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Transcriptome Sequencing and Development of Novel Genic SSR Markers From Pistacia vera L.
In this study, we aimed to develop novel genic simple sequence repeat (eSSR) markers and to study phylogenetic relationship among Pistacia species. Transcriptome sequencing was performed in different tissues of Siirt and Atl cultivars of pistachio (Pistacia vera). A total of 37.5-Gb data were used i...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2020
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7509152/ https://www.ncbi.nlm.nih.gov/pubmed/33033493 http://dx.doi.org/10.3389/fgene.2020.01021 |
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author | Karcι, Harun Paizila, Aibibula Topçu, Hayat Ilikçioğlu, Ertuğrul Kafkas, Salih |
author_facet | Karcι, Harun Paizila, Aibibula Topçu, Hayat Ilikçioğlu, Ertuğrul Kafkas, Salih |
author_sort | Karcι, Harun |
collection | PubMed |
description | In this study, we aimed to develop novel genic simple sequence repeat (eSSR) markers and to study phylogenetic relationship among Pistacia species. Transcriptome sequencing was performed in different tissues of Siirt and Atl cultivars of pistachio (Pistacia vera). A total of 37.5-Gb data were used in the assembly. The number of total contigs and unigenes was calculated as 98,831, and the length of N50 was 1,333 bp after assembly. A total of 14,308 dinucleotide, trinucleotide, tetranucleotide, pentanucleotide, and hexanucleotide SSR motifs (4–17) were detected, and the most abundant SSR repeat types were trinucleotide (29.54%), dinucleotide (24.06%), hexanucleotide (20.67%), pentanucleotide (18.88%), and tetranucleotide (6.85%), respectively. Overall 250 primer pairs were designed randomly and tested in eight Pistacia species for amplification. Of them, 233 were generated polymerase chain reaction products in at least one of the Pistacia species. A total of 55 primer pairs that had amplifications in all tested Pistacia species were used to characterize 11 P. vera cultivars and 78 wild Pistacia genotypes belonging to nine Pistacia species (P. khinjuk, P. eurycarpa, P. atlantica, P. mutica, P. integerrima, P. chinensis, P. terebinthus, P. palaestina, and P. lentiscus). A total of 434 alleles were generated from 55 polymorphic eSSR loci with an average of 7.89 alleles per locus. The mean number of effective allele was 3.40 per locus. Polymorphism information content was 0.61, whereas observed (Ho) and expected heterozygosity (He) values were 0.39 and 0.65, respectively. UPGMA (unweighted pair-group method with arithmetic averages) and STRUCTURE analysis divided 89 Pistacia genotypes into seven populations. The closest species to P. vera was P. khinjuk. P. eurycarpa was closer P. atlantica than P. khinjuk. P. atlantica–P. mutica and P. terebinthus–P. palaestina pairs of species were not clearly separated from each other, and they were suggested as the same species. The present study demonstrated that eSSR markers can be used in the characterization and phylogenetic analysis of Pistacia species and cultivars, as well as genetic linkage mapping and QTL (quantitative trait locus) analysis. |
format | Online Article Text |
id | pubmed-7509152 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-75091522020-10-07 Transcriptome Sequencing and Development of Novel Genic SSR Markers From Pistacia vera L. Karcι, Harun Paizila, Aibibula Topçu, Hayat Ilikçioğlu, Ertuğrul Kafkas, Salih Front Genet Genetics In this study, we aimed to develop novel genic simple sequence repeat (eSSR) markers and to study phylogenetic relationship among Pistacia species. Transcriptome sequencing was performed in different tissues of Siirt and Atl cultivars of pistachio (Pistacia vera). A total of 37.5-Gb data were used in the assembly. The number of total contigs and unigenes was calculated as 98,831, and the length of N50 was 1,333 bp after assembly. A total of 14,308 dinucleotide, trinucleotide, tetranucleotide, pentanucleotide, and hexanucleotide SSR motifs (4–17) were detected, and the most abundant SSR repeat types were trinucleotide (29.54%), dinucleotide (24.06%), hexanucleotide (20.67%), pentanucleotide (18.88%), and tetranucleotide (6.85%), respectively. Overall 250 primer pairs were designed randomly and tested in eight Pistacia species for amplification. Of them, 233 were generated polymerase chain reaction products in at least one of the Pistacia species. A total of 55 primer pairs that had amplifications in all tested Pistacia species were used to characterize 11 P. vera cultivars and 78 wild Pistacia genotypes belonging to nine Pistacia species (P. khinjuk, P. eurycarpa, P. atlantica, P. mutica, P. integerrima, P. chinensis, P. terebinthus, P. palaestina, and P. lentiscus). A total of 434 alleles were generated from 55 polymorphic eSSR loci with an average of 7.89 alleles per locus. The mean number of effective allele was 3.40 per locus. Polymorphism information content was 0.61, whereas observed (Ho) and expected heterozygosity (He) values were 0.39 and 0.65, respectively. UPGMA (unweighted pair-group method with arithmetic averages) and STRUCTURE analysis divided 89 Pistacia genotypes into seven populations. The closest species to P. vera was P. khinjuk. P. eurycarpa was closer P. atlantica than P. khinjuk. P. atlantica–P. mutica and P. terebinthus–P. palaestina pairs of species were not clearly separated from each other, and they were suggested as the same species. The present study demonstrated that eSSR markers can be used in the characterization and phylogenetic analysis of Pistacia species and cultivars, as well as genetic linkage mapping and QTL (quantitative trait locus) analysis. Frontiers Media S.A. 2020-09-09 /pmc/articles/PMC7509152/ /pubmed/33033493 http://dx.doi.org/10.3389/fgene.2020.01021 Text en Copyright © 2020 Karcι, Paizila, Topçu, Ilikçioğlu and Kafkas. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics Karcι, Harun Paizila, Aibibula Topçu, Hayat Ilikçioğlu, Ertuğrul Kafkas, Salih Transcriptome Sequencing and Development of Novel Genic SSR Markers From Pistacia vera L. |
title | Transcriptome Sequencing and Development of Novel Genic SSR Markers From Pistacia vera L. |
title_full | Transcriptome Sequencing and Development of Novel Genic SSR Markers From Pistacia vera L. |
title_fullStr | Transcriptome Sequencing and Development of Novel Genic SSR Markers From Pistacia vera L. |
title_full_unstemmed | Transcriptome Sequencing and Development of Novel Genic SSR Markers From Pistacia vera L. |
title_short | Transcriptome Sequencing and Development of Novel Genic SSR Markers From Pistacia vera L. |
title_sort | transcriptome sequencing and development of novel genic ssr markers from pistacia vera l. |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7509152/ https://www.ncbi.nlm.nih.gov/pubmed/33033493 http://dx.doi.org/10.3389/fgene.2020.01021 |
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