Molecular characterization and distribution of a 145-bp tandem repeat family in the genus Populus.
Identifieur interne : 004875 ( Main/Exploration ); précédent : 004874; suivant : 004876Molecular characterization and distribution of a 145-bp tandem repeat family in the genus Populus.
Auteurs : J. Rajagopal [Inde] ; S. Das ; D K Khurana ; P S Srivastava ; M. LakshmikumaranSource :
- Genome [ 0831-2796 ] ; 1999.
Descripteurs français
- KwdFr :
- ADN des plantes (MeSH), ADN satellite (analyse), Alignement de séquences (MeSH), Arbres (génétique), Données de séquences moléculaires (MeSH), Génome végétal (MeSH), Méthylation de l'ADN (MeSH), Phylogenèse (MeSH), Séquence nucléotidique (MeSH), Séquences répétées en tandem (MeSH), Technique de Southern (MeSH).
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , analysis : DNA, Satellite.
- chemical : DNA, Plant.
- genetics : Trees.
- Base Sequence, Blotting, Southern, DNA Methylation, Genome, Plant, Molecular Sequence Data, Phylogeny, Sequence Alignment, Tandem Repeat Sequences.
Abstract
This report aims to describe the identification and molecular characterization of a 145-bp tandem repeat family that accounts for nearly 1.5% of the Populus genome. Three members of this repeat family were cloned and sequenced from Populus deltoides and P. ciliata. The dimers of the repeat were sequenced in order to confirm the head-to-tail organization of the repeat. Hybridization-based analysis using the 145-bp tandem repeat as a probe on genomic DNA gave rise to ladder patterns which were identified to be a result of methylation and (or) sequence heterogeneity. Analysis of the methylation pattern of the repeat family using methylation-sensitive isoschizomers revealed variable methylation of the C residues and lack of methylation of the A residues. Sequence comparisons between the monomers revealed a high degree of sequence divergence that ranged between 6% and 11% in P. deltoides and between 4.2% and 8.3% in P. ciliata. This indicated the presence of sub-families within the 145-bp tandem family of repeats. Divergence was mainly due to the accumulation of point mutations and was concentrated in the central region of the repeat. The 145-bp tandem repeat family did not show significant homology to known tandem repeats from plants. A short stretch of 36 bp was found to show homology of 66.7% to a centromeric repeat from Chironomus plumosus. Dot-blot analysis and Southern hybridization data revealed the presence of the repeat family in 13 of the 14 Populus species examined. The absence of the 145-bp repeat from P. euphratica suggested that this species is relatively distant from other members of the genus, which correlates with taxonomic classifications. The widespread occurrence of the tandem family in the genus indicated that this family may be of ancient origin.
DOI: 10.1139/g99-013
PubMed: 10584311
Affiliations:
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Das</name></author><author><name sortKey="Khurana, D K" sort="Khurana, D K" uniqKey="Khurana D" first="D K" last="Khurana">D K Khurana</name></author><author><name sortKey="Srivastava, P S" sort="Srivastava, P S" uniqKey="Srivastava P" first="P S" last="Srivastava">P S Srivastava</name></author><author><name sortKey="Lakshmikumaran, M" sort="Lakshmikumaran, M" uniqKey="Lakshmikumaran M" first="M" last="Lakshmikumaran">M. Lakshmikumaran</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="1999">1999</date><idno type="RBID">pubmed:10584311</idno><idno type="pmid">10584311</idno><idno type="doi">10.1139/g99-013</idno><idno type="wicri:Area/Main/Corpus">004887</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">004887</idno><idno type="wicri:Area/Main/Curation">004887</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">004887</idno><idno type="wicri:Area/Main/Exploration">004887</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Molecular characterization and distribution of a 145-bp tandem repeat family in the genus Populus.</title><author><name sortKey="Rajagopal, J" sort="Rajagopal, J" uniqKey="Rajagopal J" first="J" last="Rajagopal">J. Rajagopal</name><affiliation wicri:level="1"><nlm:affiliation>Biotechnology Division, TERI, New Delhi, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Biotechnology Division, TERI, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author><author><name sortKey="Das, S" sort="Das, S" uniqKey="Das S" first="S" last="Das">S. Das</name></author><author><name sortKey="Khurana, D K" sort="Khurana, D K" uniqKey="Khurana D" first="D K" last="Khurana">D K Khurana</name></author><author><name sortKey="Srivastava, P S" sort="Srivastava, P S" uniqKey="Srivastava P" first="P S" last="Srivastava">P S Srivastava</name></author><author><name sortKey="Lakshmikumaran, M" sort="Lakshmikumaran, M" uniqKey="Lakshmikumaran M" first="M" last="Lakshmikumaran">M. Lakshmikumaran</name></author></analytic><series><title level="j">Genome</title><idno type="ISSN">0831-2796</idno><imprint><date when="1999" type="published">1999</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence (MeSH)</term><term>Blotting, Southern (MeSH)</term><term>DNA Methylation (MeSH)</term><term>DNA, Plant (MeSH)</term><term>DNA, Satellite (analysis)</term><term>Genome, Plant (MeSH)</term><term>Molecular Sequence Data (MeSH)</term><term>Phylogeny (MeSH)</term><term>Sequence Alignment (MeSH)</term><term>Tandem Repeat Sequences (MeSH)</term><term>Trees (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN des plantes (MeSH)</term><term>ADN satellite (analyse)</term><term>Alignement de séquences (MeSH)</term><term>Arbres (génétique)</term><term>Données de séquences moléculaires (MeSH)</term><term>Génome végétal (MeSH)</term><term>Méthylation de l'ADN (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Séquence nucléotidique (MeSH)</term><term>Séquences répétées en tandem (MeSH)</term><term>Technique de Southern (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>DNA, Satellite</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>DNA, Plant</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>ADN satellite</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Trees</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arbres</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Blotting, Southern</term><term>DNA Methylation</term><term>Genome, Plant</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Sequence Alignment</term><term>Tandem Repeat Sequences</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN des plantes</term><term>Alignement de séquences</term><term>Données de séquences moléculaires</term><term>Génome végétal</term><term>Méthylation de l'ADN</term><term>Phylogenèse</term><term>Séquence nucléotidique</term><term>Séquences répétées en tandem</term><term>Technique de Southern</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">This report aims to describe the identification and molecular characterization of a 145-bp tandem repeat family that accounts for nearly 1.5% of the Populus genome. Three members of this repeat family were cloned and sequenced from Populus deltoides and P. ciliata. The dimers of the repeat were sequenced in order to confirm the head-to-tail organization of the repeat. Hybridization-based analysis using the 145-bp tandem repeat as a probe on genomic DNA gave rise to ladder patterns which were identified to be a result of methylation and (or) sequence heterogeneity. Analysis of the methylation pattern of the repeat family using methylation-sensitive isoschizomers revealed variable methylation of the C residues and lack of methylation of the A residues. Sequence comparisons between the monomers revealed a high degree of sequence divergence that ranged between 6% and 11% in P. deltoides and between 4.2% and 8.3% in P. ciliata. This indicated the presence of sub-families within the 145-bp tandem family of repeats. Divergence was mainly due to the accumulation of point mutations and was concentrated in the central region of the repeat. The 145-bp tandem repeat family did not show significant homology to known tandem repeats from plants. A short stretch of 36 bp was found to show homology of 66.7% to a centromeric repeat from Chironomus plumosus. Dot-blot analysis and Southern hybridization data revealed the presence of the repeat family in 13 of the 14 Populus species examined. The absence of the 145-bp repeat from P. euphratica suggested that this species is relatively distant from other members of the genus, which correlates with taxonomic classifications. The widespread occurrence of the tandem family in the genus indicated that this family may be of ancient origin.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">10584311</PMID><DateCompleted><Year>1999</Year><Month>12</Month><Day>22</Day></DateCompleted><DateRevised><Year>2019</Year><Month>09</Month><Day>15</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0831-2796</ISSN><JournalIssue CitedMedium="Print"><Volume>42</Volume><Issue>5</Issue><PubDate><Year>1999</Year><Month>Oct</Month></PubDate></JournalIssue><Title>Genome</Title><ISOAbbreviation>Genome</ISOAbbreviation></Journal><ArticleTitle>Molecular characterization and distribution of a 145-bp tandem repeat family in the genus Populus.</ArticleTitle><Pagination><MedlinePgn>909-18</MedlinePgn></Pagination><Abstract><AbstractText>This report aims to describe the identification and molecular characterization of a 145-bp tandem repeat family that accounts for nearly 1.5% of the Populus genome. Three members of this repeat family were cloned and sequenced from Populus deltoides and P. ciliata. The dimers of the repeat were sequenced in order to confirm the head-to-tail organization of the repeat. Hybridization-based analysis using the 145-bp tandem repeat as a probe on genomic DNA gave rise to ladder patterns which were identified to be a result of methylation and (or) sequence heterogeneity. Analysis of the methylation pattern of the repeat family using methylation-sensitive isoschizomers revealed variable methylation of the C residues and lack of methylation of the A residues. Sequence comparisons between the monomers revealed a high degree of sequence divergence that ranged between 6% and 11% in P. deltoides and between 4.2% and 8.3% in P. ciliata. This indicated the presence of sub-families within the 145-bp tandem family of repeats. Divergence was mainly due to the accumulation of point mutations and was concentrated in the central region of the repeat. The 145-bp tandem repeat family did not show significant homology to known tandem repeats from plants. A short stretch of 36 bp was found to show homology of 66.7% to a centromeric repeat from Chironomus plumosus. Dot-blot analysis and Southern hybridization data revealed the presence of the repeat family in 13 of the 14 Populus species examined. The absence of the 145-bp repeat from P. euphratica suggested that this species is relatively distant from other members of the genus, which correlates with taxonomic classifications. The widespread occurrence of the tandem family in the genus indicated that this family may be of ancient origin.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Rajagopal</LastName><ForeName>J</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Biotechnology Division, TERI, New Delhi, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Das</LastName><ForeName>S</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Khurana</LastName><ForeName>D K</ForeName><Initials>DK</Initials></Author><Author ValidYN="Y"><LastName>Srivastava</LastName><ForeName>P S</ForeName><Initials>PS</Initials></Author><Author ValidYN="Y"><LastName>Lakshmikumaran</LastName><ForeName>M</ForeName><Initials>M</Initials></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>GENBANK</DataBankName><AccessionNumberList><AccessionNumber>Y11371</AccessionNumber><AccessionNumber>Y11439</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>Canada</Country><MedlineTA>Genome</MedlineTA><NlmUniqueID>8704544</NlmUniqueID><ISSNLinking>0831-2796</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018744">DNA, Plant</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004276">DNA, Satellite</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015139" MajorTopicYN="N">Blotting, Southern</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019175" MajorTopicYN="N">DNA Methylation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018744" MajorTopicYN="N">DNA, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004276" MajorTopicYN="N">DNA, Satellite</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="N">analysis</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016415" MajorTopicYN="N">Sequence Alignment</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020080" MajorTopicYN="Y">Tandem Repeat Sequences</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014197" MajorTopicYN="N">Trees</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>1999</Year><Month>12</Month><Day>10</Day></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>1999</Year><Month>12</Month><Day>10</Day><Hour>0</Hour><Minute>1</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>1999</Year><Month>12</Month><Day>10</Day><Hour>0</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">10584311</ArticleId><ArticleId IdType="doi">10.1139/g99-013</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Inde</li></country></list><tree><noCountry><name sortKey="Das, S" sort="Das, S" uniqKey="Das S" first="S" last="Das">S. Das</name><name sortKey="Khurana, D K" sort="Khurana, D K" uniqKey="Khurana D" first="D K" last="Khurana">D K Khurana</name><name sortKey="Lakshmikumaran, M" sort="Lakshmikumaran, M" uniqKey="Lakshmikumaran M" first="M" last="Lakshmikumaran">M. Lakshmikumaran</name><name sortKey="Srivastava, P S" sort="Srivastava, P S" uniqKey="Srivastava P" first="P S" last="Srivastava">P S Srivastava</name></noCountry><country name="Inde"><noRegion><name sortKey="Rajagopal, J" sort="Rajagopal, J" uniqKey="Rajagopal J" first="J" last="Rajagopal">J. Rajagopal</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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