A set of universal primers for amplification of polymorphic non‐coding regions of mitochondrial and chloroplast DNA in plants

Demesure, Brigitte; Sodzi, N.; Petit, Rémy J.

doi:10.1111/j.1365-294x.1995.tb00201.x

Cited by 1,025 publications

(768 citation statements)

References 15 publications

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“…The TF, CD and AS primer pairs designed by Taberlet et al (1991) and Demesure et al (1995), which amplify non-coding regions of the chloroplast genome, were chosen, because they are known to reveal genetic variation in other Betula species (Palmé et al 2003(Palmé et al , 2004Maliouchenko et al 2007). For each individual, the PCR reaction was set up in 10 μl mixture containing 3.4 μl of Multiplex PCR Master Mix (Qiagen), 2.0 μl of RNase-free water (Qiagen), 0.6 μl of primer mixture (0.2 μM of each primer) and 4.0 μl of diluted DNA.…”

Section: Laboratory Analysesmentioning

confidence: 99%

Chloroplast DNA variation of Betula humilis Schrk. in Poland and Belarus

Jadwiszczak

Banaszek

Jabłońska

et al. 2012

Tree Genetics & Genomes

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Betula humilis is an endangered plant species in Central Europe. In order to protect this species, it is necessary to document its genetic diversity in this region and to identify areas for conservation prioritisation. As molecular investigations conducted throughout the ranges of many plant species have shown that the highest genetic diversities are found within former glacial refugia and/or within the contact zones of different phylogenetic lineages, we investigated the reasons underlying the considerable genetic variation of B. humilis in northeastern Poland revealed previously using nuclear microsatellites. We analysed 365 individuals of B. humilis from 19 populations and 67 specimens of Betula pendula and Betula pubescens sampled in four geographical regions in Poland and Belarus for polymorphism in chloroplast PCR-restriction fragment length polymorphism markers. Genetic data strongly suggested that B. humilis could have survived the Last Glacial Maximum at higher latitudes, but the hypothesis of a refugium in southeastern Poland was rejected. Chloroplast DNA analysis confirmed high genetic diversity in some populations in northeastern Poland. This phenomenon can likely be explained in terms of a suture zone, as the high haplotypic richness was followed by h T ≤v T . Similar patterns of haplotype distributions in the birches under study and high introgression ratio (IG00.71) among B. humilis and congeneric trees suggested that postglacial recolonisation of the shrub birch was complicated by haplotype sharing with other birches.

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Section: Laboratory Analysesmentioning

confidence: 99%

Chloroplast DNA variation of Betula humilis Schrk. in Poland and Belarus

Jadwiszczak

Banaszek

Jabłońska

et al. 2012

Tree Genetics & Genomes

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“…Each amplification was performed on four samples as well as on two negative DNA isolation controls and on four negative PCR controls (PCR mixture without addition of target DNA). For chloroplast DNA, the seven pairs of primers were all located in the intergenic spacer between trnD and trnT (DT) (Demesure et al 1995). One of these primer pairs had already been tested on wood DNA in a previous study (Dumolin-Lapègue et al 1999) and six new primer pairs were designed to amplify fragments of increasing size, ranging from 87 to 1483 bp.…”

Section: (B) Dna Isolationmentioning

confidence: 99%

“…All chloroplast DNA primer pairs used in this study were designed using oak sequences as a reference; however, one of them (D7T7) turned out to be relatively conserved, allowing amplification of many dicotyledonous tree species (M.-F. Deguilloux, unpublished data). Conversely, the primers used to amplify the 5S nuclear ribosomal gene and the two mitochondrial introns cox2-1/2 and nad4-3/4 are highly conserved (Demesure et al 1995). The 5S fragment was amplified according to Szymanski et al (1999) on 2.5 µl of pure DNA extract.…”

Section: (B) Dna Isolationmentioning

confidence: 99%

“…Three pairs of primers were used to amplify nuclear fragments: ssrQrZAG20 (80 bp) and ssrQrZAG119 (178 bp) correspond to two microsatellites (Kampfer et al 1998;Steinkellner et al 1997) and 5S to the 5S ribosomal DNA (230 bp) (Szymanski et al 1999). Two pairs of primers, cox2-1/2 and nad4-3/4, were used to amplify mitochondrial fragments of 378 and 2430 bp (Demesure et al 1995). All chloroplast DNA primer pairs used in this study were designed using oak sequences as a reference; however, one of them (D7T7) turned out to be relatively conserved, allowing amplification of many dicotyledonous tree species (M.-F. Deguilloux, unpublished data).…”

Section: (B) Dna Isolationmentioning

confidence: 99%

See 1 more Smart Citation

Novel perspectives in wood certification and forensics: dry wood as a source of DNA

Deguilloux

Pémonge

Petit

2002

Proc. R. Soc. Lond. B

143

159

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The importance of wood for human societies can hardly be understated. If dry wood were amenable to molecular genetic investigations, this could lead to major applications in wood forensics, certification, archaeology and palaeobotany. To evaluate the potential of wood for molecular genetic investigations, we have attempted to isolate and amplify, by PCR, DNA fragments of increasing size corresponding to all three plant genomes from different regions of 10 oak logs. Stringent procedures to avoid contamination with external DNA were used in order to demonstrate the authenticity of the fragments amplified. This authenticity was further confirmed by demonstrating genetic uniformity within each log using both nuclear and chloroplast microsatellites. For most wood samples DNA was degraded, and the sequences that gave the best results were those of small size and present in high copy number (chloroplast, mitochondrial, or repeated nuclear sequences). Both storage conditions and storage duration play a role in DNA conservation. Overall, this work demonstrates that molecular markers from all three plant genomes can be used for genetic analysis on dry oak wood, but outlines some limitations and the need for further evaluation of the potential of wood for DNA analysis.

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“…The intergenic spacer between the atpB and rbcL genes was amplified using primers 2 and 5 (Manen & al., 1994). The intergenic spacer psbJ-petA was amplified using primers psbJ and petA (Shaw & al., 2007) and part of the intergenic spacer trnD-trnT was amplified using primers trnE (Shaw & al., 2005) and trnD (Demesure & al., 1995). A portion of the matK gene was amplified for four species (Arenifera spinescens, A. stylosa, Octopoma nanum, O. tetrasepalum) using DNA barcoding primers 3F-Kim and 1R-Kim (Cuenoud & al., 2002).…”

Section: Version Of Recordmentioning

confidence: 99%

Phylogenetic placement and generic re‐circumscriptions of the multilocular generaArenifera,OctopomaandSchlechteranthus(Aizoaceae: Ruschieae): Evidence from anatomical, morphological and plastid DNA data

Powell

Boatwright

Klak

et al. 2016

TAXON

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Ruschieae is the largest tribe in the highly speciose subfamily Ruschioideae (Aizoaceae). A generic-level phylogeny for the tribe was recently produced, providing new insights into relationships between the taxa. Octopoma and Arenifera are woody shrubs with multilocular capsules and are distributed across the Succulent Karoo. Octopoma was shown to be polyphyletic in the tribal phylogeny, but comprehensive sampling is required to confirm its polyphyly. Arenifera has not previously been sampled and therefore its phylogenetic placement in the tribe is uncertain. In this study, phylogenetic sampling for nine plastid regions matK, rpl16, rps16, was expanded to include all species of Octopoma and Arenifera, to assess phylogenetic placement and relationships of these genera. Three phylogenetic analyses were carried out, maximum parsimony, maximum likelihood and Bayesian inference. Leaf anatomical sections were studied to further inform generic circumscriptions. The phylogenies showed Octopoma to be polyphyletic, with the type, O. octojuge, and the related O. nanum, resolved as sister to Zeuktophyllum and Smicrostigma, while the other species were placed in the Conophytum-clade. Arenifera was also shown to be polyphyletic, with the type, A. pillansii, placed in the xeromorphic-clade, and the remainder of the species recovered among the Octopoma species in the Conophytum-clade (forming the Octopoma subglobosum-Arenifera spinescens subclade). Generic affinities of the O. subglobosum-A. spinescens subclade were assessed in relation to the sister taxon Schlechteranthus. The leaf anatomy was found to be informative within the study group. Bladder cells were observed in Arenifera pillansii, a hypodermis in Little Karoo Octopoma (O. octojuge, O. nanum, O. quadrisepalum) and epidermal cells forming blunt papillae in Schlechteranthus and the O. subglobosum-A. spinescens subclade. Upon assessment of the anatomical, morphological and phylogenetic data, Schlechteranthus is here expanded to include the species in the O. subglobosum-A. spinescens subclade. Eight new combinations are made in Schlechteranthus. As a result, Arenifera is again monotypic and the circumscription of Octopoma is refined to include three species restricted to the Little Karoo. Two subgenera within Schlechteranthus s.l. (subg. Schlechteranthus, subg. Microphyllus) are erected to accommodate differences in leaf size, capsule size, closing body size and locule number.

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A set of universal primers for amplification of polymorphic non‐coding regions of mitochondrial and chloroplast DNA in plants

Cited by 1,025 publications

References 15 publications

Chloroplast DNA variation of Betula humilis Schrk. in Poland and Belarus

Chloroplast DNA variation of Betula humilis Schrk. in Poland and Belarus

Novel perspectives in wood certification and forensics: dry wood as a source of DNA

Phylogenetic placement and generic re‐circumscriptions of the multilocular generaArenifera,OctopomaandSchlechteranthus(Aizoaceae: Ruschieae): Evidence from anatomical, morphological and plastid DNA data

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