Genome-wide analysis of simple sequence repeats in the model medicinal mushroom Ganoderma lucidum.
Identifieur interne : 000373 ( Main/Exploration ); précédent : 000372; suivant : 000374Genome-wide analysis of simple sequence repeats in the model medicinal mushroom Ganoderma lucidum.
Auteurs : Jun Qian [République populaire de Chine] ; Haibin Xu ; Jingyuan Song ; Jiang Xu ; Yingjie Zhu ; Shilin ChenSource :
- Gene [ 1879-0038 ] ; 2013.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Introns, Protéines fongiques, Reishi.
- métabolisme : Protéines fongiques, Reishi.
- Gènes fongiques, Marqueurs génétiques, Répétitions microsatellites, Étude d'association pangénomique.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Fungal Proteins.
- chemical , metabolism : Fungal Proteins.
- genetics : Introns, Reishi.
- metabolism : Reishi.
- Genes, Fungal, Genetic Markers, Genome-Wide Association Study, Microsatellite Repeats.
Abstract
Simple sequence repeats (SSRs) or microsatellites are one of the most popular sources of genetic markers and play a significant role in gene function and genome organization. We identified SSRs in the genome of Ganoderma lucidum and analyzed their frequency and distribution in different genomic regions. We also compared the SSRs in G. lucidum with six other Agaricomycetes genomes: Coprinopsis cinerea, Laccaria bicolor, Phanerochaete chrysosporium, Postia placenta, Schizophyllum commune and Serpula lacrymans. Based on our search criteria, the total number of SSRs found ranged from 1206 to 6104 and covered from 0.04% to 0.15% of the fungal genomes. The SSR abundance was not correlated with the genome size, and mono- to tri-nucleotide repeats outnumbered other SSR categories in all of the species examined. In G. lucidum, a repertoire of 2674 SSRs was detected, with mono-nucleotides being the most abundant. SSRs were found in all genomic regions and were more abundant in non-coding regions than coding regions. The highest SSR relative abundance was found in introns (108 SSRs/Mb), followed by intergenic regions (84 SSRs/Mb). A total of 684 SSRs were found in the protein-coding sequences (CDSs) of 588 gene models, with 81.4% of them being tri- or hexa-nucleotides. After scanning for InterPro domains, 280 of these genes were successfully annotated, and 215 of them could be assigned to Gene Ontology (GO) terms. SSRs were also identified in 28 bioactive compound synthesis-related gene models, including one 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), three polysaccharide biosynthesis genes and 24 cytochrome P450 monooxygenases (CYPs). Primers were designed for the identified SSR loci, providing the basis for the future development of SSR markers of this medicinal fungus.
DOI: 10.1016/j.gene.2012.09.127
PubMed: 23069850
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genome-wide analysis of simple sequence repeats in the model medicinal mushroom Ganoderma lucidum.</title><author><name sortKey="Qian, Jun" sort="Qian, Jun" uniqKey="Qian J" first="Jun" last="Qian">Jun Qian</name><affiliation wicri:level="1"><nlm:affiliation>The National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Xu, Haibin" sort="Xu, Haibin" uniqKey="Xu H" first="Haibin" last="Xu">Haibin Xu</name></author><author><name sortKey="Song, Jingyuan" sort="Song, Jingyuan" uniqKey="Song J" first="Jingyuan" last="Song">Jingyuan Song</name></author><author><name sortKey="Xu, Jiang" sort="Xu, Jiang" uniqKey="Xu J" first="Jiang" last="Xu">Jiang Xu</name></author><author><name sortKey="Zhu, Yingjie" sort="Zhu, Yingjie" uniqKey="Zhu Y" first="Yingjie" last="Zhu">Yingjie Zhu</name></author><author><name sortKey="Chen, Shilin" sort="Chen, Shilin" uniqKey="Chen S" first="Shilin" last="Chen">Shilin Chen</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2013">2013</date><idno type="RBID">pubmed:23069850</idno><idno type="pmid">23069850</idno><idno type="doi">10.1016/j.gene.2012.09.127</idno><idno type="wicri:Area/Main/Corpus">000397</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000397</idno><idno type="wicri:Area/Main/Curation">000397</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000397</idno><idno type="wicri:Area/Main/Exploration">000397</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Genome-wide analysis of simple sequence repeats in the model medicinal mushroom Ganoderma lucidum.</title><author><name sortKey="Qian, Jun" sort="Qian, Jun" uniqKey="Qian J" first="Jun" last="Qian">Jun Qian</name><affiliation wicri:level="1"><nlm:affiliation>The National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Xu, Haibin" sort="Xu, Haibin" uniqKey="Xu H" first="Haibin" last="Xu">Haibin Xu</name></author><author><name sortKey="Song, Jingyuan" sort="Song, Jingyuan" uniqKey="Song J" first="Jingyuan" last="Song">Jingyuan Song</name></author><author><name sortKey="Xu, Jiang" sort="Xu, Jiang" uniqKey="Xu J" first="Jiang" last="Xu">Jiang Xu</name></author><author><name sortKey="Zhu, Yingjie" sort="Zhu, Yingjie" uniqKey="Zhu Y" first="Yingjie" last="Zhu">Yingjie Zhu</name></author><author><name sortKey="Chen, Shilin" sort="Chen, Shilin" uniqKey="Chen S" first="Shilin" last="Chen">Shilin Chen</name></author></analytic><series><title level="j">Gene</title><idno type="eISSN">1879-0038</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Fungal Proteins (genetics)</term><term>Fungal Proteins (metabolism)</term><term>Genes, Fungal (MeSH)</term><term>Genetic Markers (MeSH)</term><term>Genome-Wide Association Study (MeSH)</term><term>Introns (genetics)</term><term>Microsatellite Repeats (MeSH)</term><term>Reishi (genetics)</term><term>Reishi (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Gènes fongiques (MeSH)</term><term>Introns (génétique)</term><term>Marqueurs génétiques (MeSH)</term><term>Protéines fongiques (génétique)</term><term>Protéines fongiques (métabolisme)</term><term>Reishi (génétique)</term><term>Reishi (métabolisme)</term><term>Répétitions microsatellites (MeSH)</term><term>Étude d'association pangénomique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Fungal Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Fungal Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Introns</term><term>Reishi</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Introns</term><term>Protéines fongiques</term><term>Reishi</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Reishi</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Protéines fongiques</term><term>Reishi</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genes, Fungal</term><term>Genetic Markers</term><term>Genome-Wide Association Study</term><term>Microsatellite Repeats</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Gènes fongiques</term><term>Marqueurs génétiques</term><term>Répétitions microsatellites</term><term>Étude d'association pangénomique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Simple sequence repeats (SSRs) or microsatellites are one of the most popular sources of genetic markers and play a significant role in gene function and genome organization. We identified SSRs in the genome of Ganoderma lucidum and analyzed their frequency and distribution in different genomic regions. We also compared the SSRs in G. lucidum with six other Agaricomycetes genomes: Coprinopsis cinerea, Laccaria bicolor, Phanerochaete chrysosporium, Postia placenta, Schizophyllum commune and Serpula lacrymans. Based on our search criteria, the total number of SSRs found ranged from 1206 to 6104 and covered from 0.04% to 0.15% of the fungal genomes. The SSR abundance was not correlated with the genome size, and mono- to tri-nucleotide repeats outnumbered other SSR categories in all of the species examined. In G. lucidum, a repertoire of 2674 SSRs was detected, with mono-nucleotides being the most abundant. SSRs were found in all genomic regions and were more abundant in non-coding regions than coding regions. The highest SSR relative abundance was found in introns (108 SSRs/Mb), followed by intergenic regions (84 SSRs/Mb). A total of 684 SSRs were found in the protein-coding sequences (CDSs) of 588 gene models, with 81.4% of them being tri- or hexa-nucleotides. After scanning for InterPro domains, 280 of these genes were successfully annotated, and 215 of them could be assigned to Gene Ontology (GO) terms. SSRs were also identified in 28 bioactive compound synthesis-related gene models, including one 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), three polysaccharide biosynthesis genes and 24 cytochrome P450 monooxygenases (CYPs). Primers were designed for the identified SSR loci, providing the basis for the future development of SSR markers of this medicinal fungus.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23069850</PMID><DateCompleted><Year>2013</Year><Month>02</Month><Day>01</Day></DateCompleted><DateRevised><Year>2012</Year><Month>12</Month><Day>03</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1879-0038</ISSN><JournalIssue CitedMedium="Internet"><Volume>512</Volume><Issue>2</Issue><PubDate><Year>2013</Year><Month>Jan</Month><Day>10</Day></PubDate></JournalIssue><Title>Gene</Title><ISOAbbreviation>Gene</ISOAbbreviation></Journal><ArticleTitle>Genome-wide analysis of simple sequence repeats in the model medicinal mushroom Ganoderma lucidum.</ArticleTitle><Pagination><MedlinePgn>331-6</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.gene.2012.09.127</ELocationID><ELocationID EIdType="pii" ValidYN="Y">S0378-1119(12)01236-X</ELocationID><Abstract><AbstractText>Simple sequence repeats (SSRs) or microsatellites are one of the most popular sources of genetic markers and play a significant role in gene function and genome organization. We identified SSRs in the genome of Ganoderma lucidum and analyzed their frequency and distribution in different genomic regions. We also compared the SSRs in G. lucidum with six other Agaricomycetes genomes: Coprinopsis cinerea, Laccaria bicolor, Phanerochaete chrysosporium, Postia placenta, Schizophyllum commune and Serpula lacrymans. Based on our search criteria, the total number of SSRs found ranged from 1206 to 6104 and covered from 0.04% to 0.15% of the fungal genomes. The SSR abundance was not correlated with the genome size, and mono- to tri-nucleotide repeats outnumbered other SSR categories in all of the species examined. In G. lucidum, a repertoire of 2674 SSRs was detected, with mono-nucleotides being the most abundant. SSRs were found in all genomic regions and were more abundant in non-coding regions than coding regions. The highest SSR relative abundance was found in introns (108 SSRs/Mb), followed by intergenic regions (84 SSRs/Mb). A total of 684 SSRs were found in the protein-coding sequences (CDSs) of 588 gene models, with 81.4% of them being tri- or hexa-nucleotides. After scanning for InterPro domains, 280 of these genes were successfully annotated, and 215 of them could be assigned to Gene Ontology (GO) terms. SSRs were also identified in 28 bioactive compound synthesis-related gene models, including one 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), three polysaccharide biosynthesis genes and 24 cytochrome P450 monooxygenases (CYPs). Primers were designed for the identified SSR loci, providing the basis for the future development of SSR markers of this medicinal fungus.</AbstractText><CopyrightInformation>Copyright © 2012 Elsevier B.V. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Qian</LastName><ForeName>Jun</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>The National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, PR China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Haibin</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Song</LastName><ForeName>Jingyuan</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Jiang</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Zhu</LastName><ForeName>Yingjie</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Shilin</ForeName><Initials>S</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>2012</Year><Month>10</Month><Day>13</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>Gene</MedlineTA><NlmUniqueID>7706761</NlmUniqueID><ISSNLinking>0378-1119</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005656">Fungal Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005819">Genetic Markers</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D005656" MajorTopicYN="N">Fungal Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005800" MajorTopicYN="Y">Genes, Fungal</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005819" MajorTopicYN="N">Genetic Markers</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055106" MajorTopicYN="N">Genome-Wide Association Study</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D007438" MajorTopicYN="N">Introns</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018895" MajorTopicYN="Y">Microsatellite Repeats</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020940" MajorTopicYN="N">Reishi</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2012</Year><Month>08</Month><Day>15</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2012</Year><Month>09</Month><Day>11</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2012</Year><Month>09</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2012</Year><Month>10</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2012</Year><Month>10</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2013</Year><Month>2</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">23069850</ArticleId><ArticleId IdType="pii">S0378-1119(12)01236-X</ArticleId><ArticleId IdType="doi">10.1016/j.gene.2012.09.127</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country><settlement><li>Pékin</li></settlement></list><tree><noCountry><name sortKey="Chen, Shilin" sort="Chen, Shilin" uniqKey="Chen S" first="Shilin" last="Chen">Shilin Chen</name><name sortKey="Song, Jingyuan" sort="Song, Jingyuan" uniqKey="Song J" first="Jingyuan" last="Song">Jingyuan Song</name><name sortKey="Xu, Haibin" sort="Xu, Haibin" uniqKey="Xu H" first="Haibin" last="Xu">Haibin Xu</name><name sortKey="Xu, Jiang" sort="Xu, Jiang" uniqKey="Xu J" first="Jiang" last="Xu">Jiang Xu</name><name sortKey="Zhu, Yingjie" sort="Zhu, Yingjie" uniqKey="Zhu Y" first="Yingjie" last="Zhu">Yingjie Zhu</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Qian, Jun" sort="Qian, Jun" uniqKey="Qian J" first="Jun" last="Qian">Jun Qian</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/PhanerochaeteV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000373 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000373 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= PhanerochaeteV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:23069850
|texte= Genome-wide analysis of simple sequence repeats in the model medicinal mushroom Ganoderma lucidum.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:23069850" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PhanerochaeteV1
| This area was generated with Dilib version V0.6.37. |  |