Analysis of expressed sequence tags from Prunus mume flower and fruit and development of simple sequence repeat markers
Identifieur interne : 001B09 ( Main/Exploration ); précédent : 001B08; suivant : 001B10Analysis 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
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000E04
- to stream Pmc, to step Curation: 000E03
- to stream Pmc, to step Checkpoint: 000F74
- to stream Ncbi, to step Merge: 000C00
- to stream Ncbi, to step Curation: 000C00
- to stream Ncbi, to step Checkpoint: 000C00
- to stream Main, to step Merge: 001B47
- to stream Main, to step Curation: 001B09
Le document en format XML
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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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<affiliations><list><country><li>République populaire de Chine</li>
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<tree><country name="République populaire de Chine"><noRegion><name sortKey="Li, Xiaoying" sort="Li, Xiaoying" uniqKey="Li X" first="Xiaoying" last="Li">Xiaoying Li</name>
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<name sortKey="Gao, Zhihong" sort="Gao, Zhihong" uniqKey="Gao Z" first="Zhihong" last="Gao">Zhihong Gao</name>
<name sortKey="Shangguan, Lingfei" sort="Shangguan, Lingfei" uniqKey="Shangguan L" first="Lingfei" last="Shangguan">Lingfei Shangguan</name>
<name sortKey="Song, Changnian" sort="Song, Changnian" uniqKey="Song C" first="Changnian" last="Song">Changnian Song</name>
<name sortKey="Wang, Chen" sort="Wang, Chen" uniqKey="Wang C" first="Chen" last="Wang">Chen Wang</name>
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