16S-23S rRNA intergenic spacer region variability in the genus Frankia.
Identifieur interne : 000099 ( Main/Exploration ); précédent : 000098; suivant : 00010016S-23S rRNA intergenic spacer region variability in the genus Frankia.
Auteurs : Faten Ghodhbane-Gtari [Tunisie] ; Imen Nouioui ; Mohamed Chair ; Abdellatif Boudabous ; Maher GtariSource :
- Microbial ecology [ 1432-184X ] ; 2010.
Descripteurs français
- KwdFr :
- ADN bactérien (génétique), ADN intergénique (MeSH), ARN ribosomique 16S (génétique), ARN ribosomique 23S (génétique), Alignement de séquences (MeSH), Analyse de séquence d'ADN (MeSH), Données de séquences moléculaires (MeSH), Frankia (génétique), Phylogenèse (MeSH), Polymorphisme génétique (MeSH), Réaction de polymérisation en chaîne (MeSH), Séquence nucléotidique (MeSH).
- MESH :
English descriptors
- KwdEn :
- Base Sequence (MeSH), DNA, Bacterial (genetics), DNA, Intergenic (MeSH), Frankia (genetics), Molecular Sequence Data (MeSH), Phylogeny (MeSH), Polymerase Chain Reaction (MeSH), Polymorphism, Genetic (MeSH), RNA, Ribosomal, 16S (genetics), RNA, Ribosomal, 23S (genetics), Sequence Alignment (MeSH), Sequence Analysis, DNA (MeSH).
- MESH :
- chemical , genetics : DNA, Bacterial, RNA, Ribosomal, 16S, RNA, Ribosomal, 23S.
- genetics : Frankia.
- Base Sequence, DNA, Intergenic, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, Polymorphism, Genetic, Sequence Alignment, Sequence Analysis, DNA.
Abstract
16S-23S rRNA internally transcribed spacer (ITS) sequences from 53 Frankia strains were sequenced and sized from polymerase chain reaction amplification products and compiled with 14 selected 16S-23S ITS sequences from public database. Frankia genomes included two to three ITS copies lacking length polymorphism except for nine strains. No tRNA gene was encountered in this region. Frankia strains exhibited various lengths (369 to 452 nt) and a wide range of sequence similarity (35-100%) in the ITS region. The average pairwise distance varied from 0.368 (clusters 1 and 2) to 0.964 (clusters 3 and 4) and was 0.397, 0.138, 0.129, and 0.016, respectively, for cluster 4 (saprophytic non-infective/non-effective), clusters 1 and 3 (facultative symbiotic), and cluster 2 (obligate symbiotic). This suggests a gradual erosion of Frankia diversity concomitantly with a shift from saprophytic non-infective/non-effective to facultative and symbiotic lifestyle. Comparative sequence analyses of the 16S-23S rRNA intergenic spacer region of Frankia strains are not useful to assign them to their respective cluster or host infection group. Accurate assignment required the inclusion of the adjacent 16S and 23S rRNA gene fragments.
DOI: 10.1007/s00248-010-9641-6
PubMed: 20179918
Affiliations:
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Le document en format XML
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scheme="KwdEn" xml:lang="en"><term>Base Sequence (MeSH)</term><term>DNA, Bacterial (genetics)</term><term>DNA, Intergenic (MeSH)</term><term>Frankia (genetics)</term><term>Molecular Sequence Data (MeSH)</term><term>Phylogeny (MeSH)</term><term>Polymerase Chain Reaction (MeSH)</term><term>Polymorphism, Genetic (MeSH)</term><term>RNA, Ribosomal, 16S (genetics)</term><term>RNA, Ribosomal, 23S (genetics)</term><term>Sequence Alignment (MeSH)</term><term>Sequence Analysis, DNA (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN bactérien (génétique)</term><term>ADN intergénique (MeSH)</term><term>ARN ribosomique 16S (génétique)</term><term>ARN ribosomique 23S (génétique)</term><term>Alignement de séquences (MeSH)</term><term>Analyse de séquence d'ADN (MeSH)</term><term>Données de séquences moléculaires (MeSH)</term><term>Frankia (génétique)</term><term>Phylogenèse (MeSH)</term><term>Polymorphisme génétique (MeSH)</term><term>Réaction de polymérisation en chaîne (MeSH)</term><term>Séquence nucléotidique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Bacterial</term><term>RNA, Ribosomal, 16S</term><term>RNA, Ribosomal, 23S</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Frankia</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN bactérien</term><term>ARN ribosomique 16S</term><term>ARN ribosomique 23S</term><term>Frankia</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>DNA, Intergenic</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Polymerase Chain Reaction</term><term>Polymorphism, Genetic</term><term>Sequence Alignment</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN intergénique</term><term>Alignement de séquences</term><term>Analyse de séquence d'ADN</term><term>Données de séquences moléculaires</term><term>Phylogenèse</term><term>Polymorphisme génétique</term><term>Réaction de polymérisation en chaîne</term><term>Séquence nucléotidique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">16S-23S rRNA internally transcribed spacer (ITS) sequences from 53 Frankia strains were sequenced and sized from polymerase chain reaction amplification products and compiled with 14 selected 16S-23S ITS sequences from public database. Frankia genomes included two to three ITS copies lacking length polymorphism except for nine strains. No tRNA gene was encountered in this region. Frankia strains exhibited various lengths (369 to 452 nt) and a wide range of sequence similarity (35-100%) in the ITS region. The average pairwise distance varied from 0.368 (clusters 1 and 2) to 0.964 (clusters 3 and 4) and was 0.397, 0.138, 0.129, and 0.016, respectively, for cluster 4 (saprophytic non-infective/non-effective), clusters 1 and 3 (facultative symbiotic), and cluster 2 (obligate symbiotic). This suggests a gradual erosion of Frankia diversity concomitantly with a shift from saprophytic non-infective/non-effective to facultative and symbiotic lifestyle. Comparative sequence analyses of the 16S-23S rRNA intergenic spacer region of Frankia strains are not useful to assign them to their respective cluster or host infection group. Accurate assignment required the inclusion of the adjacent 16S and 23S rRNA gene fragments.</div></front></TEI><affiliations><list><country><li>Tunisie</li></country><region><li>Gouvernorat de Tunis</li></region><settlement><li>Tunis</li></settlement></list><tree><noCountry><name sortKey="Boudabous, Abdellatif" sort="Boudabous, Abdellatif" uniqKey="Boudabous A" first="Abdellatif" last="Boudabous">Abdellatif Boudabous</name><name sortKey="Chair, Mohamed" sort="Chair, Mohamed" uniqKey="Chair M" first="Mohamed" last="Chair">Mohamed Chair</name><name sortKey="Gtari, Maher" sort="Gtari, Maher" uniqKey="Gtari M" first="Maher" last="Gtari">Maher Gtari</name><name sortKey="Nouioui, Imen" sort="Nouioui, Imen" uniqKey="Nouioui I" first="Imen" last="Nouioui">Imen Nouioui</name></noCountry><country name="Tunisie"><region name="Gouvernorat de Tunis"><name sortKey="Ghodhbane Gtari, Faten" sort="Ghodhbane Gtari, Faten" uniqKey="Ghodhbane Gtari F" first="Faten" last="Ghodhbane-Gtari">Faten Ghodhbane-Gtari</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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