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A set of 100 chloroplast DNA primer pairs to study population genetics and phylogeny in monocotyledons.

Scarcelli N, Barnaud A, Eiserhardt W, Treier UA, Seveno M, d'Anfray A, Vigouroux Y, Pintaud JC - PLoS ONE (2011)

Bottom Line: The diversity found in Dioscorea, Digitaria and Pennisetum mainly corresponded to Single Nucleotide Polymorphism (SNP) while the diversity found in Arecaceae also comprises Variable Number Tandem Repeat (VNTR).We observed that the most variable loci (rps15-ycf1, rpl32-ccsA, ndhF-rpl32, ndhG-ndhI and ccsA) are located in the SSC.Through the analysis of the genetic structure of a wild-cultivated species complex in Dioscorea, we demonstrated that this new set of primers is of great interest for population genetics and we anticipate that it will also be useful for phylogeny and bar-coding studies.

View Article: PubMed Central - PubMed

Affiliation: UMR Diversité, Adaptation et Développement des Plantes (DIADE), Institut de Recherche pour le Développement, Montpellier, France. nora.scarcelli@ird.fr

ABSTRACT
Chloroplast DNA sequences are of great interest for population genetics and phylogenetic studies. However, only a small set of markers are commonly used. Most of them have been designed for amplification in a large range of Angiosperms and are located in the Large Single Copy (LSC). Here we developed a new set of 100 primer pairs optimized for amplification in Monocotyledons. Primer pairs amplify coding (exon) and non-coding regions (intron and intergenic spacer). They span the different chloroplast regions: 72 are located in the LSC, 13 in the Small Single Copy (SSC) and 15 in the Inverted Repeat region (IR). Amplification and sequencing were tested in 13 species of Monocotyledons: Dioscorea abyssinica, D. praehensilis, D. rotundata, D. dumetorum, D. bulbifera, Trichopus sempervirens (Dioscoreaceae), Phoenix canariensis, P. dactylifera, Astrocaryum scopatum, A. murumuru, Ceroxylon echinulatum (Arecaceae), Digitaria excilis and Pennisetum glaucum (Poaceae). The diversity found in Dioscorea, Digitaria and Pennisetum mainly corresponded to Single Nucleotide Polymorphism (SNP) while the diversity found in Arecaceae also comprises Variable Number Tandem Repeat (VNTR). We observed that the most variable loci (rps15-ycf1, rpl32-ccsA, ndhF-rpl32, ndhG-ndhI and ccsA) are located in the SSC. Through the analysis of the genetic structure of a wild-cultivated species complex in Dioscorea, we demonstrated that this new set of primers is of great interest for population genetics and we anticipate that it will also be useful for phylogeny and bar-coding studies.

Show MeSH
Inter-generic diversity found in Dioscorea, Arecaceae and Poaceae.Inter-generic diversity was estimated as the number of SNP in the LSC, SSC and IR. Numbers of SNP have been standardised to 1 kb. Bars represent the 95% confidence intervals.
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pone-0019954-g001: Inter-generic diversity found in Dioscorea, Arecaceae and Poaceae.Inter-generic diversity was estimated as the number of SNP in the LSC, SSC and IR. Numbers of SNP have been standardised to 1 kb. Bars represent the 95% confidence intervals.

Mentions: The occurrence of SNP among the three regions of the chloroplast (LSC, SSC and IR) varies (Figure 1). LSC and SSC exhibit similar levels of diversity while IR exhibits significantly lower numbers of SNP. The difference in number of SNP is significant for LSC vs. IR and SSC vs. IR (p<0.001 for Dioscorea, Arecaceae and Poaceae) but is not significant for LSC vs. SSC (p>0.05 for Dioscorea, Arecaceae and Poaceae). Variation in SNP number in the SSC region is, however, mostly driven by the ndhF-rpl32 locus. This locus exhibits a very high genetic diversity: 92 and 118 SNP per 1 kb for Dioscorea and Poaceae, compared to the mean of 16, 10 and 62 SNP per 1 kb for Dioscorea, Arecaceae and Poaceae, respectively and of 11, 7 and 30 SNP per 1 kb in the whole chloroplast.


A set of 100 chloroplast DNA primer pairs to study population genetics and phylogeny in monocotyledons.

Scarcelli N, Barnaud A, Eiserhardt W, Treier UA, Seveno M, d'Anfray A, Vigouroux Y, Pintaud JC - PLoS ONE (2011)

Inter-generic diversity found in Dioscorea, Arecaceae and Poaceae.Inter-generic diversity was estimated as the number of SNP in the LSC, SSC and IR. Numbers of SNP have been standardised to 1 kb. Bars represent the 95% confidence intervals.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3102674&req=5

pone-0019954-g001: Inter-generic diversity found in Dioscorea, Arecaceae and Poaceae.Inter-generic diversity was estimated as the number of SNP in the LSC, SSC and IR. Numbers of SNP have been standardised to 1 kb. Bars represent the 95% confidence intervals.
Mentions: The occurrence of SNP among the three regions of the chloroplast (LSC, SSC and IR) varies (Figure 1). LSC and SSC exhibit similar levels of diversity while IR exhibits significantly lower numbers of SNP. The difference in number of SNP is significant for LSC vs. IR and SSC vs. IR (p<0.001 for Dioscorea, Arecaceae and Poaceae) but is not significant for LSC vs. SSC (p>0.05 for Dioscorea, Arecaceae and Poaceae). Variation in SNP number in the SSC region is, however, mostly driven by the ndhF-rpl32 locus. This locus exhibits a very high genetic diversity: 92 and 118 SNP per 1 kb for Dioscorea and Poaceae, compared to the mean of 16, 10 and 62 SNP per 1 kb for Dioscorea, Arecaceae and Poaceae, respectively and of 11, 7 and 30 SNP per 1 kb in the whole chloroplast.

Bottom Line: The diversity found in Dioscorea, Digitaria and Pennisetum mainly corresponded to Single Nucleotide Polymorphism (SNP) while the diversity found in Arecaceae also comprises Variable Number Tandem Repeat (VNTR).We observed that the most variable loci (rps15-ycf1, rpl32-ccsA, ndhF-rpl32, ndhG-ndhI and ccsA) are located in the SSC.Through the analysis of the genetic structure of a wild-cultivated species complex in Dioscorea, we demonstrated that this new set of primers is of great interest for population genetics and we anticipate that it will also be useful for phylogeny and bar-coding studies.

View Article: PubMed Central - PubMed

Affiliation: UMR Diversité, Adaptation et Développement des Plantes (DIADE), Institut de Recherche pour le Développement, Montpellier, France. nora.scarcelli@ird.fr

ABSTRACT
Chloroplast DNA sequences are of great interest for population genetics and phylogenetic studies. However, only a small set of markers are commonly used. Most of them have been designed for amplification in a large range of Angiosperms and are located in the Large Single Copy (LSC). Here we developed a new set of 100 primer pairs optimized for amplification in Monocotyledons. Primer pairs amplify coding (exon) and non-coding regions (intron and intergenic spacer). They span the different chloroplast regions: 72 are located in the LSC, 13 in the Small Single Copy (SSC) and 15 in the Inverted Repeat region (IR). Amplification and sequencing were tested in 13 species of Monocotyledons: Dioscorea abyssinica, D. praehensilis, D. rotundata, D. dumetorum, D. bulbifera, Trichopus sempervirens (Dioscoreaceae), Phoenix canariensis, P. dactylifera, Astrocaryum scopatum, A. murumuru, Ceroxylon echinulatum (Arecaceae), Digitaria excilis and Pennisetum glaucum (Poaceae). The diversity found in Dioscorea, Digitaria and Pennisetum mainly corresponded to Single Nucleotide Polymorphism (SNP) while the diversity found in Arecaceae also comprises Variable Number Tandem Repeat (VNTR). We observed that the most variable loci (rps15-ycf1, rpl32-ccsA, ndhF-rpl32, ndhG-ndhI and ccsA) are located in the SSC. Through the analysis of the genetic structure of a wild-cultivated species complex in Dioscorea, we demonstrated that this new set of primers is of great interest for population genetics and we anticipate that it will also be useful for phylogeny and bar-coding studies.

Show MeSH