Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon (Salmo salar)
Identifieur interne : 002813 ( Main/Exploration ); précédent : 002812; suivant : 002814Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon (Salmo salar)
Auteurs : Rune Andreassen [Norvège] ; Sigbj Rn Lunner [Norvège] ; Bj Rn H Yheim [Norvège]Source :
- BMC Genomics [ 1471-2164 ] ; 2009.
Descripteurs français
- KwdFr :
- ADN complémentaire (génétique), ARN messager (génétique), ARN messager (métabolisme), Animaux, Cadres ouverts de lecture, Clonage moléculaire, Isoformes de protéines (génétique), Muscles squelettiques (cytologie), Muscles squelettiques (métabolisme), Polyadénylation, Régions non traduites (génétique), Salmo salar (croissance et développement), Salmo salar (génétique), Séquence consensus, Séquence nucléotidique.
- MESH :
- croissance et développement : Salmo salar.
- cytologie : Muscles squelettiques.
- génétique : ADN complémentaire, ARN messager, Isoformes de protéines, Régions non traduites, Salmo salar.
- métabolisme : ARN messager, Muscles squelettiques.
- Animaux, Cadres ouverts de lecture, Clonage moléculaire, Polyadénylation, Séquence consensus, Séquence nucléotidique.
English descriptors
- KwdEn :
- Animals, Base Sequence, Cloning, Molecular, Consensus Sequence, DNA, Complementary (genetics), Muscle, Skeletal (cytology), Muscle, Skeletal (metabolism), Open Reading Frames, Polyadenylation, Protein Isoforms (genetics), RNA, Messenger (genetics), RNA, Messenger (metabolism), Salmo salar (genetics), Salmo salar (growth & development), Untranslated Regions (genetics).
- MESH :
- chemical , genetics : DNA, Complementary, Protein Isoforms, RNA, Messenger, Untranslated Regions.
- cytology : Muscle, Skeletal.
- genetics : Salmo salar.
- growth & development : Salmo salar.
- metabolism : Muscle, Skeletal, RNA, Messenger.
- Animals, Base Sequence, Cloning, Molecular, Consensus Sequence, Open Reading Frames, Polyadenylation.
Abstract
Sequencing of the Atlantic salmon genome is now being planned by an international research consortium. Full-length sequenced inserts from cDNAs (FLIcs) are an important tool for correct annotation and clustering of the genomic sequence in any species. The large amount of highly similar duplicate sequences caused by the relatively recent genome duplication in the salmonid ancestor represents a particular challenge for the genome project. FLIcs will therefore be an extremely useful resource for the Atlantic salmon sequencing project. In addition to be helpful in order to distinguish between duplicate genome regions and in determining correct gene structures, FLIcs are an important resource for functional genomic studies and for investigation of regulatory elements controlling gene expression. In contrast to the large number of ESTs available, including the ESTs from 23 developmental and tissue specific cDNA libraries contributed by the Salmon Genome Project (SGP), the number of sequences where the full-length of the cDNA insert has been determined has been small.
High quality full-length insert sequences from 560 pre-smolt white muscle tissue specific cDNAs were generated, accession numbers [GenBank:
This paper describes the first Atlantic salmon FLIcs from a tissue and developmental stage specific cDNA library. We have demonstrated that many FLIcs contained a complete coding sequence (cCDS). This suggests that the remaining cDNA libraries generated by SGP represent a valuable cCDS FLIc source. The conservation of 7-mers in 3'UTRs indicates that these motifs are functionally important. Identity between some of these 7-mers and miRNA target sequences suggests that they are miRNA targets in
Url:
DOI: 10.1186/1471-2164-10-502
PubMed: 19878547
PubMed Central: 2774873
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000552
- to stream Pmc, to step Curation: 000552
- to stream Pmc, to step Checkpoint: 001381
- to stream PubMed, to step Corpus: 001F85
- to stream PubMed, to step Curation: 001F85
- to stream PubMed, to step Checkpoint: 001F30
- to stream Ncbi, to step Merge: 000720
- to stream Ncbi, to step Curation: 000720
- to stream Ncbi, to step Checkpoint: 000720
- to stream Main, to step Merge: 002839
- to stream Main, to step Curation: 002813
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon (<italic>Salmo salar</italic>
)</title>
<author><name sortKey="Andreassen, Rune" sort="Andreassen, Rune" uniqKey="Andreassen R" first="Rune" last="Andreassen">Rune Andreassen</name>
<affiliation wicri:level="1"><nlm:aff id="I1">BasAM-Genetics, Norwegian School of Veterinary Science, PO Box 8146 DEP, NO-0033 Oslo, Norway</nlm:aff>
<country xml:lang="fr">Norvège</country>
<wicri:regionArea>BasAM-Genetics, Norwegian School of Veterinary Science, PO Box 8146 DEP, NO-0033 Oslo</wicri:regionArea>
<wicri:noRegion>NO-0033 Oslo</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="I2">CIGENE-Centre for Integrative Genetics, Ås, Norway</nlm:aff>
<country xml:lang="fr">Norvège</country>
<wicri:regionArea>CIGENE-Centre for Integrative Genetics, Ås</wicri:regionArea>
<wicri:noRegion>Ås</wicri:noRegion>
</affiliation>
<affiliation wicri:level="3"><nlm:aff id="I3">Faculty of Health Sciences, Oslo University College, Oslo, Norway</nlm:aff>
<country xml:lang="fr">Norvège</country>
<wicri:regionArea>Faculty of Health Sciences, Oslo University College, Oslo</wicri:regionArea>
<placeName><settlement type="city">Oslo</settlement>
<region nuts="2">Østlandet</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Lunner, Sigbj Rn" sort="Lunner, Sigbj Rn" uniqKey="Lunner S" first="Sigbj Rn" last="Lunner">Sigbj Rn Lunner</name>
<affiliation wicri:level="1"><nlm:aff id="I1">BasAM-Genetics, Norwegian School of Veterinary Science, PO Box 8146 DEP, NO-0033 Oslo, Norway</nlm:aff>
<country xml:lang="fr">Norvège</country>
<wicri:regionArea>BasAM-Genetics, Norwegian School of Veterinary Science, PO Box 8146 DEP, NO-0033 Oslo</wicri:regionArea>
<wicri:noRegion>NO-0033 Oslo</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="H Yheim, Bj Rn" sort="H Yheim, Bj Rn" uniqKey="H Yheim B" first="Bj Rn" last="H Yheim">Bj Rn H Yheim</name>
<affiliation wicri:level="1"><nlm:aff id="I1">BasAM-Genetics, Norwegian School of Veterinary Science, PO Box 8146 DEP, NO-0033 Oslo, Norway</nlm:aff>
<country xml:lang="fr">Norvège</country>
<wicri:regionArea>BasAM-Genetics, Norwegian School of Veterinary Science, PO Box 8146 DEP, NO-0033 Oslo</wicri:regionArea>
<wicri:noRegion>NO-0033 Oslo</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="I2">CIGENE-Centre for Integrative Genetics, Ås, Norway</nlm:aff>
<country xml:lang="fr">Norvège</country>
<wicri:regionArea>CIGENE-Centre for Integrative Genetics, Ås</wicri:regionArea>
<wicri:noRegion>Ås</wicri:noRegion>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">19878547</idno>
<idno type="pmc">2774873</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774873</idno>
<idno type="RBID">PMC:2774873</idno>
<idno type="doi">10.1186/1471-2164-10-502</idno>
<date when="2009">2009</date>
<idno type="wicri:Area/Pmc/Corpus">000552</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000552</idno>
<idno type="wicri:Area/Pmc/Curation">000552</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000552</idno>
<idno type="wicri:Area/Pmc/Checkpoint">001381</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001381</idno>
<idno type="wicri:source">PubMed</idno>
<idno type="RBID">pubmed:19878547</idno>
<idno type="wicri:Area/PubMed/Corpus">001F85</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001F85</idno>
<idno type="wicri:Area/PubMed/Curation">001F85</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001F85</idno>
<idno type="wicri:Area/PubMed/Checkpoint">001F30</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001F30</idno>
<idno type="wicri:Area/Ncbi/Merge">000720</idno>
<idno type="wicri:Area/Ncbi/Curation">000720</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">000720</idno>
<idno type="wicri:Area/Main/Merge">002839</idno>
<idno type="wicri:Area/Main/Curation">002813</idno>
<idno type="wicri:Area/Main/Exploration">002813</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon (<italic>Salmo salar</italic>
)</title>
<author><name sortKey="Andreassen, Rune" sort="Andreassen, Rune" uniqKey="Andreassen R" first="Rune" last="Andreassen">Rune Andreassen</name>
<affiliation wicri:level="1"><nlm:aff id="I1">BasAM-Genetics, Norwegian School of Veterinary Science, PO Box 8146 DEP, NO-0033 Oslo, Norway</nlm:aff>
<country xml:lang="fr">Norvège</country>
<wicri:regionArea>BasAM-Genetics, Norwegian School of Veterinary Science, PO Box 8146 DEP, NO-0033 Oslo</wicri:regionArea>
<wicri:noRegion>NO-0033 Oslo</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="I2">CIGENE-Centre for Integrative Genetics, Ås, Norway</nlm:aff>
<country xml:lang="fr">Norvège</country>
<wicri:regionArea>CIGENE-Centre for Integrative Genetics, Ås</wicri:regionArea>
<wicri:noRegion>Ås</wicri:noRegion>
</affiliation>
<affiliation wicri:level="3"><nlm:aff id="I3">Faculty of Health Sciences, Oslo University College, Oslo, Norway</nlm:aff>
<country xml:lang="fr">Norvège</country>
<wicri:regionArea>Faculty of Health Sciences, Oslo University College, Oslo</wicri:regionArea>
<placeName><settlement type="city">Oslo</settlement>
<region nuts="2">Østlandet</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Lunner, Sigbj Rn" sort="Lunner, Sigbj Rn" uniqKey="Lunner S" first="Sigbj Rn" last="Lunner">Sigbj Rn Lunner</name>
<affiliation wicri:level="1"><nlm:aff id="I1">BasAM-Genetics, Norwegian School of Veterinary Science, PO Box 8146 DEP, NO-0033 Oslo, Norway</nlm:aff>
<country xml:lang="fr">Norvège</country>
<wicri:regionArea>BasAM-Genetics, Norwegian School of Veterinary Science, PO Box 8146 DEP, NO-0033 Oslo</wicri:regionArea>
<wicri:noRegion>NO-0033 Oslo</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="H Yheim, Bj Rn" sort="H Yheim, Bj Rn" uniqKey="H Yheim B" first="Bj Rn" last="H Yheim">Bj Rn H Yheim</name>
<affiliation wicri:level="1"><nlm:aff id="I1">BasAM-Genetics, Norwegian School of Veterinary Science, PO Box 8146 DEP, NO-0033 Oslo, Norway</nlm:aff>
<country xml:lang="fr">Norvège</country>
<wicri:regionArea>BasAM-Genetics, Norwegian School of Veterinary Science, PO Box 8146 DEP, NO-0033 Oslo</wicri:regionArea>
<wicri:noRegion>NO-0033 Oslo</wicri:noRegion>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="I2">CIGENE-Centre for Integrative Genetics, Ås, Norway</nlm:aff>
<country xml:lang="fr">Norvège</country>
<wicri:regionArea>CIGENE-Centre for Integrative Genetics, Ås</wicri:regionArea>
<wicri:noRegion>Ås</wicri:noRegion>
</affiliation>
</author>
</analytic>
<series><title level="j">BMC Genomics</title>
<idno type="eISSN">1471-2164</idno>
<imprint><date when="2009">2009</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term>
<term>Base Sequence</term>
<term>Cloning, Molecular</term>
<term>Consensus Sequence</term>
<term>DNA, Complementary (genetics)</term>
<term>Muscle, Skeletal (cytology)</term>
<term>Muscle, Skeletal (metabolism)</term>
<term>Open Reading Frames</term>
<term>Polyadenylation</term>
<term>Protein Isoforms (genetics)</term>
<term>RNA, Messenger (genetics)</term>
<term>RNA, Messenger (metabolism)</term>
<term>Salmo salar (genetics)</term>
<term>Salmo salar (growth & development)</term>
<term>Untranslated Regions (genetics)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>ADN complémentaire (génétique)</term>
<term>ARN messager (génétique)</term>
<term>ARN messager (métabolisme)</term>
<term>Animaux</term>
<term>Cadres ouverts de lecture</term>
<term>Clonage moléculaire</term>
<term>Isoformes de protéines (génétique)</term>
<term>Muscles squelettiques (cytologie)</term>
<term>Muscles squelettiques (métabolisme)</term>
<term>Polyadénylation</term>
<term>Régions non traduites (génétique)</term>
<term>Salmo salar (croissance et développement)</term>
<term>Salmo salar (génétique)</term>
<term>Séquence consensus</term>
<term>Séquence nucléotidique</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Complementary</term>
<term>Protein Isoforms</term>
<term>RNA, Messenger</term>
<term>Untranslated Regions</term>
</keywords>
<keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Salmo salar</term>
</keywords>
<keywords scheme="MESH" qualifier="cytologie" xml:lang="fr"><term>Muscles squelettiques</term>
</keywords>
<keywords scheme="MESH" qualifier="cytology" xml:lang="en"><term>Muscle, Skeletal</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Salmo salar</term>
</keywords>
<keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Salmo salar</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN complémentaire</term>
<term>ARN messager</term>
<term>Isoformes de protéines</term>
<term>Régions non traduites</term>
<term>Salmo salar</term>
</keywords>
<keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Muscle, Skeletal</term>
<term>RNA, Messenger</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ARN messager</term>
<term>Muscles squelettiques</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Animals</term>
<term>Base Sequence</term>
<term>Cloning, Molecular</term>
<term>Consensus Sequence</term>
<term>Open Reading Frames</term>
<term>Polyadenylation</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Animaux</term>
<term>Cadres ouverts de lecture</term>
<term>Clonage moléculaire</term>
<term>Polyadénylation</term>
<term>Séquence consensus</term>
<term>Séquence nucléotidique</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Sequencing of the Atlantic salmon genome is now being planned by an international research consortium. Full-length sequenced inserts from cDNAs (FLIcs) are an important tool for correct annotation and clustering of the genomic sequence in any species. The large amount of highly similar duplicate sequences caused by the relatively recent genome duplication in the salmonid ancestor represents a particular challenge for the genome project. FLIcs will therefore be an extremely useful resource for the Atlantic salmon sequencing project. In addition to be helpful in order to distinguish between duplicate genome regions and in determining correct gene structures, FLIcs are an important resource for functional genomic studies and for investigation of regulatory elements controlling gene expression. In contrast to the large number of ESTs available, including the ESTs from 23 developmental and tissue specific cDNA libraries contributed by the Salmon Genome Project (SGP), the number of sequences where the full-length of the cDNA insert has been determined has been small.</p>
</sec>
<sec><title>Results</title>
<p>High quality full-length insert sequences from 560 pre-smolt white muscle tissue specific cDNAs were generated, accession numbers [GenBank: <ext-link ext-link-type="gen" xlink:href="BT043497">BT043497</ext-link>
- <ext-link ext-link-type="gen" xlink:href="BT044056">BT044056</ext-link>
]. Five hundred and ten (91%) of the transcripts were annotated using Gene Ontology (GO) terms and 440 of the FLIcs are likely to contain a complete coding sequence (cCDS). The sequence information was used to identify putative paralogs, characterize salmon Kozak motifs, polyadenylation signal variation and to identify motifs likely to be involved in the regulation of particular genes. Finally, conserved 7-mers in the 3'UTRs were identified, of which some were identical to miRNA target sequences.</p>
</sec>
<sec><title>Conclusion</title>
<p>This paper describes the first Atlantic salmon FLIcs from a tissue and developmental stage specific cDNA library. We have demonstrated that many FLIcs contained a complete coding sequence (cCDS). This suggests that the remaining cDNA libraries generated by SGP represent a valuable cCDS FLIc source. The conservation of 7-mers in 3'UTRs indicates that these motifs are functionally important. Identity between some of these 7-mers and miRNA target sequences suggests that they are miRNA targets in <italic>Salmo salar </italic>
transcripts as well.</p>
</sec>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
</listBibl>
</div1>
</back>
</TEI>
<affiliations><list><country><li>Norvège</li>
</country>
<region><li>Østlandet</li>
</region>
<settlement><li>Oslo</li>
</settlement>
</list>
<tree><country name="Norvège"><noRegion><name sortKey="Andreassen, Rune" sort="Andreassen, Rune" uniqKey="Andreassen R" first="Rune" last="Andreassen">Rune Andreassen</name>
</noRegion>
<name sortKey="Andreassen, Rune" sort="Andreassen, Rune" uniqKey="Andreassen R" first="Rune" last="Andreassen">Rune Andreassen</name>
<name sortKey="Andreassen, Rune" sort="Andreassen, Rune" uniqKey="Andreassen R" first="Rune" last="Andreassen">Rune Andreassen</name>
<name sortKey="H Yheim, Bj Rn" sort="H Yheim, Bj Rn" uniqKey="H Yheim B" first="Bj Rn" last="H Yheim">Bj Rn H Yheim</name>
<name sortKey="H Yheim, Bj Rn" sort="H Yheim, Bj Rn" uniqKey="H Yheim B" first="Bj Rn" last="H Yheim">Bj Rn H Yheim</name>
<name sortKey="Lunner, Sigbj Rn" sort="Lunner, Sigbj Rn" uniqKey="Lunner S" first="Sigbj Rn" last="Lunner">Sigbj Rn Lunner</name>
</country>
</tree>
</affiliations>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002813 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 002813 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= MersV1 |flux= Main |étape= Exploration |type= RBID |clé= PMC:2774873 |texte= Characterization of full-length sequenced cDNA inserts (FLIcs) from Atlantic salmon (Salmo salar) }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:19878547" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \ | NlmPubMed2Wicri -a MersV1
This area was generated with Dilib version V0.6.33. |