An overview of the Phalaenopsis orchid genome through BAC end sequence analysis.
Identifieur interne : 002F98 ( Main/Exploration ); précédent : 002F97; suivant : 002F99An overview of the Phalaenopsis orchid genome through BAC end sequence analysis.
Auteurs : Chia-Chi Hsu [Taïwan] ; Yu-Lin Chung ; Tien-Chih Chen ; Yu-Ling Lee ; Yi-Tzu Kuo ; Wen-Chieh Tsai ; Yu-Yun Hsiao ; Yun-Wen Chen ; Wen-Luan Wu ; Hong-Hwa ChenSource :
- BMC plant biology [ 1471-2229 ] ; 2011.
Descripteurs français
- KwdFr :
- ADN des chloroplastes (génétique), Analyse de séquence d'ADN (méthodes), Annotation de séquence moléculaire (MeSH), Bases de données d'acides nucléiques (MeSH), Cartographie chromosomique (MeSH), Chromosomes artificiels de bactérie (génétique), Données de séquences moléculaires (MeSH), Génome végétal (génétique), Marqueurs génétiques (MeSH), Noyau de la cellule (génétique), Orchidaceae (génétique), Réaction de polymérisation en chaîne (MeSH), Répétitions minisatellites (génétique), Spécificité d'espèce (MeSH), Synténie (génétique), Séquence nucléotidique (MeSH), Séquence riche en AT (génétique).
- MESH :
- génétique : ADN des chloroplastes, Chromosomes artificiels de bactérie, Génome végétal, Noyau de la cellule, Orchidaceae, Répétitions minisatellites, Synténie, Séquence riche en AT.
- méthodes : Analyse de séquence d'ADN.
- Annotation de séquence moléculaire, Bases de données d'acides nucléiques, Cartographie chromosomique, Données de séquences moléculaires, Marqueurs génétiques, Réaction de polymérisation en chaîne, Spécificité d'espèce, Séquence nucléotidique.
English descriptors
- KwdEn :
- AT Rich Sequence (genetics), Base Sequence (MeSH), Cell Nucleus (genetics), Chromosome Mapping (MeSH), Chromosomes, Artificial, Bacterial (genetics), DNA, Chloroplast (genetics), Databases, Nucleic Acid (MeSH), Genetic Markers (MeSH), Genome, Plant (genetics), Minisatellite Repeats (genetics), Molecular Sequence Annotation (MeSH), Molecular Sequence Data (MeSH), Orchidaceae (genetics), Polymerase Chain Reaction (MeSH), Sequence Analysis, DNA (methods), Species Specificity (MeSH), Synteny (genetics).
- MESH :
- chemical , genetics : DNA, Chloroplast.
- genetics : AT Rich Sequence, Cell Nucleus, Chromosomes, Artificial, Bacterial, Genome, Plant, Minisatellite Repeats, Orchidaceae, Synteny.
- methods : Sequence Analysis, DNA.
- Base Sequence, Chromosome Mapping, Databases, Nucleic Acid, Genetic Markers, Molecular Sequence Annotation, Molecular Sequence Data, Polymerase Chain Reaction, Species Specificity.
Abstract
BACKGROUND
Phalaenopsis orchids are popular floral crops, and development of new cultivars is economically important to floricultural industries worldwide. Analysis of orchid genes could facilitate orchid improvement. Bacterial artificial chromosome (BAC) end sequences (BESs) can provide the first glimpses into the sequence composition of a novel genome and can yield molecular markers for use in genetic mapping and breeding.
RESULTS
We used two BAC libraries (constructed using the BamHI and HindIII restriction enzymes) of Phalaenopsis equestris to generate pair-end sequences from 2,920 BAC clones (71.4% and 28.6% from the BamHI and HindIII libraries, respectively), at a success rate of 95.7%. A total of 5,535 BESs were generated, representing 4.5 Mb, or about 0.3% of the Phalaenopsis genome. The trimmed sequences ranged from 123 to 1,397 base pairs (bp) in size, with an average edited read length of 821 bp. When these BESs were subjected to sequence homology searches, it was found that 641 (11.6%) were predicted to represent protein-encoding regions, whereas 1,272 (23.0%) contained repetitive DNA. Most of the repetitive DNA sequences were gypsy- and copia-like retrotransposons (41.9% and 12.8%, respectively), whereas only 10.8% were DNA transposons. Further, 950 potential simple sequence repeats (SSRs) were discovered. Dinucleotides were the most abundant repeat motifs; AT/TA dimer repeats were the most frequent SSRs, representing 253 (26.6%) of all identified SSRs. Microsynteny analysis revealed that more BESs mapped to the whole-genome sequences of poplar than to those of grape or Arabidopsis, and even fewer mapped to the rice genome. This work will facilitate analysis of the Phalaenopsis genome, and will help clarify similarities and differences in genome composition between orchids and other plant species.
CONCLUSION
Using BES analysis, we obtained an overview of the Phalaenopsis genome in terms of gene abundance, the presence of repetitive DNA and SSR markers, and the extent of microsynteny with other plant species. This work provides a basis for future physical mapping of the Phalaenopsis genome and advances our knowledge thereof.
DOI: 10.1186/1471-2229-11-3
PubMed: 21208460
PubMed Central: PMC3027094
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Chen</name></author><author><name sortKey="Wu, Wen Luan" sort="Wu, Wen Luan" uniqKey="Wu W" first="Wen-Luan" last="Wu">Wen-Luan Wu</name></author><author><name sortKey="Chen, Hong Hwa" sort="Chen, Hong Hwa" uniqKey="Chen H" first="Hong-Hwa" last="Chen">Hong-Hwa Chen</name></author></analytic><series><title level="j">BMC plant biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>AT Rich Sequence (genetics)</term><term>Base Sequence (MeSH)</term><term>Cell Nucleus (genetics)</term><term>Chromosome Mapping (MeSH)</term><term>Chromosomes, Artificial, Bacterial (genetics)</term><term>DNA, Chloroplast (genetics)</term><term>Databases, Nucleic Acid (MeSH)</term><term>Genetic Markers (MeSH)</term><term>Genome, Plant (genetics)</term><term>Minisatellite Repeats (genetics)</term><term>Molecular Sequence Annotation (MeSH)</term><term>Molecular Sequence Data (MeSH)</term><term>Orchidaceae (genetics)</term><term>Polymerase Chain Reaction (MeSH)</term><term>Sequence Analysis, DNA (methods)</term><term>Species Specificity (MeSH)</term><term>Synteny (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN des chloroplastes (génétique)</term><term>Analyse de séquence d'ADN (méthodes)</term><term>Annotation de séquence moléculaire (MeSH)</term><term>Bases de données d'acides nucléiques (MeSH)</term><term>Cartographie chromosomique (MeSH)</term><term>Chromosomes artificiels de bactérie (génétique)</term><term>Données de séquences moléculaires (MeSH)</term><term>Génome végétal (génétique)</term><term>Marqueurs génétiques (MeSH)</term><term>Noyau de la cellule (génétique)</term><term>Orchidaceae (génétique)</term><term>Réaction de polymérisation en chaîne (MeSH)</term><term>Répétitions minisatellites (génétique)</term><term>Spécificité d'espèce (MeSH)</term><term>Synténie 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xml:lang="fr"><term>Analyse de séquence d'ADN</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Chromosome Mapping</term><term>Databases, Nucleic Acid</term><term>Genetic Markers</term><term>Molecular Sequence Annotation</term><term>Molecular Sequence Data</term><term>Polymerase Chain Reaction</term><term>Species Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Annotation de séquence moléculaire</term><term>Bases de données d'acides nucléiques</term><term>Cartographie chromosomique</term><term>Données de séquences moléculaires</term><term>Marqueurs génétiques</term><term>Réaction de polymérisation en chaîne</term><term>Spécificité d'espèce</term><term>Séquence nucléotidique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Phalaenopsis orchids are popular floral crops, and development of new cultivars is economically important to floricultural industries worldwide. Analysis of orchid genes could facilitate orchid improvement. Bacterial artificial chromosome (BAC) end sequences (BESs) can provide the first glimpses into the sequence composition of a novel genome and can yield molecular markers for use in genetic mapping and breeding.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We used two BAC libraries (constructed using the BamHI and HindIII restriction enzymes) of Phalaenopsis equestris to generate pair-end sequences from 2,920 BAC clones (71.4% and 28.6% from the BamHI and HindIII libraries, respectively), at a success rate of 95.7%. A total of 5,535 BESs were generated, representing 4.5 Mb, or about 0.3% of the Phalaenopsis genome. The trimmed sequences ranged from 123 to 1,397 base pairs (bp) in size, with an average edited read length of 821 bp. When these BESs were subjected to sequence homology searches, it was found that 641 (11.6%) were predicted to represent protein-encoding regions, whereas 1,272 (23.0%) contained repetitive DNA. Most of the repetitive DNA sequences were gypsy- and copia-like retrotransposons (41.9% and 12.8%, respectively), whereas only 10.8% were DNA transposons. Further, 950 potential simple sequence repeats (SSRs) were discovered. Dinucleotides were the most abundant repeat motifs; AT/TA dimer repeats were the most frequent SSRs, representing 253 (26.6%) of all identified SSRs. Microsynteny analysis revealed that more BESs mapped to the whole-genome sequences of poplar than to those of grape or Arabidopsis, and even fewer mapped to the rice genome. This work will facilitate analysis of the Phalaenopsis genome, and will help clarify similarities and differences in genome composition between orchids and other plant species.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSION</b></p><p>Using BES analysis, we obtained an overview of the Phalaenopsis genome in terms of gene abundance, the presence of repetitive DNA and SSR markers, and the extent of microsynteny with other plant species. This work provides a basis for future physical mapping of the Phalaenopsis genome and advances our knowledge thereof.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21208460</PMID><DateCompleted><Year>2011</Year><Month>04</Month><Day>25</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>11</Volume><PubDate><Year>2011</Year><Month>Jan</Month><Day>06</Day></PubDate></JournalIssue><Title>BMC plant biology</Title><ISOAbbreviation>BMC Plant Biol</ISOAbbreviation></Journal><ArticleTitle>An overview of the Phalaenopsis orchid genome through BAC end sequence analysis.</ArticleTitle><Pagination><MedlinePgn>3</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2229-11-3</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Phalaenopsis orchids are popular floral crops, and development of new cultivars is economically important to floricultural industries worldwide. Analysis of orchid genes could facilitate orchid improvement. Bacterial artificial chromosome (BAC) end sequences (BESs) can provide the first glimpses into the sequence composition of a novel genome and can yield molecular markers for use in genetic mapping and breeding.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We used two BAC libraries (constructed using the BamHI and HindIII restriction enzymes) of Phalaenopsis equestris to generate pair-end sequences from 2,920 BAC clones (71.4% and 28.6% from the BamHI and HindIII libraries, respectively), at a success rate of 95.7%. A total of 5,535 BESs were generated, representing 4.5 Mb, or about 0.3% of the Phalaenopsis genome. The trimmed sequences ranged from 123 to 1,397 base pairs (bp) in size, with an average edited read length of 821 bp. When these BESs were subjected to sequence homology searches, it was found that 641 (11.6%) were predicted to represent protein-encoding regions, whereas 1,272 (23.0%) contained repetitive DNA. Most of the repetitive DNA sequences were gypsy- and copia-like retrotransposons (41.9% and 12.8%, respectively), whereas only 10.8% were DNA transposons. Further, 950 potential simple sequence repeats (SSRs) were discovered. Dinucleotides were the most abundant repeat motifs; AT/TA dimer repeats were the most frequent SSRs, representing 253 (26.6%) of all identified SSRs. Microsynteny analysis revealed that more BESs mapped to the whole-genome sequences of poplar than to those of grape or Arabidopsis, and even fewer mapped to the rice genome. This work will facilitate analysis of the Phalaenopsis genome, and will help clarify similarities and differences in genome composition between orchids and other plant species.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">Using BES analysis, we obtained an overview of the Phalaenopsis genome in terms of gene abundance, the presence of repetitive DNA and SSR markers, and the extent of microsynteny with other plant species. This work provides a basis for future physical mapping of the Phalaenopsis genome and advances our knowledge thereof.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hsu</LastName><ForeName>Chia-Chi</ForeName><Initials>CC</Initials><AffiliationInfo><Affiliation>Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chung</LastName><ForeName>Yu-Lin</ForeName><Initials>YL</Initials></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Tien-Chih</ForeName><Initials>TC</Initials></Author><Author ValidYN="Y"><LastName>Lee</LastName><ForeName>Yu-Ling</ForeName><Initials>YL</Initials></Author><Author ValidYN="Y"><LastName>Kuo</LastName><ForeName>Yi-Tzu</ForeName><Initials>YT</Initials></Author><Author ValidYN="Y"><LastName>Tsai</LastName><ForeName>Wen-Chieh</ForeName><Initials>WC</Initials></Author><Author ValidYN="Y"><LastName>Hsiao</LastName><ForeName>Yu-Yun</ForeName><Initials>YY</Initials></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Yun-Wen</ForeName><Initials>YW</Initials></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Wen-Luan</ForeName><Initials>WL</Initials></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Hong-Hwa</ForeName><Initials>HH</Initials></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>GENBANK</DataBankName><AccessionNumberList><AccessionNumber>HN176659</AccessionNumber><AccessionNumber>HN176660</AccessionNumber><AccessionNumber>HN176661</AccessionNumber><AccessionNumber>HN176662</AccessionNumber><AccessionNumber>HN176663</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. 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IdType="pubmed">17721507</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>Taïwan</li></country></list><tree><noCountry><name sortKey="Chen, Hong Hwa" sort="Chen, Hong Hwa" uniqKey="Chen H" first="Hong-Hwa" last="Chen">Hong-Hwa Chen</name><name sortKey="Chen, Tien Chih" sort="Chen, Tien Chih" uniqKey="Chen T" first="Tien-Chih" last="Chen">Tien-Chih Chen</name><name sortKey="Chen, Yun Wen" sort="Chen, Yun Wen" uniqKey="Chen Y" first="Yun-Wen" last="Chen">Yun-Wen Chen</name><name sortKey="Chung, Yu Lin" sort="Chung, Yu Lin" uniqKey="Chung Y" first="Yu-Lin" last="Chung">Yu-Lin Chung</name><name sortKey="Hsiao, Yu Yun" sort="Hsiao, Yu Yun" uniqKey="Hsiao Y" first="Yu-Yun" last="Hsiao">Yu-Yun Hsiao</name><name sortKey="Kuo, Yi Tzu" sort="Kuo, Yi Tzu" uniqKey="Kuo Y" first="Yi-Tzu" last="Kuo">Yi-Tzu Kuo</name><name sortKey="Lee, Yu Ling" sort="Lee, Yu Ling" uniqKey="Lee Y" first="Yu-Ling" last="Lee">Yu-Ling Lee</name><name sortKey="Tsai, Wen Chieh" sort="Tsai, Wen Chieh" uniqKey="Tsai W" first="Wen-Chieh" last="Tsai">Wen-Chieh Tsai</name><name sortKey="Wu, Wen Luan" sort="Wu, Wen Luan" uniqKey="Wu W" first="Wen-Luan" last="Wu">Wen-Luan Wu</name></noCountry><country name="Taïwan"><noRegion><name sortKey="Hsu, Chia Chi" sort="Hsu, Chia Chi" uniqKey="Hsu C" first="Chia-Chi" last="Hsu">Chia-Chi Hsu</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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