Transposable elements in Coffea (Gentianales: Rubiacea) transcripts and their role in the origin of protein diversity in flowering plants.
Identifieur interne : 003771 ( Main/Exploration ); précédent : 003770; suivant : 003772Transposable elements in Coffea (Gentianales: Rubiacea) transcripts and their role in the origin of protein diversity in flowering plants.
Auteurs : Fabrício Ramon Lopes [Brésil] ; Marcelo Falsarella Carazzolle ; Gonçalo Amarante Guimarães Pereira ; Carlos Augusto Colombo ; Claudia Marcia Aparecida CararetoSource :
- Molecular genetics and genomics : MGG [ 1617-4615 ] ; 2008.
Descripteurs français
- KwdFr :
- ADN des plantes (génétique), Analyse de profil d'expression de gènes (MeSH), Arabidopsis (génétique), Coffea (classification), Coffea (génétique), Données de séquences moléculaires (MeSH), Exons (MeSH), Génome végétal (MeSH), Magnoliopsida (classification), Magnoliopsida (génétique), Phosphotransferases (génétique), Phylogenèse (MeSH), Protéines végétales (génétique), Protéome (MeSH), Similitude de séquences d'acides aminés (MeSH), Similitude de séquences d'acides nucléiques (MeSH), Séquence d'acides aminés (MeSH), Séquence nucléotidique (MeSH), Transcription génétique (MeSH), Variation génétique (MeSH), Éléments transposables d'ADN (génétique), Étiquettes de séquences exprimées (MeSH), Évolution moléculaire (MeSH).
- MESH :
- génétique : ADN des plantes, Arabidopsis, Coffea, Magnoliopsida, Phosphotransferases, Protéines végétales, Éléments transposables d'ADN.
- Analyse de profil d'expression de gènes, Données de séquences moléculaires, Exons, Génome végétal, Phylogenèse, Protéome, Similitude de séquences d'acides aminés, Similitude de séquences d'acides nucléiques, Séquence d'acides aminés, Séquence nucléotidique, Transcription génétique, Variation génétique, Étiquettes de séquences exprimées, Évolution moléculaire.
English descriptors
- KwdEn :
- Amino Acid Sequence (MeSH), Arabidopsis (genetics), Base Sequence (MeSH), Coffea (classification), Coffea (genetics), DNA Transposable Elements (genetics), DNA, Plant (genetics), Evolution, Molecular (MeSH), Exons (MeSH), Expressed Sequence Tags (MeSH), Gene Expression Profiling (MeSH), Genetic Variation (MeSH), Genome, Plant (MeSH), Magnoliopsida (classification), Magnoliopsida (genetics), Molecular Sequence Data (MeSH), Phosphotransferases (genetics), Phylogeny (MeSH), Plant Proteins (genetics), Proteome (MeSH), Sequence Homology, Amino Acid (MeSH), Sequence Homology, Nucleic Acid (MeSH), Transcription, Genetic (MeSH).
- MESH :
- chemical , genetics : DNA Transposable Elements, DNA, Plant, Phosphotransferases, Plant Proteins.
- classification : Coffea, Magnoliopsida.
- genetics : Arabidopsis, Coffea, Magnoliopsida.
- Amino Acid Sequence, Base Sequence, Evolution, Molecular, Exons, Expressed Sequence Tags, Gene Expression Profiling, Genetic Variation, Genome, Plant, Molecular Sequence Data, Phylogeny, Proteome, Sequence Homology, Amino Acid, Sequence Homology, Nucleic Acid, Transcription, Genetic.
Abstract
Transposable elements are major components of plant genomes and they influence their evolution, acting as recombination hot spots, acquiring specific cell functions or becoming part of protein-coding regions. The latter is the subject of the present analysis. This study is a report on the annotation of transposable elements (TEs) in expressed sequences of Coffea arabica, Coffea canephora and Coffea racemosa, showing the occurrence of 383 ESTs and 142 unigenes with TE fragments in these three Coffea species. Based on selected unigenes, it was possible to suggest 26 putative proteins with TE-cassette insertions, demonstrating a likely contribution to protein variability. The genes for two of those proteins, the fertility restorer (FR) and the pyrophosphate-dependent phosphofructokinase (PPi-PFKs) genes, were selected for evaluating the impact of TE-cassettes on host gene evolution of other plant genomes (Arabidopsis thaliana, Oryza sativa and Populus trichocarpa). This survey allowed identifying a FR gene in O. sativa harboring multiple insertions of LTR retrotransposons that originated new exons, which however does not necessarily mean a case of molecular domestication. A possible transduction event of a fragment of the PPi-PFK beta-subunit gene mediated by Helitron ATREPX1 in Arabidopsis thaliana was also highlighted.
DOI: 10.1007/s00438-008-0319-4
PubMed: 18231813
Affiliations:
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(MeSH)</term><term>Phosphotransferases (genetics)</term><term>Phylogeny (MeSH)</term><term>Plant Proteins (genetics)</term><term>Proteome (MeSH)</term><term>Sequence Homology, Amino Acid (MeSH)</term><term>Sequence Homology, Nucleic Acid (MeSH)</term><term>Transcription, Genetic (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN des plantes (génétique)</term><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Arabidopsis (génétique)</term><term>Coffea (classification)</term><term>Coffea (génétique)</term><term>Données de séquences moléculaires (MeSH)</term><term>Exons (MeSH)</term><term>Génome végétal (MeSH)</term><term>Magnoliopsida (classification)</term><term>Magnoliopsida (génétique)</term><term>Phosphotransferases (génétique)</term><term>Phylogenèse (MeSH)</term><term>Protéines végétales (génétique)</term><term>Protéome (MeSH)</term><term>Similitude de séquences d'acides aminés (MeSH)</term><term>Similitude de séquences d'acides nucléiques (MeSH)</term><term>Séquence d'acides aminés (MeSH)</term><term>Séquence nucléotidique (MeSH)</term><term>Transcription génétique (MeSH)</term><term>Variation génétique (MeSH)</term><term>Éléments transposables d'ADN (génétique)</term><term>Étiquettes de séquences exprimées (MeSH)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA Transposable Elements</term><term>DNA, Plant</term><term>Phosphotransferases</term><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Coffea</term><term>Magnoliopsida</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Coffea</term><term>Magnoliopsida</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN des 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The latter is the subject of the present analysis. This study is a report on the annotation of transposable elements (TEs) in expressed sequences of Coffea arabica, Coffea canephora and Coffea racemosa, showing the occurrence of 383 ESTs and 142 unigenes with TE fragments in these three Coffea species. Based on selected unigenes, it was possible to suggest 26 putative proteins with TE-cassette insertions, demonstrating a likely contribution to protein variability. The genes for two of those proteins, the fertility restorer (FR) and the pyrophosphate-dependent phosphofructokinase (PPi-PFKs) genes, were selected for evaluating the impact of TE-cassettes on host gene evolution of other plant genomes (Arabidopsis thaliana, Oryza sativa and Populus trichocarpa). This survey allowed identifying a FR gene in O. sativa harboring multiple insertions of LTR retrotransposons that originated new exons, which however does not necessarily mean a case of molecular domestication. A possible transduction event of a fragment of the PPi-PFK beta-subunit gene mediated by Helitron ATREPX1 in Arabidopsis thaliana was also highlighted.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18231813</PMID><DateCompleted><Year>2008</Year><Month>06</Month><Day>27</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">1617-4615</ISSN><JournalIssue CitedMedium="Print"><Volume>279</Volume><Issue>4</Issue><PubDate><Year>2008</Year><Month>Apr</Month></PubDate></JournalIssue><Title>Molecular genetics and genomics : MGG</Title><ISOAbbreviation>Mol Genet Genomics</ISOAbbreviation></Journal><ArticleTitle>Transposable elements in Coffea (Gentianales: Rubiacea) transcripts and their role in the origin of protein diversity in flowering plants.</ArticleTitle><Pagination><MedlinePgn>385-401</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00438-008-0319-4</ELocationID><Abstract><AbstractText>Transposable elements are major components of plant genomes and they influence their evolution, acting as recombination hot spots, acquiring specific cell functions or becoming part of protein-coding regions. The latter is the subject of the present analysis. This study is a report on the annotation of transposable elements (TEs) in expressed sequences of Coffea arabica, Coffea canephora and Coffea racemosa, showing the occurrence of 383 ESTs and 142 unigenes with TE fragments in these three Coffea species. Based on selected unigenes, it was possible to suggest 26 putative proteins with TE-cassette insertions, demonstrating a likely contribution to protein variability. The genes for two of those proteins, the fertility restorer (FR) and the pyrophosphate-dependent phosphofructokinase (PPi-PFKs) genes, were selected for evaluating the impact of TE-cassettes on host gene evolution of other plant genomes (Arabidopsis thaliana, Oryza sativa and Populus trichocarpa). This survey allowed identifying a FR gene in O. sativa harboring multiple insertions of LTR retrotransposons that originated new exons, which however does not necessarily mean a case of molecular domestication. A possible transduction event of a fragment of the PPi-PFK beta-subunit gene mediated by Helitron ATREPX1 in Arabidopsis thaliana was also highlighted.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Lopes</LastName><ForeName>Fabrício Ramon</ForeName><Initials>FR</Initials><AffiliationInfo><Affiliation>Laboratory of Molecular Evolution, Department of Biology, UNESP, São Paulo State University, 15054-000, São José do Rio Preto, São Paulo, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Carazzolle</LastName><ForeName>Marcelo Falsarella</ForeName><Initials>MF</Initials></Author><Author ValidYN="Y"><LastName>Pereira</LastName><ForeName>Gonçalo Amarante Guimarães</ForeName><Initials>GA</Initials></Author><Author ValidYN="Y"><LastName>Colombo</LastName><ForeName>Carlos Augusto</ForeName><Initials>CA</Initials></Author><Author ValidYN="Y"><LastName>Carareto</LastName><ForeName>Claudia Marcia Aparecida</ForeName><Initials>CM</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2008</Year><Month>01</Month><Day>30</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Mol Genet Genomics</MedlineTA><NlmUniqueID>101093320</NlmUniqueID><ISSNLinking>1617-4623</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004251">DNA Transposable Elements</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018744">DNA, Plant</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D020543">Proteome</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 2.7.-</RegistryNumber><NameOfSubstance UI="D010770">Phosphotransferases</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 2.7.1.90</RegistryNumber><NameOfSubstance UI="C022502">pyrophosphate-fructose 6-phosphate 1-phosphotransferase</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017360" MajorTopicYN="N">Arabidopsis</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D040503" MajorTopicYN="N">Coffea</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004251" MajorTopicYN="N">DNA Transposable Elements</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018744" MajorTopicYN="N">DNA, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005091" MajorTopicYN="N">Exons</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020224" MajorTopicYN="N">Expressed Sequence Tags</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="N">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019684" MajorTopicYN="N">Magnoliopsida</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010770" MajorTopicYN="N">Phosphotransferases</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020543" MajorTopicYN="N">Proteome</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017386" MajorTopicYN="N">Sequence Homology, Amino Acid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012689" MajorTopicYN="N">Sequence Homology, Nucleic Acid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014158" MajorTopicYN="N">Transcription, Genetic</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2007</Year><Month>06</Month><Day>25</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2008</Year><Month>01</Month><Day>02</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2008</Year><Month>1</Month><Day>31</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2008</Year><Month>6</Month><Day>28</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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