexpressedsequencetagssuggestsdifferentialhomeologousgeneexpressionintheallotetraploidcoffeaarabica1w AT batistaambrosioalinne ahighthroughputdataminingofsinglenucleotidepolymorphismsincoffeaspeciesexpressedsequencetagssuggestsdifferentialhomeologousgeneexpressionintheallotetraploidcoffeaarabica1w AT carvalhoandradealan ahighthroughputdataminingofsinglenucleotidepolymorphismsincoffeaspeciesexpressedsequencetagssuggestsdifferentialhomeologousgeneexpressionintheallotetraploidcoffeaarabica1w AT protasiopereiraluizfilipe ahighthroughputdataminingofsinglenucleotidepolymorphismsincoffeaspeciesexpressedsequencetagssuggestsdifferentialhomeologousgeneexpressionintheallotetraploidcoffeaarabica1w AT colombocarlosaugusto ahighthroughputdataminingofsinglenucleotidepolymorphismsincoffeaspeciesexpressedsequencetagssuggestsdifferentialhomeologousgeneexpressionintheallotetraploidcoffeaarabica1w AT vieiraluizgonzagaesteves ahighthroughputdataminingofsinglenucleotidepolymorphismsincoffeaspeciesexpressedsequencetagssuggestsdifferentialhomeologousgeneexpressionintheallotetraploidcoffeaarabica1w AT carazzollemarcelofalsarella ahighthroughputdataminingofsinglenucleotidepolymorphismsincoffeaspeciesexpressedsequencetagssuggestsdifferentialhomeologousgeneexpressionintheallotetraploidcoffeaarabica1w AT guimaraespereiragoncaloamarante ahighthroughputdataminingofsinglenucleotidepolymorphismsincoffeaspeciesexpressedsequencetagssuggestsdifferentialhomeologousgeneexpressionintheallotetraploidcoffeaarabica1w AT vidalramonoliveira highthroughputdataminingofsinglenucleotidepolymorphismsincoffeaspeciesexpressedsequencetagssuggestsdifferentialhomeologousgeneexpressionintheallotetraploidcoffeaarabica1w AT mondegojorgemc highthroughputdataminingofsinglenucleotidepolymorphismsincoffeaspeciesexpressedsequencetagssuggestsdifferentialhomeologousgeneexpressionintheallotetraploidcoffeaarabica1w AT potdavid highthroughputdataminingofsinglenucleotidepolymorphismsincoffeaspeciesexpressedsequencetagssuggestsdifferentialhomeologousgeneexpressionintheallotetraploidcoffeaarabica1w AT batistaambrosioalinne highthroughputdataminingofsinglenucleotidepolymorphismsincoffeaspeciesexpressedsequencetagssuggestsdifferentialhomeologousgeneexpressionintheallotetraploidcoffeaarabica1w AT carvalhoandradealan highthroughputdataminingofsinglenucleotidepolymorphismsincoffeaspeciesexpressedsequencetagssuggestsdifferentialhomeologousgeneexpressionintheallotetraploidcoffeaarabica1w AT protasiopereiraluizfilipe highthroughputdataminingofsinglenucleotidepolymorphismsincoffeaspeciesexpressedsequencetagssuggestsdifferentialhomeologousgeneexpressionintheallotetraploidcoffeaarabica1w AT colombocarlosaugusto highthroughputdataminingofsinglenucleotidepolymorphismsincoffeaspeciesexpressedsequencetagssuggestsdifferentialhomeologousgeneexpressionintheallotetraploidcoffeaarabica1w AT vieiraluizgonzagaesteves highthroughputdataminingofsinglenucleotidepolymorphismsincoffeaspeciesexpressedsequencetagssuggestsdifferentialhomeologousgeneexpressionintheallotetraploidcoffeaarabica1w AT carazzollemarcelofalsarella highthroughputdataminingofsinglenucleotidepolymorphismsincoffeaspeciesexpressedsequencetagssuggestsdifferentialhomeologousgeneexpressionintheallotetraploidcoffeaarabica1w AT guimaraespereiragoncaloamarante highthroughputdataminingofsinglenucleotidepolymorphismsincoffeaspeciesexpressedsequencetagssuggestsdifferentialhomeologousgeneexpressionintheallotetraploidcoffeaarabica1w |
_version_ |
1792497669459935232 |
spelling |
dig-cirad-fr-5571172024-01-28T18:41:16Z http://agritrop.cirad.fr/557117/ http://agritrop.cirad.fr/557117/ A high-throughput data mining of single nucleotide polymorphisms in Coffea species expressed sequence tags suggests differential homeologous gene expression in the allotetraploid Coffea arabica 1[W]. Vidal Ramon Oliveira, Mondego Jorge M.C., Pot David, Batista Ambrosio Alinne, Carvalho Andrade Alan, Protasio Pereira Luiz Filipe, Colombo Carlos Augusto, Vieira Luiz Gonzaga Esteves, Carazzolle Marcelo Falsarella, Guimarães Pereira Gonçalo Amarante. 2010. Plant Physiology, 154 (3) : 1053-1066.https://doi.org/10.1104/pp.110.162438 <https://doi.org/10.1104/pp.110.162438> A high-throughput data mining of single nucleotide polymorphisms in Coffea species expressed sequence tags suggests differential homeologous gene expression in the allotetraploid Coffea arabica 1[W] Vidal, Ramon Oliveira Mondego, Jorge M.C. Pot, David Batista Ambrosio, Alinne Carvalho Andrade, Alan Protasio Pereira, Luiz Filipe Colombo, Carlos Augusto Vieira, Luiz Gonzaga Esteves Carazzolle, Marcelo Falsarella Guimarães Pereira, Gonçalo Amarante eng 2010 Plant Physiology F30 - Génétique et amélioration des plantes U30 - Méthodes de recherche Coffea Coffea arabica Coffea canephora Coffea eugenioides expression des gènes polymorphisme génétique variation génétique séquence nucléotidique gène génome PCR http://aims.fao.org/aos/agrovoc/c_1720 http://aims.fao.org/aos/agrovoc/c_1721 http://aims.fao.org/aos/agrovoc/c_1723 http://aims.fao.org/aos/agrovoc/c_1725 http://aims.fao.org/aos/agrovoc/c_27527 http://aims.fao.org/aos/agrovoc/c_24031 http://aims.fao.org/aos/agrovoc/c_15975 http://aims.fao.org/aos/agrovoc/c_27583 http://aims.fao.org/aos/agrovoc/c_3214 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_34079 Brésil http://aims.fao.org/aos/agrovoc/c_1070 Polyploidization constitutes a common mode of evolution in flowering plants. This event provides the raw material for the divergence of function in homeologous genes, leading to phenotypic novelty that can contribute to the success of polyploids in nature or their selection for use in agriculture. Mounting evidence underlined the existence of homeologous expression biases in polyploid genomes; however, strategies to analyze such transcriptome regulation remained scarce. Important factors regarding homeologous expression biases remain to be explored, such as whether this phenomenon influences specific genes, how paralogs are affected by genome doubling, and what is the importance of the variability of homeologous expression bias to genotype differences. This study reports the expressed sequence tag assembly of the allopolyploid Coffea arabica and one of its direct ancestors, Coffea canephora. The assembly was used for the discovery of single nucleotide polymorphisms through the identification of high-quality discrepancies in overlapped expressed sequence tags and for gene expression information indirectly estimated by the transcript redundancy. Sequence diversity profiles were evaluated within C. arabica (Ca) and C. canephora (Cc) and used to deduce the transcript contribution of the Coffea eugenioides (Ce) ancestor. The assignment of the C. arabica haplotypes to the C. canephora (CaCc) or C. eugenioides (CaCe) ancestral genomes allowed us to analyze gene expression contributions of each subgenome in C. arabica. In silico data were validated by the quantitative polymerase chain reaction and allele-specific combination TaqMAMA-based method. The presence of differential expression of C. arabica homeologous genes and its implications in coffee gene expression, ontology, and physiology are discussed. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/557117/1/document_557117.pdf application/pdf Cirad license info:eu-repo/semantics/restrictedAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1104/pp.110.162438 10.1104/pp.110.162438 info:eu-repo/semantics/altIdentifier/doi/10.1104/pp.110.162438 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1104/pp.110.162438 |