In silico search, characterization and validation of new EST-SSR markers in the genus Prunus
Identifieur interne : 000163 ( Main/Exploration ); précédent : 000162; suivant : 000164In silico search, characterization and validation of new EST-SSR markers in the genus Prunus
Auteurs : Karim Sorkheh [Iran] ; Angela S. Prudencio [Espagne] ; Azim Ghebinejad [Iran] ; Mehrana Kohei Dehkordi [Iran] ; Deniz Erogul [Turquie] ; Manuel Rubio [Espagne] ; Pedro Martínez-G Mez [Espagne]Source :
- BMC Research Notes [ 1756-0500 ] ; 2016.
Abstract
Simple sequence repeats (SSRs) are defined as sequence repeat units between 1 and 6 bp that occur in both coding and non-coding regions abundant in eukaryotic genomes, which may affect the expression of genes. In this study, expressed sequence tags (ESTs) of eight
A total of 316 SSRs were identified using MISA software. Dinucleotide SSR motifs (26.31 %) were found to be the most abundant type of repeats, followed by tri- (14.58 %), tetra- (0.53 %), and penta- (0.27 %) nucleotide motifs. An attempt was made to design primer pairs for 316 identified SSRs but these were successful for only 175 SSR sequences. The positions of SSRs with respect to ORFs were detected, and annotation of sequences containing SSRs was performed to assign function to each sequence. SSRs were also characterized (in terms of position in the reference genome and associated gene) using the two available
Findings will aid analysis of functionally important molecular markers and facilitate the analysis of genetic diversity.
The online version of this article (doi:10.1186/s13104-016-2143-y) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s13104-016-2143-y
PubMed: 27389023
PubMed Central: 4937603
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">In silico search, characterization and validation of new EST-SSR markers in the genus <italic>Prunus</italic></title><author><name sortKey="Sorkheh, Karim" sort="Sorkheh, Karim" uniqKey="Sorkheh K" first="Karim" last="Sorkheh">Karim Sorkheh</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P.O. Box. 61355/144, Ahvaz, Iran</nlm:aff><country xml:lang="fr">Iran</country><wicri:regionArea>Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P.O. Box. 61355/144, Ahvaz</wicri:regionArea><wicri:noRegion>Ahvaz</wicri:noRegion></affiliation></author><author><name sortKey="Prudencio, Angela S" sort="Prudencio, Angela S" uniqKey="Prudencio A" first="Angela S." last="Prudencio">Angela S. Prudencio</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), PO Box 164, E-30100 Espinardo-Murcia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), PO Box 164, E-30100 Espinardo-Murcia</wicri:regionArea><placeName><region nuts="2" type="communauté">Région de Murcie</region></placeName></affiliation></author><author><name sortKey="Ghebinejad, Azim" sort="Ghebinejad, Azim" uniqKey="Ghebinejad A" first="Azim" last="Ghebinejad">Azim Ghebinejad</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P.O. Box. 61355/144, Ahvaz, Iran</nlm:aff><country xml:lang="fr">Iran</country><wicri:regionArea>Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P.O. Box. 61355/144, Ahvaz</wicri:regionArea><wicri:noRegion>Ahvaz</wicri:noRegion></affiliation></author><author><name sortKey="Dehkordi, Mehrana Kohei" sort="Dehkordi, Mehrana Kohei" uniqKey="Dehkordi M" first="Mehrana Kohei" last="Dehkordi">Mehrana Kohei Dehkordi</name><affiliation wicri:level="1"><nlm:aff id="Aff3">Department of Agronomy, Faculty of Agriculture, Payame Noor University, P.O. Box. 19395-3697, Tehran, Iran</nlm:aff><country xml:lang="fr">Iran</country><wicri:regionArea>Department of Agronomy, Faculty of Agriculture, Payame Noor University, P.O. Box. 19395-3697, Tehran</wicri:regionArea><wicri:noRegion>Tehran</wicri:noRegion></affiliation></author><author><name sortKey="Erogul, Deniz" sort="Erogul, Deniz" uniqKey="Erogul D" first="Deniz" last="Erogul">Deniz Erogul</name><affiliation wicri:level="1"><nlm:aff id="Aff4">Department of Horticulture, Faculty of Agriculture, University of Ege, Bornova, 35100 Izmir, Turkey</nlm:aff><country xml:lang="fr">Turquie</country><wicri:regionArea>Department of Horticulture, Faculty of Agriculture, University of Ege, Bornova, 35100 Izmir</wicri:regionArea><wicri:noRegion>35100 Izmir</wicri:noRegion></affiliation></author><author><name sortKey="Rubio, Manuel" sort="Rubio, Manuel" uniqKey="Rubio M" first="Manuel" last="Rubio">Manuel Rubio</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), PO Box 164, E-30100 Espinardo-Murcia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), PO Box 164, E-30100 Espinardo-Murcia</wicri:regionArea><placeName><region nuts="2" type="communauté">Région de Murcie</region></placeName></affiliation></author><author><name sortKey="Martinez G Mez, Pedro" sort="Martinez G Mez, Pedro" uniqKey="Martinez G Mez P" first="Pedro" last="Martínez-G Mez">Pedro Martínez-G Mez</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), PO Box 164, E-30100 Espinardo-Murcia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), PO Box 164, E-30100 Espinardo-Murcia</wicri:regionArea><placeName><region nuts="2" type="communauté">Région de Murcie</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27389023</idno><idno type="pmc">4937603</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937603</idno><idno type="RBID">PMC:4937603</idno><idno type="doi">10.1186/s13104-016-2143-y</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000652</idno><idno type="wicri:Area/Pmc/Curation">000651</idno><idno type="wicri:Area/Pmc/Checkpoint">000133</idno><idno type="wicri:Area/Ncbi/Merge">002102</idno><idno type="wicri:Area/Ncbi/Curation">002102</idno><idno type="wicri:Area/Ncbi/Checkpoint">002102</idno><idno type="wicri:Area/Main/Merge">000163</idno><idno type="wicri:Area/Main/Curation">000163</idno><idno type="wicri:Area/Main/Exploration">000163</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">In silico search, characterization and validation of new EST-SSR markers in the genus <italic>Prunus</italic></title><author><name sortKey="Sorkheh, Karim" sort="Sorkheh, Karim" uniqKey="Sorkheh K" first="Karim" last="Sorkheh">Karim Sorkheh</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P.O. Box. 61355/144, Ahvaz, Iran</nlm:aff><country xml:lang="fr">Iran</country><wicri:regionArea>Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P.O. Box. 61355/144, Ahvaz</wicri:regionArea><wicri:noRegion>Ahvaz</wicri:noRegion></affiliation></author><author><name sortKey="Prudencio, Angela S" sort="Prudencio, Angela S" uniqKey="Prudencio A" first="Angela S." last="Prudencio">Angela S. Prudencio</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), PO Box 164, E-30100 Espinardo-Murcia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), PO Box 164, E-30100 Espinardo-Murcia</wicri:regionArea><placeName><region nuts="2" type="communauté">Région de Murcie</region></placeName></affiliation></author><author><name sortKey="Ghebinejad, Azim" sort="Ghebinejad, Azim" uniqKey="Ghebinejad A" first="Azim" last="Ghebinejad">Azim Ghebinejad</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P.O. Box. 61355/144, Ahvaz, Iran</nlm:aff><country xml:lang="fr">Iran</country><wicri:regionArea>Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P.O. Box. 61355/144, Ahvaz</wicri:regionArea><wicri:noRegion>Ahvaz</wicri:noRegion></affiliation></author><author><name sortKey="Dehkordi, Mehrana Kohei" sort="Dehkordi, Mehrana Kohei" uniqKey="Dehkordi M" first="Mehrana Kohei" last="Dehkordi">Mehrana Kohei Dehkordi</name><affiliation wicri:level="1"><nlm:aff id="Aff3">Department of Agronomy, Faculty of Agriculture, Payame Noor University, P.O. Box. 19395-3697, Tehran, Iran</nlm:aff><country xml:lang="fr">Iran</country><wicri:regionArea>Department of Agronomy, Faculty of Agriculture, Payame Noor University, P.O. Box. 19395-3697, Tehran</wicri:regionArea><wicri:noRegion>Tehran</wicri:noRegion></affiliation></author><author><name sortKey="Erogul, Deniz" sort="Erogul, Deniz" uniqKey="Erogul D" first="Deniz" last="Erogul">Deniz Erogul</name><affiliation wicri:level="1"><nlm:aff id="Aff4">Department of Horticulture, Faculty of Agriculture, University of Ege, Bornova, 35100 Izmir, Turkey</nlm:aff><country xml:lang="fr">Turquie</country><wicri:regionArea>Department of Horticulture, Faculty of Agriculture, University of Ege, Bornova, 35100 Izmir</wicri:regionArea><wicri:noRegion>35100 Izmir</wicri:noRegion></affiliation></author><author><name sortKey="Rubio, Manuel" sort="Rubio, Manuel" uniqKey="Rubio M" first="Manuel" last="Rubio">Manuel Rubio</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), PO Box 164, E-30100 Espinardo-Murcia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), PO Box 164, E-30100 Espinardo-Murcia</wicri:regionArea><placeName><region nuts="2" type="communauté">Région de Murcie</region></placeName></affiliation></author><author><name sortKey="Martinez G Mez, Pedro" sort="Martinez G Mez, Pedro" uniqKey="Martinez G Mez P" first="Pedro" last="Martínez-G Mez">Pedro Martínez-G Mez</name><affiliation wicri:level="2"><nlm:aff id="Aff2">Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), PO Box 164, E-30100 Espinardo-Murcia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), PO Box 164, E-30100 Espinardo-Murcia</wicri:regionArea><placeName><region nuts="2" type="communauté">Région de Murcie</region></placeName></affiliation></author></analytic><series><title level="j">BMC Research Notes</title><idno type="eISSN">1756-0500</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Simple sequence repeats (SSRs) are defined as sequence repeat units between 1 and 6 bp that occur in both coding and non-coding regions abundant in eukaryotic genomes, which may affect the expression of genes. In this study, expressed sequence tags (ESTs) of eight <italic>Prunus</italic> species were analyzed for in silico mining of EST-SSRs, protein annotation, and open reading frames (ORFs), and the identification of codon repetitions.</p></sec><sec><title>Results</title><p>A total of 316 SSRs were identified using MISA software. Dinucleotide SSR motifs (26.31 %) were found to be the most abundant type of repeats, followed by tri- (14.58 %), tetra- (0.53 %), and penta- (0.27 %) nucleotide motifs. An attempt was made to design primer pairs for 316 identified SSRs but these were successful for only 175 SSR sequences. The positions of SSRs with respect to ORFs were detected, and annotation of sequences containing SSRs was performed to assign function to each sequence. SSRs were also characterized (in terms of position in the reference genome and associated gene) using the two available <italic>Prunus</italic> reference genomes (mei and peach). Finally, 38 SSR markers were validated across peach, almond, plum, and apricot genotypes. This validation showed a higher transferability level of EST-SSR developed in <italic>P. mume</italic> (mei) in comparison with the rest of species analyzed.</p></sec><sec><title>Conclusions</title><p>Findings will aid analysis of functionally important molecular markers and facilitate the analysis of genetic diversity.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s13104-016-2143-y) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Potter, D" uniqKey="Potter D">D Potter</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kantety, Rv" uniqKey="Kantety R">RV Kantety</name></author><author><name sortKey="La Rota, M" uniqKey="La Rota M">M La Rota</name></author><author><name sortKey="Matthews, De" uniqKey="Matthews D">DE Matthews</name></author><author><name 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uniqKey="Ballester J">J Ballester</name></author><author><name sortKey="Dicenta, F" uniqKey="Dicenta F">F Dicenta</name></author><author><name sortKey="Arus, P" uniqKey="Arus P">P Arús</name></author><author><name sortKey="Martinez G Mez, P" uniqKey="Martinez G Mez P">P Martínez-Gómez</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Espagne</li><li>Iran</li><li>Turquie</li></country><region><li>Région de Murcie</li></region></list><tree><country name="Iran"><noRegion><name sortKey="Sorkheh, Karim" sort="Sorkheh, Karim" uniqKey="Sorkheh K" first="Karim" last="Sorkheh">Karim Sorkheh</name></noRegion><name sortKey="Dehkordi, Mehrana Kohei" sort="Dehkordi, Mehrana Kohei" uniqKey="Dehkordi M" first="Mehrana Kohei" last="Dehkordi">Mehrana Kohei Dehkordi</name><name sortKey="Ghebinejad, Azim" sort="Ghebinejad, Azim" uniqKey="Ghebinejad A" first="Azim" last="Ghebinejad">Azim Ghebinejad</name></country><country name="Espagne"><region name="Région de Murcie"><name sortKey="Prudencio, Angela S" sort="Prudencio, Angela S" uniqKey="Prudencio A" first="Angela S." last="Prudencio">Angela S. Prudencio</name></region><name sortKey="Martinez G Mez, Pedro" sort="Martinez G Mez, Pedro" uniqKey="Martinez G Mez P" first="Pedro" last="Martínez-G Mez">Pedro Martínez-G Mez</name><name sortKey="Rubio, Manuel" sort="Rubio, Manuel" uniqKey="Rubio M" first="Manuel" last="Rubio">Manuel Rubio</name></country><country name="Turquie"><noRegion><name sortKey="Erogul, Deniz" sort="Erogul, Deniz" uniqKey="Erogul D" first="Deniz" last="Erogul">Deniz Erogul</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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