A full-length enriched cDNA library and expressed sequence tag analysis of the parasitic weed, Striga hermonthica.
Identifieur interne : 003395 ( Main/Exploration ); précédent : 003394; suivant : 003396A full-length enriched cDNA library and expressed sequence tag analysis of the parasitic weed, Striga hermonthica.
Auteurs : Satoko Yoshida [Japon] ; Juliane K. Ishida ; Nasrein M. Kamal ; Abdelbagi M. Ali ; Shigetou Namba ; Ken ShirasuSource :
- BMC plant biology [ 1471-2229 ] ; 2010.
Descripteurs français
- KwdFr :
- Analyse de regroupements (MeSH), Analyse de séquence d'ADN (MeSH), Banque de gènes (MeSH), Bases de données génétiques (MeSH), Cytométrie en flux (MeSH), Dynamique des populations (MeSH), Gènes de plante (MeSH), Internet (MeSH), Plantes (parasitologie), Réaction de polymérisation en chaîne (MeSH), Répétitions microsatellites (MeSH), Similitude de séquences d'acides nucléiques (MeSH), Spécificité d'espèce (MeSH), Striga (génétique), Séquence nucléotidique (MeSH), Variation génétique (MeSH), Étiquettes de séquences exprimées (MeSH), Évolution moléculaire (MeSH).
- MESH :
- génétique : Striga.
- parasitologie : Plantes.
- Analyse de regroupements, Analyse de séquence d'ADN, Banque de gènes, Bases de données génétiques, Cytométrie en flux, Dynamique des populations, Gènes de plante, Internet, Réaction de polymérisation en chaîne, Répétitions microsatellites, Similitude de séquences d'acides nucléiques, Spécificité d'espèce, Séquence nucléotidique, Variation génétique, Étiquettes de séquences exprimées, Évolution moléculaire.
English descriptors
- KwdEn :
- Base Sequence (MeSH), Cluster Analysis (MeSH), Databases, Genetic (MeSH), Evolution, Molecular (MeSH), Expressed Sequence Tags (MeSH), Flow Cytometry (MeSH), Gene Library (MeSH), Genes, Plant (MeSH), Genetic Variation (MeSH), Internet (MeSH), Microsatellite Repeats (MeSH), Plants (parasitology), Polymerase Chain Reaction (MeSH), Population Dynamics (MeSH), Sequence Analysis, DNA (MeSH), Sequence Homology, Nucleic Acid (MeSH), Species Specificity (MeSH), Striga (genetics).
- MESH :
- genetics : Striga.
- parasitology : Plants.
- Base Sequence, Cluster Analysis, Databases, Genetic, Evolution, Molecular, Expressed Sequence Tags, Flow Cytometry, Gene Library, Genes, Plant, Genetic Variation, Internet, Microsatellite Repeats, Polymerase Chain Reaction, Population Dynamics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Species Specificity.
Abstract
BACKGROUND
The obligate parasitic plant witchweed (Striga hermonthica) infects major cereal crops such as sorghum, maize, and millet, and is the most devastating weed pest in Africa. An understanding of the nature of its parasitism would contribute to the development of more sophisticated management methods. However, the molecular and genomic resources currently available for the study of S. hermonthica are limited.
RESULTS
We constructed a full-length enriched cDNA library of S. hermonthica, sequenced 37,710 clones from the library, and obtained 67,814 expressed sequence tag (EST) sequences. The ESTs were assembled into 17,317 unigenes that included 10,319 contigs and 6,818 singletons. The S. hermonthica unigene dataset was subjected to a comparative analysis with other plant genomes or ESTs. Approximately 80% of the unigenes have homologs in other dicotyledonous plants including Arabidopsis, poplar, and grape. We found that 589 unigenes are conserved in the hemiparasitic Triphysaria species but not in other plant species. These are good candidates for genes specifically involved in plant parasitism. Furthermore, we found 1,445 putative simple sequence repeats (SSRs) in the S. hermonthica unigene dataset. We tested 64 pairs of PCR primers flanking the SSRs to develop genetic markers for the detection of polymorphisms. Most primer sets amplified polymorphicbands from individual plants collected at a single location, indicating high genetic diversity in S. hermonthica. We selected 10 primer pairs to analyze S. hermonthica harvested in the field from different host species and geographic locations. A clustering analysis suggests that genetic distances are not correlated with host specificity.
CONCLUSIONS
Our data provide the first extensive set of molecular resources for studying S. hermonthica, and include EST sequences, a comparative analysis with other plant genomes, and useful genetic markers. All the data are stored in a web-based database and freely available. These resources will be useful for genome annotation, gene discovery, functional analysis, molecular breeding, epidemiological studies, and studies of plant evolution.
DOI: 10.1186/1471-2229-10-55
PubMed: 20353604
PubMed Central: PMC2923529
Affiliations:
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Kamal</name></author><author><name sortKey="Ali, Abdelbagi M" sort="Ali, Abdelbagi M" uniqKey="Ali A" first="Abdelbagi M" last="Ali">Abdelbagi M. Ali</name></author><author><name sortKey="Namba, Shigetou" sort="Namba, Shigetou" uniqKey="Namba S" first="Shigetou" last="Namba">Shigetou Namba</name></author><author><name sortKey="Shirasu, Ken" sort="Shirasu, Ken" uniqKey="Shirasu K" first="Ken" last="Shirasu">Ken Shirasu</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2010">2010</date><idno type="RBID">pubmed:20353604</idno><idno type="pmid">20353604</idno><idno type="doi">10.1186/1471-2229-10-55</idno><idno type="pmc">PMC2923529</idno><idno type="wicri:Area/Main/Corpus">003249</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">003249</idno><idno type="wicri:Area/Main/Curation">003249</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">003249</idno><idno type="wicri:Area/Main/Exploration">003249</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">A full-length enriched cDNA library and expressed sequence tag analysis of the parasitic weed, Striga hermonthica.</title><author><name sortKey="Yoshida, Satoko" sort="Yoshida, Satoko" uniqKey="Yoshida S" first="Satoko" last="Yoshida">Satoko Yoshida</name><affiliation wicri:level="1"><nlm:affiliation>Plant Science Center, RIKEN, Tsurumi-ku, Yokohama, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Plant Science Center, RIKEN, Tsurumi-ku, Yokohama</wicri:regionArea><wicri:noRegion>Yokohama</wicri:noRegion></affiliation></author><author><name sortKey="Ishida, Juliane K" sort="Ishida, Juliane K" uniqKey="Ishida J" first="Juliane K" last="Ishida">Juliane K. Ishida</name></author><author><name sortKey="Kamal, Nasrein M" sort="Kamal, Nasrein M" uniqKey="Kamal N" first="Nasrein M" last="Kamal">Nasrein M. Kamal</name></author><author><name sortKey="Ali, Abdelbagi M" sort="Ali, Abdelbagi M" uniqKey="Ali A" first="Abdelbagi M" last="Ali">Abdelbagi M. Ali</name></author><author><name sortKey="Namba, Shigetou" sort="Namba, Shigetou" uniqKey="Namba S" first="Shigetou" last="Namba">Shigetou Namba</name></author><author><name sortKey="Shirasu, Ken" sort="Shirasu, Ken" uniqKey="Shirasu K" first="Ken" last="Shirasu">Ken Shirasu</name></author></analytic><series><title level="j">BMC plant biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2010" type="published">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence (MeSH)</term><term>Cluster Analysis (MeSH)</term><term>Databases, Genetic (MeSH)</term><term>Evolution, Molecular (MeSH)</term><term>Expressed Sequence Tags (MeSH)</term><term>Flow Cytometry (MeSH)</term><term>Gene Library (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Genetic Variation (MeSH)</term><term>Internet (MeSH)</term><term>Microsatellite Repeats (MeSH)</term><term>Plants (parasitology)</term><term>Polymerase Chain Reaction (MeSH)</term><term>Population Dynamics (MeSH)</term><term>Sequence Analysis, DNA (MeSH)</term><term>Sequence Homology, Nucleic Acid (MeSH)</term><term>Species Specificity (MeSH)</term><term>Striga (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de regroupements (MeSH)</term><term>Analyse de séquence d'ADN (MeSH)</term><term>Banque de gènes (MeSH)</term><term>Bases de données génétiques (MeSH)</term><term>Cytométrie en flux (MeSH)</term><term>Dynamique des populations (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Internet (MeSH)</term><term>Plantes (parasitologie)</term><term>Réaction de polymérisation en chaîne (MeSH)</term><term>Répétitions microsatellites (MeSH)</term><term>Similitude de séquences d'acides nucléiques (MeSH)</term><term>Spécificité d'espèce (MeSH)</term><term>Striga (génétique)</term><term>Séquence nucléotidique (MeSH)</term><term>Variation génétique (MeSH)</term><term>Étiquettes de séquences exprimées (MeSH)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Striga</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Striga</term></keywords><keywords scheme="MESH" qualifier="parasitologie" xml:lang="fr"><term>Plantes</term></keywords><keywords scheme="MESH" qualifier="parasitology" xml:lang="en"><term>Plants</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Cluster Analysis</term><term>Databases, Genetic</term><term>Evolution, Molecular</term><term>Expressed Sequence Tags</term><term>Flow Cytometry</term><term>Gene Library</term><term>Genes, Plant</term><term>Genetic Variation</term><term>Internet</term><term>Microsatellite Repeats</term><term>Polymerase Chain Reaction</term><term>Population Dynamics</term><term>Sequence Analysis, DNA</term><term>Sequence Homology, Nucleic Acid</term><term>Species Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de regroupements</term><term>Analyse de séquence d'ADN</term><term>Banque de gènes</term><term>Bases de données génétiques</term><term>Cytométrie en flux</term><term>Dynamique des populations</term><term>Gènes de plante</term><term>Internet</term><term>Réaction de polymérisation en chaîne</term><term>Répétitions microsatellites</term><term>Similitude de séquences d'acides nucléiques</term><term>Spécificité d'espèce</term><term>Séquence nucléotidique</term><term>Variation génétique</term><term>Étiquettes de séquences exprimées</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>The obligate parasitic plant witchweed (Striga hermonthica) infects major cereal crops such as sorghum, maize, and millet, and is the most devastating weed pest in Africa. An understanding of the nature of its parasitism would contribute to the development of more sophisticated management methods. However, the molecular and genomic resources currently available for the study of S. hermonthica are limited.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We constructed a full-length enriched cDNA library of S. hermonthica, sequenced 37,710 clones from the library, and obtained 67,814 expressed sequence tag (EST) sequences. The ESTs were assembled into 17,317 unigenes that included 10,319 contigs and 6,818 singletons. The S. hermonthica unigene dataset was subjected to a comparative analysis with other plant genomes or ESTs. Approximately 80% of the unigenes have homologs in other dicotyledonous plants including Arabidopsis, poplar, and grape. We found that 589 unigenes are conserved in the hemiparasitic Triphysaria species but not in other plant species. These are good candidates for genes specifically involved in plant parasitism. Furthermore, we found 1,445 putative simple sequence repeats (SSRs) in the S. hermonthica unigene dataset. We tested 64 pairs of PCR primers flanking the SSRs to develop genetic markers for the detection of polymorphisms. Most primer sets amplified polymorphicbands from individual plants collected at a single location, indicating high genetic diversity in S. hermonthica. We selected 10 primer pairs to analyze S. hermonthica harvested in the field from different host species and geographic locations. A clustering analysis suggests that genetic distances are not correlated with host specificity.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>Our data provide the first extensive set of molecular resources for studying S. hermonthica, and include EST sequences, a comparative analysis with other plant genomes, and useful genetic markers. All the data are stored in a web-based database and freely available. These resources will be useful for genome annotation, gene discovery, functional analysis, molecular breeding, epidemiological studies, and studies of plant evolution.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">20353604</PMID><DateCompleted><Year>2010</Year><Month>07</Month><Day>05</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2229</ISSN><JournalIssue CitedMedium="Internet"><Volume>10</Volume><PubDate><Year>2010</Year><Month>Mar</Month><Day>30</Day></PubDate></JournalIssue><Title>BMC plant biology</Title><ISOAbbreviation>BMC Plant Biol</ISOAbbreviation></Journal><ArticleTitle>A full-length enriched cDNA library and expressed sequence tag analysis of the parasitic weed, Striga hermonthica.</ArticleTitle><Pagination><MedlinePgn>55</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2229-10-55</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">The obligate parasitic plant witchweed (Striga hermonthica) infects major cereal crops such as sorghum, maize, and millet, and is the most devastating weed pest in Africa. An understanding of the nature of its parasitism would contribute to the development of more sophisticated management methods. However, the molecular and genomic resources currently available for the study of S. hermonthica are limited.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We constructed a full-length enriched cDNA library of S. hermonthica, sequenced 37,710 clones from the library, and obtained 67,814 expressed sequence tag (EST) sequences. The ESTs were assembled into 17,317 unigenes that included 10,319 contigs and 6,818 singletons. The S. hermonthica unigene dataset was subjected to a comparative analysis with other plant genomes or ESTs. Approximately 80% of the unigenes have homologs in other dicotyledonous plants including Arabidopsis, poplar, and grape. We found that 589 unigenes are conserved in the hemiparasitic Triphysaria species but not in other plant species. These are good candidates for genes specifically involved in plant parasitism. Furthermore, we found 1,445 putative simple sequence repeats (SSRs) in the S. hermonthica unigene dataset. We tested 64 pairs of PCR primers flanking the SSRs to develop genetic markers for the detection of polymorphisms. Most primer sets amplified polymorphicbands from individual plants collected at a single location, indicating high genetic diversity in S. hermonthica. We selected 10 primer pairs to analyze S. hermonthica harvested in the field from different host species and geographic locations. A clustering analysis suggests that genetic distances are not correlated with host specificity.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">Our data provide the first extensive set of molecular resources for studying S. hermonthica, and include EST sequences, a comparative analysis with other plant genomes, and useful genetic markers. All the data are stored in a web-based database and freely available. These resources will be useful for genome annotation, gene discovery, functional analysis, molecular breeding, epidemiological studies, and studies of plant evolution.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Yoshida</LastName><ForeName>Satoko</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Plant Science Center, RIKEN, Tsurumi-ku, Yokohama, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ishida</LastName><ForeName>Juliane K</ForeName><Initials>JK</Initials></Author><Author ValidYN="Y"><LastName>Kamal</LastName><ForeName>Nasrein M</ForeName><Initials>NM</Initials></Author><Author ValidYN="Y"><LastName>Ali</LastName><ForeName>Abdelbagi M</ForeName><Initials>AM</Initials></Author><Author ValidYN="Y"><LastName>Namba</LastName><ForeName>Shigetou</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Shirasu</LastName><ForeName>Ken</ForeName><Initials>K</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>2010</Year><Month>03</Month><Day>30</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Plant Biol</MedlineTA><NlmUniqueID>100967807</NlmUniqueID><ISSNLinking>1471-2229</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016000" MajorTopicYN="N">Cluster Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D030541" MajorTopicYN="N">Databases, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020224" MajorTopicYN="Y">Expressed Sequence Tags</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005434" MajorTopicYN="N">Flow Cytometry</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015723" MajorTopicYN="Y">Gene Library</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="N">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020407" MajorTopicYN="N">Internet</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018895" MajorTopicYN="N">Microsatellite Repeats</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010944" MajorTopicYN="N">Plants</DescriptorName><QualifierName UI="Q000469" MajorTopicYN="Y">parasitology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016133" MajorTopicYN="N">Polymerase Chain Reaction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011157" MajorTopicYN="N">Population Dynamics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012689" MajorTopicYN="N">Sequence Homology, Nucleic Acid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013045" MajorTopicYN="N">Species Specificity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D034362" MajorTopicYN="N">Striga</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2009</Year><Month>12</Month><Day>02</Day></PubMedPubDate><PubMedPubDate 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M" uniqKey="Ali A" first="Abdelbagi M" last="Ali">Abdelbagi M. Ali</name><name sortKey="Ishida, Juliane K" sort="Ishida, Juliane K" uniqKey="Ishida J" first="Juliane K" last="Ishida">Juliane K. Ishida</name><name sortKey="Kamal, Nasrein M" sort="Kamal, Nasrein M" uniqKey="Kamal N" first="Nasrein M" last="Kamal">Nasrein M. Kamal</name><name sortKey="Namba, Shigetou" sort="Namba, Shigetou" uniqKey="Namba S" first="Shigetou" last="Namba">Shigetou Namba</name><name sortKey="Shirasu, Ken" sort="Shirasu, Ken" uniqKey="Shirasu K" first="Ken" last="Shirasu">Ken Shirasu</name></noCountry><country name="Japon"><noRegion><name sortKey="Yoshida, Satoko" sort="Yoshida, Satoko" uniqKey="Yoshida S" first="Satoko" last="Yoshida">Satoko Yoshida</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|clé= pubmed:20353604
|texte= A full-length enriched cDNA library and expressed sequence tag analysis of the parasitic weed, Striga hermonthica.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:20353604" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PoplarV1
| This area was generated with Dilib version V0.6.37. |  |