Analysis of expressed sequence tags from Prunus mume flower and fruit and development of simple sequence repeat markers
Identifieur interne : 000E03 ( Pmc/Curation ); précédent : 000E02; suivant : 000E04Analysis of expressed sequence tags from Prunus mume flower and fruit and development of simple sequence repeat markers
Auteurs : Xiaoying Li [République populaire de Chine] ; Lingfei Shangguan [République populaire de Chine] ; Changnian Song [République populaire de Chine] ; Chen Wang [République populaire de Chine] ; Zhihong Gao [République populaire de Chine] ; Huaping Yu [République populaire de Chine] ; Jinggui Fang [République populaire de Chine]Source :
- BMC Genetics [ 1471-2156 ] ; 2010.
Abstract
Expressed Sequence Tag (EST) has been a cost-effective tool in molecular biology and represents an abundant valuable resource for genome annotation, gene expression, and comparative genomics in plants.
In this study, we constructed a cDNA library of
We have constructed the first cDNA library of
Url:
DOI: 10.1186/1471-2156-11-66
PubMed: 20626882
PubMed Central: 2920227
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PMC:2920227Le document en format XML
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flower and fruit and development of simple sequence repeat markers</title>
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flower and fruit and development of simple sequence repeat markers</title>
<author><name sortKey="Li, Xiaoying" sort="Li, Xiaoying" uniqKey="Li X" first="Xiaoying" last="Li">Xiaoying Li</name>
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<author><name sortKey="Shangguan, Lingfei" sort="Shangguan, Lingfei" uniqKey="Shangguan L" first="Lingfei" last="Shangguan">Lingfei Shangguan</name>
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<wicri:regionArea>College of Horticulture, Nanjing Agricultural University, Nanjing 210095</wicri:regionArea>
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<author><name sortKey="Song, Changnian" sort="Song, Changnian" uniqKey="Song C" first="Changnian" last="Song">Changnian Song</name>
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<author><name sortKey="Wang, Chen" sort="Wang, Chen" uniqKey="Wang C" first="Chen" last="Wang">Chen Wang</name>
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<wicri:regionArea>College of Horticulture, Nanjing Agricultural University, Nanjing 210095</wicri:regionArea>
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<author><name sortKey="Yu, Huaping" sort="Yu, Huaping" uniqKey="Yu H" first="Huaping" last="Yu">Huaping Yu</name>
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<author><name sortKey="Fang, Jinggui" sort="Fang, Jinggui" uniqKey="Fang J" first="Jinggui" last="Fang">Jinggui Fang</name>
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<series><title level="j">BMC Genetics</title>
<idno type="eISSN">1471-2156</idno>
<imprint><date when="2010">2010</date>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Expressed Sequence Tag (EST) has been a cost-effective tool in molecular biology and represents an abundant valuable resource for genome annotation, gene expression, and comparative genomics in plants.</p>
</sec>
<sec><title>Results</title>
<p>In this study, we constructed a cDNA library of <italic>Prunus mume </italic>
flower and fruit, sequenced 10,123 clones of the library, and obtained 8,656 expressed sequence tag (EST) sequences with high quality. The ESTs were assembled into 4,473 unigenes composed of 1,492 contigs and 2,981 singletons and that have been deposited in NCBI (accession IDs: GW868575 - GW873047), among which 1,294 unique ESTs were with known or putative functions. Furthermore, we found 1,233 putative simple sequence repeats (SSRs) in the <italic>P. mume </italic>
unigene dataset. We randomly tested 42 pairs of PCR primers flanking potential SSRs, and 14 pairs were identified as true-to-type SSR loci and could amplify polymorphic bands from 20 individual plants of <italic>P. mume</italic>
. We further used the 14 EST-SSR primer pairs to test the transferability on peach and plum. The result showed that nearly 89% of the primer pairs produced target PCR bands in the two species. A high level of marker polymorphism was observed in the plum species (65%) and low in the peach (46%), and the clustering analysis of the three species indicated that these SSR markers were useful in the evaluation of genetic relationships and diversity between and within the <italic>Prunus </italic>
species.</p>
</sec>
<sec><title>Conclusions</title>
<p>We have constructed the first cDNA library of <italic>P. mume </italic>
flower and fruit, and our data provide sets of molecular biology resources for <italic>P. mume </italic>
and other <italic>Prunus </italic>
species. These resources will be useful for further study such as genome annotation, new gene discovery, gene functional analysis, molecular breeding, evolution and comparative genomics between <italic>Prunus </italic>
species.</p>
</sec>
</div>
</front>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Genet</journal-id>
<journal-title-group><journal-title>BMC Genetics</journal-title>
</journal-title-group>
<issn pub-type="epub">1471-2156</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">20626882</article-id>
<article-id pub-id-type="pmc">2920227</article-id>
<article-id pub-id-type="publisher-id">1471-2156-11-66</article-id>
<article-id pub-id-type="doi">10.1186/1471-2156-11-66</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Analysis of expressed sequence tags from <italic>Prunus mume </italic>
flower and fruit and development of simple sequence repeat markers</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" id="A1"><name><surname>Li</surname>
<given-names>Xiaoying</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>2009204001@njau.edu.cn</email>
</contrib>
<contrib contrib-type="author" id="A2"><name><surname>Shangguan</surname>
<given-names>Lingfei</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>2008104020@njau.edu.cn</email>
</contrib>
<contrib contrib-type="author" id="A3"><name><surname>Song</surname>
<given-names>Changnian</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>2008204002@njau.edu.cn</email>
</contrib>
<contrib contrib-type="author" id="A4"><name><surname>Wang</surname>
<given-names>Chen</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>2008104022@njau.edu.cn</email>
</contrib>
<contrib contrib-type="author" id="A5"><name><surname>Gao</surname>
<given-names>Zhihong</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>gaozhihong@njau.edu.cn</email>
</contrib>
<contrib contrib-type="author" id="A6"><name><surname>Yu</surname>
<given-names>Huaping</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>2008104024@njau.edu.cn</email>
</contrib>
<contrib contrib-type="author" corresp="yes" id="A7"><name><surname>Fang</surname>
<given-names>Jinggui</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>fanggg@njau.edu.cn</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China</aff>
<pub-date pub-type="collection"><year>2010</year>
</pub-date>
<pub-date pub-type="epub"><day>13</day>
<month>7</month>
<year>2010</year>
</pub-date>
<volume>11</volume>
<fpage>66</fpage>
<lpage>66</lpage>
<history><date date-type="received"><day>13</day>
<month>5</month>
<year>2010</year>
</date>
<date date-type="accepted"><day>13</day>
<month>7</month>
<year>2010</year>
</date>
</history>
<permissions><copyright-statement>Copyright ©2010 Li et al; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2010</copyright-year>
<copyright-holder>Li et al; licensee BioMed Central Ltd.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<self-uri xlink:href="http://www.biomedcentral.com/1471-2156/11/66"></self-uri>
<abstract><sec><title>Background</title>
<p>Expressed Sequence Tag (EST) has been a cost-effective tool in molecular biology and represents an abundant valuable resource for genome annotation, gene expression, and comparative genomics in plants.</p>
</sec>
<sec><title>Results</title>
<p>In this study, we constructed a cDNA library of <italic>Prunus mume </italic>
flower and fruit, sequenced 10,123 clones of the library, and obtained 8,656 expressed sequence tag (EST) sequences with high quality. The ESTs were assembled into 4,473 unigenes composed of 1,492 contigs and 2,981 singletons and that have been deposited in NCBI (accession IDs: GW868575 - GW873047), among which 1,294 unique ESTs were with known or putative functions. Furthermore, we found 1,233 putative simple sequence repeats (SSRs) in the <italic>P. mume </italic>
unigene dataset. We randomly tested 42 pairs of PCR primers flanking potential SSRs, and 14 pairs were identified as true-to-type SSR loci and could amplify polymorphic bands from 20 individual plants of <italic>P. mume</italic>
. We further used the 14 EST-SSR primer pairs to test the transferability on peach and plum. The result showed that nearly 89% of the primer pairs produced target PCR bands in the two species. A high level of marker polymorphism was observed in the plum species (65%) and low in the peach (46%), and the clustering analysis of the three species indicated that these SSR markers were useful in the evaluation of genetic relationships and diversity between and within the <italic>Prunus </italic>
species.</p>
</sec>
<sec><title>Conclusions</title>
<p>We have constructed the first cDNA library of <italic>P. mume </italic>
flower and fruit, and our data provide sets of molecular biology resources for <italic>P. mume </italic>
and other <italic>Prunus </italic>
species. These resources will be useful for further study such as genome annotation, new gene discovery, gene functional analysis, molecular breeding, evolution and comparative genomics between <italic>Prunus </italic>
species.</p>
</sec>
</abstract>
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