Length and sequence heterogeneity in 5S rDNA of Populus deltoides.
Identifieur interne : 004566 ( Main/Exploration ); précédent : 004565; suivant : 004567Length and sequence heterogeneity in 5S rDNA of Populus deltoides.
Auteurs : Madan S. Negi [Inde] ; Jyothi Rajagopal ; Neeti Chauhan ; Richard Cronn ; Malathi LakshmikumaranSource :
- Genome [ 0831-2796 ] ; 2002.
Descripteurs français
- KwdFr :
- ADN ribosomique (composition chimique), ADN ribosomique (génétique), ARN ribosomique 5S (génétique), Données de séquences moléculaires (MeSH), Populus (génétique), Répétitions microsatellites (génétique), Similitude de séquences d'acides nucléiques (MeSH), Séquence nucléotidique (MeSH), Technique de Southern (MeSH).
- MESH :
- composition chimique : ADN ribosomique.
- génétique : ADN ribosomique, ARN ribosomique 5S, Populus, Répétitions microsatellites.
- Données de séquences moléculaires, Similitude de séquences d'acides nucléiques, Séquence nucléotidique, Technique de Southern.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA, Ribosomal.
- chemical , genetics : DNA, Ribosomal, RNA, Ribosomal, 5S.
- genetics : Microsatellite Repeats, Populus.
- Base Sequence, Blotting, Southern, Molecular Sequence Data, Sequence Homology, Nucleic Acid.
Abstract
The 5S rRNA genes and their associated non-transcribed spacer (NTS) regions are present as repeat units arranged in tandem arrays in plant genomes. Length heterogeneity in 5S rDNA repeats was previously identified in Populus deltoides and was also observed in the present study. Primers were designed to amplify the 5S rDNA NTS variants from the P. deltoides genome. The PCR-amplified products from the two accessions of P. deltoides (G3 and G48) suggested the presence of length heterogeneity of 5S rDNA units within and among accessions, and the size of the spacers ranged from 385 to 434 bp. Sequence analysis of the non-transcribed spacer (NTS) revealed two distinct classes of 5S rDNA within both accessions: class 1, which contained GAA trinucleotide microsatellite repeats, and class 2, which lacked the repeats. The class 1 spacer shows length variation owing to the microsatellite, with two clones exhibiting 10 GAA repeat units and one clone exhibiting 16 such repeat units. However, distance analysis shows that class 1 spacer sequences are highly similar inter se, yielding nucleotide diversity (pi) estimates that are less than 0.15% of those obtained for class 2 spacers (pi = 0.0183 vs. 0.1433, respectively). The presence of microsatellite in the NTS region leading to variation in spacer length is reported and discussed for the first time in P. deltoides.
DOI: 10.1139/g02-094
PubMed: 12502265
Affiliations:
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Negi</name><affiliation wicri:level="1"><nlm:affiliation>Biotechnology and Bioresources Division, TERI, Darbari Seth Block, Habitat Place, Lodhi Road, New Delhi 110003, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Biotechnology and Bioresources Division, TERI, Darbari Seth Block, Habitat Place, Lodhi Road, New Delhi 110003</wicri:regionArea><wicri:noRegion>New Delhi 110003</wicri:noRegion></affiliation></author><author><name sortKey="Rajagopal, Jyothi" sort="Rajagopal, Jyothi" uniqKey="Rajagopal J" first="Jyothi" last="Rajagopal">Jyothi Rajagopal</name></author><author><name sortKey="Chauhan, Neeti" sort="Chauhan, Neeti" uniqKey="Chauhan N" first="Neeti" last="Chauhan">Neeti Chauhan</name></author><author><name sortKey="Cronn, Richard" sort="Cronn, Richard" uniqKey="Cronn R" first="Richard" last="Cronn">Richard Cronn</name></author><author><name sortKey="Lakshmikumaran, Malathi" sort="Lakshmikumaran, Malathi" uniqKey="Lakshmikumaran M" first="Malathi" last="Lakshmikumaran">Malathi Lakshmikumaran</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2002">2002</date><idno type="RBID">pubmed:12502265</idno><idno type="pmid">12502265</idno><idno type="doi">10.1139/g02-094</idno><idno type="wicri:Area/Main/Corpus">004564</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">004564</idno><idno type="wicri:Area/Main/Curation">004564</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">004564</idno><idno type="wicri:Area/Main/Exploration">004564</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Length and sequence heterogeneity in 5S rDNA of Populus deltoides.</title><author><name sortKey="Negi, Madan S" sort="Negi, Madan S" uniqKey="Negi M" first="Madan S" last="Negi">Madan S. Negi</name><affiliation wicri:level="1"><nlm:affiliation>Biotechnology and Bioresources Division, TERI, Darbari Seth Block, Habitat Place, Lodhi Road, New Delhi 110003, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Biotechnology and Bioresources Division, TERI, Darbari Seth Block, Habitat Place, Lodhi Road, New Delhi 110003</wicri:regionArea><wicri:noRegion>New Delhi 110003</wicri:noRegion></affiliation></author><author><name sortKey="Rajagopal, Jyothi" sort="Rajagopal, Jyothi" uniqKey="Rajagopal J" first="Jyothi" last="Rajagopal">Jyothi Rajagopal</name></author><author><name sortKey="Chauhan, Neeti" sort="Chauhan, Neeti" uniqKey="Chauhan N" first="Neeti" last="Chauhan">Neeti Chauhan</name></author><author><name sortKey="Cronn, Richard" sort="Cronn, Richard" uniqKey="Cronn R" first="Richard" last="Cronn">Richard Cronn</name></author><author><name sortKey="Lakshmikumaran, Malathi" sort="Lakshmikumaran, Malathi" uniqKey="Lakshmikumaran M" first="Malathi" last="Lakshmikumaran">Malathi Lakshmikumaran</name></author></analytic><series><title level="j">Genome</title><idno type="ISSN">0831-2796</idno><imprint><date when="2002" type="published">2002</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, Ribosomal (chemistry)</term><term>DNA, Ribosomal (genetics)</term><term>Microsatellite Repeats (genetics)</term><term>Molecular Sequence Data (MeSH)</term><term>Populus (genetics)</term><term>RNA, Ribosomal, 5S (genetics)</term><term>Sequence Homology, Nucleic Acid (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN ribosomique (composition chimique)</term><term>ADN ribosomique (génétique)</term><term>ARN ribosomique 5S (génétique)</term><term>Données de séquences moléculaires (MeSH)</term><term>Populus (génétique)</term><term>Répétitions microsatellites (génétique)</term><term>Similitude de séquences d'acides nucléiques (MeSH)</term><term>Séquence nucléotidique (MeSH)</term><term>Technique de Southern (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA, Ribosomal</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Ribosomal</term><term>RNA, Ribosomal, 5S</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>ADN ribosomique</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Microsatellite Repeats</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN ribosomique</term><term>ARN ribosomique 5S</term><term>Populus</term><term>Répétitions microsatellites</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Blotting, Southern</term><term>Molecular Sequence Data</term><term>Sequence Homology, Nucleic Acid</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Données de séquences moléculaires</term><term>Similitude de séquences d'acides nucléiques</term><term>Séquence nucléotidique</term><term>Technique de Southern</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The 5S rRNA genes and their associated non-transcribed spacer (NTS) regions are present as repeat units arranged in tandem arrays in plant genomes. Length heterogeneity in 5S rDNA repeats was previously identified in Populus deltoides and was also observed in the present study. Primers were designed to amplify the 5S rDNA NTS variants from the P. deltoides genome. The PCR-amplified products from the two accessions of P. deltoides (G3 and G48) suggested the presence of length heterogeneity of 5S rDNA units within and among accessions, and the size of the spacers ranged from 385 to 434 bp. Sequence analysis of the non-transcribed spacer (NTS) revealed two distinct classes of 5S rDNA within both accessions: class 1, which contained GAA trinucleotide microsatellite repeats, and class 2, which lacked the repeats. The class 1 spacer shows length variation owing to the microsatellite, with two clones exhibiting 10 GAA repeat units and one clone exhibiting 16 such repeat units. However, distance analysis shows that class 1 spacer sequences are highly similar inter se, yielding nucleotide diversity (pi) estimates that are less than 0.15% of those obtained for class 2 spacers (pi = 0.0183 vs. 0.1433, respectively). The presence of microsatellite in the NTS region leading to variation in spacer length is reported and discussed for the first time in P. deltoides.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">12502265</PMID><DateCompleted><Year>2003</Year><Month>05</Month><Day>28</Day></DateCompleted><DateRevised><Year>2019</Year><Month>09</Month><Day>16</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0831-2796</ISSN><JournalIssue CitedMedium="Print"><Volume>45</Volume><Issue>6</Issue><PubDate><Year>2002</Year><Month>Dec</Month></PubDate></JournalIssue><Title>Genome</Title><ISOAbbreviation>Genome</ISOAbbreviation></Journal><ArticleTitle>Length and sequence heterogeneity in 5S rDNA of Populus deltoides.</ArticleTitle><Pagination><MedlinePgn>1181-8</MedlinePgn></Pagination><Abstract><AbstractText>The 5S rRNA genes and their associated non-transcribed spacer (NTS) regions are present as repeat units arranged in tandem arrays in plant genomes. Length heterogeneity in 5S rDNA repeats was previously identified in Populus deltoides and was also observed in the present study. Primers were designed to amplify the 5S rDNA NTS variants from the P. deltoides genome. The PCR-amplified products from the two accessions of P. deltoides (G3 and G48) suggested the presence of length heterogeneity of 5S rDNA units within and among accessions, and the size of the spacers ranged from 385 to 434 bp. Sequence analysis of the non-transcribed spacer (NTS) revealed two distinct classes of 5S rDNA within both accessions: class 1, which contained GAA trinucleotide microsatellite repeats, and class 2, which lacked the repeats. The class 1 spacer shows length variation owing to the microsatellite, with two clones exhibiting 10 GAA repeat units and one clone exhibiting 16 such repeat units. However, distance analysis shows that class 1 spacer sequences are highly similar inter se, yielding nucleotide diversity (pi) estimates that are less than 0.15% of those obtained for class 2 spacers (pi = 0.0183 vs. 0.1433, respectively). The presence of microsatellite in the NTS region leading to variation in spacer length is reported and discussed for the first time in P. deltoides.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Negi</LastName><ForeName>Madan S</ForeName><Initials>MS</Initials><AffiliationInfo><Affiliation>Biotechnology and Bioresources Division, TERI, Darbari Seth Block, Habitat Place, Lodhi Road, New Delhi 110003, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rajagopal</LastName><ForeName>Jyothi</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Chauhan</LastName><ForeName>Neeti</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Cronn</LastName><ForeName>Richard</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Lakshmikumaran</LastName><ForeName>Malathi</ForeName><Initials>M</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></Article><MedlineJournalInfo><Country>Canada</Country><MedlineTA>Genome</MedlineTA><NlmUniqueID>8704544</NlmUniqueID><ISSNLinking>0831-2796</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004275">DNA, Ribosomal</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012341">RNA, Ribosomal, 5S</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="D004275" MajorTopicYN="N">DNA, Ribosomal</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018895" MajorTopicYN="N">Microsatellite Repeats</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012341" MajorTopicYN="N">RNA, Ribosomal, 5S</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012689" MajorTopicYN="N">Sequence Homology, Nucleic Acid</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2002</Year><Month>12</Month><Day>28</Day><Hour>4</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2003</Year><Month>5</Month><Day>29</Day><Hour>5</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2002</Year><Month>12</Month><Day>28</Day><Hour>4</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">12502265</ArticleId><ArticleId IdType="doi">10.1139/g02-094</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Inde</li></country></list><tree><noCountry><name sortKey="Chauhan, Neeti" sort="Chauhan, Neeti" uniqKey="Chauhan N" first="Neeti" last="Chauhan">Neeti Chauhan</name><name sortKey="Cronn, Richard" sort="Cronn, Richard" uniqKey="Cronn R" first="Richard" last="Cronn">Richard Cronn</name><name sortKey="Lakshmikumaran, Malathi" sort="Lakshmikumaran, Malathi" uniqKey="Lakshmikumaran M" first="Malathi" last="Lakshmikumaran">Malathi Lakshmikumaran</name><name sortKey="Rajagopal, Jyothi" sort="Rajagopal, Jyothi" uniqKey="Rajagopal J" first="Jyothi" last="Rajagopal">Jyothi Rajagopal</name></noCountry><country name="Inde"><noRegion><name sortKey="Negi, Madan S" sort="Negi, Madan S" uniqKey="Negi M" first="Madan S" last="Negi">Madan S. 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