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Analysis of Variation in Chloroplast DNA Sequences

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Molecular Plant Taxonomy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1115))

Abstract

This chapter introduces and reviews methods for analyzing variation in chloroplast DNA, mainly by polymerase chain reaction (PCR) and subsequent revelation of polymorphisms. Sources for chloroplast primers are discussed, as well as methods such as Sanger sequencing, PCR followed by restriction fragment length polymorphism (RFLP), gel electrophoresis, fragment analysis on automated DNA sequencers, denaturing high-performance liquid chromatography (dHPLC), and next-generation sequencing (NGS). A special section deals with peculiarities of chloroplast DNA variation, such as tandem repeats and mini- and microsatellites.

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References

  1. Clegg MT, Zurawski G (1992) Chloroplast DNA and the study of plant phylogeny: present status and future prospects. In: Soltis PS, Soltis DE, Doyle JJ (eds) Molecular systematics of plants. Chapman & Hall, New York, pp 1–13

    Chapter  Google Scholar 

  2. Bovenberg WA, Kool AJ, Nijkamp HJJ (1981) Isolation, characterization and restriction endonuclease mapping of the Petunia hybrida chloroplast DNA. Nucleic Acids Res 9:503–517

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  3. Palmer JD et al (1983) Chloroplast DNA evolution and the origin of amphidiploid Brassica species. Theor Appl Genet 65:181–189

    Article  CAS  PubMed  Google Scholar 

  4. Clark EM, Izhar S, Hanson MR (1985) Independent segregation of the plastid genome and cytoplasmic male sterility in Petunia somatic hybrids. Mol Gen Genet 199:440–445

    Article  CAS  Google Scholar 

  5. Shinozaki K et al (1986) The complete nucleotide sequence of the tobacco chloroplast genome. Plant Mol Biol Rep 4:111–147

    Article  CAS  Google Scholar 

  6. Sugiura M (1987) Structure and function of the tobacco chloroplast genome. J Plant Res 100:407–436

    CAS  Google Scholar 

  7. Sugiura M (1992) The chloroplast genome. Plant Mol Biol 19:149–168

    Article  CAS  PubMed  Google Scholar 

  8. Olmstead RG, Sweere JA, Wolfe KH (1993) Ninety extra nucleotide in ndhF gene of tobacco chloroplast DNA: a summary of revisions to the 1986 genome sequence. Plant Mol Biol 22:1191–1193

    Article  CAS  PubMed  Google Scholar 

  9. Wakasugi T et al (1998) Updated gene map of tobacco chloroplast DNA. Plant Mol Biol Rep 16:231–241

    Article  CAS  Google Scholar 

  10. Sugiura M (2003) History of chloroplast genomics. Photosynth Res 76:371–377

    Article  CAS  PubMed  Google Scholar 

  11. Yukawa M, Tsudzuki T, Sugiura M (2005) The 2005 version of the chloroplast DNA sequence from tobacco (Nicotiana tabacum). Plant Mol Biol Rep 23:359–365

    Article  CAS  Google Scholar 

  12. Bock R (2007) Structure, function, and inheritance of plastid genomes. In: Bock R (ed) Cell and molecular biology of plastids. Springer, Berlin, pp 29–63

    Chapter  Google Scholar 

  13. Ravi V et al (2008) An update on chloroplast genomes. Plant Syst Evol 271:101–122

    Article  CAS  Google Scholar 

  14. Taberlet P et al (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17:1105–1109

    Article  CAS  PubMed  Google Scholar 

  15. Till BJ (2006) A protocol for TILLING and Ecotilling in plants and animals. Nat Protoc 1:2465–2477

    Article  CAS  PubMed  Google Scholar 

  16. Hauser MT et al (1998) Generation of co-dominant PCR-based markers by duplex analysis on high resolution gels. Plant J 16:117–125

    Article  CAS  PubMed  Google Scholar 

  17. Hoelzel AR (1998) Molecular genetic analysis of populations. IRL Press at Oxford University Press, Oxford

    Google Scholar 

  18. Hoelzel AR, Green A (1998) PCR protocols and population analysis by direct DNA sequencing and PCR-based DNA fingerprinting. In: Hoelzel AR (ed) Molecular genetic analysis of populations. IRL Press at Oxford University Press, Oxford, pp 201–235

    Google Scholar 

  19. Sambrook J, Russell DW (2001) Molecular cloning, 3rd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

    Google Scholar 

  20. Liston A (1992) Variation in the chloroplast genes rpoC1 and rpoC2 of the genus Astralagus (Fabaceae): evidence from restriction site mapping of a PCR-amplified fragment. Am J Bot 79:953–961

    Article  CAS  Google Scholar 

  21. Zeltz P et al (1993) Editing of the chloroplast rpoB transcript is independent of chloroplast translation and shows different patterns in barley and maize. EMBO J 12:4291–4296

    CAS  PubMed  Google Scholar 

  22. Steele KP, Vilgalys R (1994) Phylogenetic analysis of Polemoniaceae using nucleotide sequences of the plastid gene matK. Syst Bot 19:126–142

    Article  Google Scholar 

  23. Graham SW, Olmstead RG (2000) Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms. Am J Bot 87:1712–1730

    Article  CAS  PubMed  Google Scholar 

  24. Demesure B, Sodzi N, Petit RJ (1995) A set of universal primers for amplification of polymorphic non-coding regions of mitochondrial and chloroplast DNA in plants. Mol Ecol 4:129–131

    Article  CAS  PubMed  Google Scholar 

  25. Dumolin-Lapegue S, Pemonge M-H, Petit RJ (1997) An enlarged set of consensus primers for the study of organelle DNA in plants. Mol Ecol 6:393–398

    Article  CAS  PubMed  Google Scholar 

  26. Small RL et al (1998) The tortoise and the hare: choosing between noncoding plastome and nuclear ADH sequences for phylogeny reconstruction in a recently diverged plant group. Am J Bot 85:1301–1315

    Article  CAS  PubMed  Google Scholar 

  27. Grivet D et al (2001) Genome walking with consensus primers: application to the large single copy region of chloroplast DNA. Mol Ecol Notes 1:345–349

    Article  CAS  Google Scholar 

  28. Dhingra A, Folta KM (2005) ASAP: amplification, sequencing & annotation of plastomes. BMC Genomics 6:176

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  29. Shaw J et al (2005) The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am J Bot 92:142–166

    Article  CAS  PubMed  Google Scholar 

  30. Shaw J et al (2007) Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am J Bot 94:275–288

    Article  CAS  PubMed  Google Scholar 

  31. Heinze B (2007) A database of PCR primers for the chloroplast genomes of higher plants. Plant Methods 3:4

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  32. Watts CD et al (2008) The D4 set: primers that target highly variable intron loops in plant chloroplast genomes. Mol Ecol Resour 8:1344–1347

    Article  CAS  PubMed  Google Scholar 

  33. Borsch T et al (2009) The petD group II intron as a species level marker: utility for tree inference and species identification in the diverse genus Campanula (Campanulaceae). Willdenowia 39:7–33

    Article  Google Scholar 

  34. Ebert D, Peakall R (2009) Chloroplast simple sequence repeats (cpSSRs): technical resources and recommendations for expanding cpSSR discovery and applications to a wide array of plant species. Mol Ecol Resour 9:673–690

    Article  CAS  PubMed  Google Scholar 

  35. Lin C-P et al (2010) Comparative chloroplast genomics reveals the evolution of Pinaceae genera and subfamilies. Genome Biol Evol 2:504–517

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  36. Scarcelli N et al (2011) A set of 100 chloroplast DNA primer pairs to study population genetics and phylogeny in monocotyledons. PLoS ONE 6:e19954

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  37. Prince LM (2011) Plastid primers for phylogenetics. Rancho Santa Ana Botanic Garden, Claremont, California, USA. https://sites.google.com/site/plastidprimersforphylogenetics/. Accessed 2 Apr 2012

  38. Haider N, Wilkinson M (2011) A set of plastid DNA-specific universal primers for flowering plants. Russ J Genet 47:1066–1077

    Article  CAS  Google Scholar 

  39. Haider N (2011) Chloroplast-specific universal primers and their uses in plant studies. Biol Plant 55:225–236

    Article  CAS  Google Scholar 

  40. Ebert D, Peakall R (2009) A new set of universal de novo sequencing primers for extensive coverage of noncoding chloroplast DNA: new opportunities for phylogenetic studies and cpSSR discovery. Mol Ecol Resour 9:777–783

    Article  CAS  PubMed  Google Scholar 

  41. Nakamura I et al (1997) A proposal for identifying the short ID sequence which addresses the plastid subtype of higher plants. Breed Sci 47:385–388/394

    CAS  Google Scholar 

  42. Brunner I et al (2001) Molecular identification of fine roots of trees from the Alps: reliable and fast DNA extraction and PCR-RFLP analyses of plastid DNA. Mol Ecol 10:2079–2087

    Article  CAS  PubMed  Google Scholar 

  43. Borsch T et al (2003) Non-coding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms. J Evol Biol 16:558–576

    Article  CAS  PubMed  Google Scholar 

  44. CBOL Plant Working Group (2009) A DNA barcode for land plants. Proc Natl Acad Sci USA 106:12794–12797

    Article  Google Scholar 

  45. Chase MW et al (2005) Land plants and DNA barcodes: short-term and long-term goals. Phil Trans R Soc B-Biol Sci 360:1889–1895

    Article  CAS  Google Scholar 

  46. Hollingsworth PM, Graham SW, Little DP (2011) Choosing and using a plant DNA barcode. PLoS ONE 6:e19254

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  47. Presting GG (2006) Identification of conserved regions in the plastid genome: implications for DNA barcoding and biological function. Can J Bot 84:1434–1443

    Article  CAS  Google Scholar 

  48. Newmaster SG, Fazekas AJ, Ragupathy S (2006) DNA barcoding in land plants: evaluation of rbcL in a multigene tiered approach. Can J Bot 84:335–341

    Article  CAS  Google Scholar 

  49. Chase MW et al (2007) A proposal for a standardised protocol to barcode all land plants. Taxon 56:295–299

    Google Scholar 

  50. Fazekas AJ et al (2008) Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well. Public Libr Sci 3:e2802

    Google Scholar 

  51. Lahaye R et al (2008) DNA barcoding the floras of biodiversity hotspots. Proc Natl Acad Sci USA 105:2923–2928

    Article  CAS  PubMed  Google Scholar 

  52. Ford CS et al (2009) Selection of candidate coding DNA barcoding regions for use on land plants. Bot J Linn Soc 159:1–11

    Article  Google Scholar 

  53. Hollingsworth ML et al (2009) Selecting barcoding loci for plants: evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants. Mol Ecol Resour 9:439–457

    Article  CAS  PubMed  Google Scholar 

  54. Taberlet P et al (2007) Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res 35:e14

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  55. Spooner DM (2009) DNA barcoding will frequently fail in complicated groups: an example in wild potatoes. Am J Bot 96:1177–1189

    Article  CAS  PubMed  Google Scholar 

  56. Fazekas AJ et al (2009) Are plant species inherently harder to discriminate than animal species using DNA barcoding markers? Mol Ecol Resour 9:130–139

    Article  CAS  PubMed  Google Scholar 

  57. Ran J-H et al (2010) A test of seven candidate barcode regions from the plastome in Picea (Pinaceae). J Integr Plant Biol 52:1109–1126

    Article  CAS  PubMed  Google Scholar 

  58. Arca M et al (2012) Deciduous trees and the application of universal DNA barcodes: a case study on the circumpolar Fraxinus. PLoS ONE 7:e34089

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  59. Tsumura Y et al (1995) Molecular phylogeny of conifers using RFLP analysis of PCR-amplified specific chloroplast genes. Theor Appl Genet 91:1222–1236

    Article  CAS  PubMed  Google Scholar 

  60. Parks M, Liston A, Cronn R (2011) Newly developed primers for complete ycf1 amplification in Pinus (Pinaceae) chloroplasts with possible family-wide utility. Am J Bot 98:e185–e188

    Article  CAS  PubMed  Google Scholar 

  61. Oefner PJ, Underhill PA (1998) Detection of nucleic acid heteroduplex molecules by denaturing high-performance liquid chromatography and methods for comparative sequencing., US Patent 5,795,976 (18 August 1998)

    Google Scholar 

  62. Gielly L, Taberlet P (1994) The use of chloroplast DNA to resolve plant phylogenies: noncoding versus rbcL sequences. Mol Biol Evol 11:769–777

    CAS  PubMed  Google Scholar 

  63. Devey DS, Chase MW, Clarkson JJ (2009) A stuttering start to plant DNA barcoding: microsatellites present a previously overlooked problem in non-coding plastid regions. Taxon 58:7–15

    Google Scholar 

  64. Powell W et al (1995) Hypervariable microsatellites provide a general source of polymorphic DNA markers for the chloroplast genome. Curr Biol 5:1023–1029

    Article  CAS  PubMed  Google Scholar 

  65. Weising K, Gardner R (1999) A set of conserved PCR primers for the analysis of simple sequence repeat polymorphisms in chloroplast genomes of dicotyledonous angiosperms. Genome 42:9–19

    Article  CAS  PubMed  Google Scholar 

  66. Vendramin GG et al (1996) A set of primers for the amplification of 20 chloroplast microsatellites in Pinaceae. Mol Ecol 5:595–598

    Article  CAS  PubMed  Google Scholar 

  67. Provan J et al (2004) Universal primers for the amplification of chloroplast microsatellites in grasses (Poaceae). Mol Ecol Notes 4:262–264

    Article  CAS  Google Scholar 

  68. Chung S-M, Staub JE (2003) The development and evaluation of consensus chloroplast primer pairs that possess highly variable sequence regions in a diverse array of plant taxa. Theor Appl Genet 107:757–767

    Article  CAS  PubMed  Google Scholar 

  69. Blasko K et al (1988) Variation in copy number of a 24-base pair tandem repeat in the chloroplast DNA of Oenothera hookeri strain Johansen. Curr Genet 14:287–292

    Article  CAS  PubMed  Google Scholar 

  70. Hipkins VD et al (1995) A mutation hotspot in the chloroplast genome of a conifer (Douglas-fir: Pseudotsuga) is caused by variability in the number of direct repeats derived from a partially duplicated tRNA gene. Curr Genet 27:572–579

    Article  CAS  PubMed  Google Scholar 

  71. Cafasso D et al (2001) Characterization of a minisatellite repeat locus in the chloroplast genome of Orchis palustris (Orchidaceae). Curr Genet 39:394–398

    Article  CAS  PubMed  Google Scholar 

  72. Fussi B, Lexer C, Heinze B (2010) Phylogeography of Populus alba (L.) and Populus tremula (L.) in Central Europe: secondary contact and hybridisation during recolonisation from disconnected refugia. Tree Genet Genomes 6:439–450

    Article  Google Scholar 

  73. Vachon N, Freeland JR (2011) Phylogeographic inferences from chloroplast DNA: quantifying the effects of mutations in repetitive and non-repetitive sequences. Mol Ecol Resour 11:279–285

    Article  CAS  PubMed  Google Scholar 

  74. Parks M, Cronn R, Liston A (2009) Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biol 7:84

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  75. Khan A et al (2012) The chloroplast genome sequence of date palm (Phoenix dactylifera L. cv. ‘Aseel’). Plant Mol Biol Rep 30:666–678

    Article  CAS  Google Scholar 

  76. Antoniw J (1995) A new method for designing PCR primers specific for groups of sequences and its application to plant viruses. Mol Biotechnol 4:111–119

    Article  CAS  PubMed  Google Scholar 

  77. Noh EW, Lee JS (1997) Molecular genetic analysis of Populus chloroplast DNA. In: Klopfenstein NB, Chun YW, Kim MS, Ahuja MR (eds) Micropropagation, genetic engineering, and molecular biology of Populus. US Dept. of Agriculture, Forest Service, Rocky Mountain Research Station, Fort Collins, CO, pp 143–149

    Google Scholar 

  78. Heinze B (1998) PCR-based chloroplast DNA assays for the identification of native Populus nigra and introduced poplar hybrids in Europe. Forest Genet 5:31–38

    Google Scholar 

  79. Hamza-Babiker N et al (2009) Chloroplast DNA identification of eight closely related European Salix species. Austrian J Forest Sci 126:175–193

    Google Scholar 

  80. Jarman SN (2004) Amplicon: software for designing PCR primers on aligned DNA sequences. Bioinformatics 20:1644–1645

    Article  CAS  PubMed  Google Scholar 

  81. Jabado OJ et al (2006) Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments. Nucleic Acids Res 34:6605–6611

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  82. Boyce R, Chilana P, Rose TM (2009) iCODEHOP: a new interactive program for designing COnsensus-DEgenerate Hybrid Oligonucleotide Primers from multiply aligned protein sequences. Nucleic Acids Res 37:W222–W228

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  83. Contreras-Moreira B et al (2009) primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies. Nucleic Acids Res 37:W95–W100

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  84. Lexer C et al (2005) Barrier to gene flow between two ecologically divergent Populus species, P. alba (white poplar) and P. tremula (European aspen): the role of ecology and life history in gene introgression. Mol Ecol 14:1045–1057

    Article  CAS  PubMed  Google Scholar 

  85. Turkec A, Sayar M, Heinze B (2006) Identification of sweet cherry cultivars (Prunus avium L.) and analysis of their genetic relationships by chloroplast sequence-characterised amplified regions (cpSCAR). Genet Resour Crop Evol 53:1635–1641

    Article  CAS  Google Scholar 

  86. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  87. Bassam BJ, Caetano-Anollés G (1993) Silver staining of DNA in polyacrylamide gels. Appl Biochem Biotechnol 42:181–188

    Article  CAS  Google Scholar 

  88. Flores-Renteria L, Whipple AV (2011) A new approach to improve the scoring of mononucleotide microsatellite loci. Am J Bot 98:e51–e53

    Article  PubMed  Google Scholar 

  89. Mariotti R et al (2010) Identification of new polymorphic regions and differentiation of cultivated olives (Olea europaea L.) through plastome sequence comparison. BMC Plant Biol 10:1–13

    Article  CAS  Google Scholar 

  90. Besnard G et al (2011) Genomic profiling of plastid DNA variation in the Mediterranean olive tree. BMC Plant Biol 11:80

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  91. Morris GP, Grabowski PP, Borevitz JO (2011) Genomic diversity in switchgrass (Panicum virgatum): from the continental scale to a dune landscape. Mol Ecol 20:4938–4952

    Article  PubMed Central  PubMed  Google Scholar 

  92. Vroh Bi I (1996) Improved RAPD amplification of recalcitrant plant DNA by the use of activated charcoal during DNA extraction. Plant Breed 115:205–206

    Article  CAS  Google Scholar 

  93. Lutz K et al (2011) Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing. BMC Biotechnol 11:1–9

    Article  CAS  Google Scholar 

  94. Nock CJ et al (2011) Chloroplast genome sequences from total DNA for plant identification. Plant Biotechnol J 9:328–333

    Article  CAS  PubMed  Google Scholar 

  95. Tuskan GA et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:1596–1604

    Article  CAS  PubMed  Google Scholar 

  96. Lin H, Walker MA (1997) Extracting DNA from cambium tissue for analysis of grape rootstocks. Hortscience 32:1264–1266

    CAS  Google Scholar 

  97. Colpaert N et al (2005) Sampling tissue for DNA analysis of trees: trunk cambium as an alternative to canopy leaves. Silvae Genetica 54:265–269

    Google Scholar 

  98. Tibbits J et al (2006) A rapid method for tissue collection and high-throughput isolation of genomic DNA from mature trees. Plant Mol Biol Rep 24:81–91

    Article  CAS  Google Scholar 

  99. Ayliffe MA, Timmis JN (1992) Tobacco nuclear DNA contains long tracts of homology to chloroplast DNA. Theor Appl Genet 85:229–238

    CAS  PubMed  Google Scholar 

  100. Ayliffe MA, Scott NS, Timmis JN (1998) Analysis of plastid DNA-like sequences within the nuclear genomes of higher plants. Mol Biol Evol 15:738–745

    Article  CAS  PubMed  Google Scholar 

  101. Huang CY, Ayliffe MA, Timmis JN (2003) Direct measurement of the transfer rate of chloroplast DNA into the nucleus. Nature 422:72–76

    Article  CAS  PubMed  Google Scholar 

  102. Kim K-J, Lee H-L (2005) Widespread occurrence of small inversions in the chloroplast genomes of land plants. Mol Cells 19:104–113

    CAS  PubMed  Google Scholar 

  103. Borsch T, Quandt D (2009) Mutational dynamics and phylogenetic utility of noncoding chloroplast DNA. Plant Syst Evol 282:169–199

    Article  CAS  Google Scholar 

  104. Dumolin-Lapegue S, Pemonge MH, Petit RJ (1998) Association between chloroplast and mitochondrial lineages in oaks. Mol Biol Evol 15:1321–1331

    Article  CAS  PubMed  Google Scholar 

  105. Ravi V et al (2006) The chloroplast genome of mulberry: complete nucleotide sequence, gene organization and comparative analysis. Tree Genet Genomes 3:49–59

    Article  Google Scholar 

  106. Ochoterena H (2009) Homology in coding and non-coding DNA sequences: a parsimony perspective. Plant Syst Evol 282:151–168

    Article  CAS  Google Scholar 

  107. Tangphatsornruang S et al (2011) Characterization of the complete chloroplast genome of Hevea brasiliensis reveals genome rearrangement, RNA editing sites and phylogenetic relationships. Gene 475:104–112

    Article  CAS  PubMed  Google Scholar 

  108. Schmitz-Linneweber C et al (2002) The plastid chromosome of Atropa belladonna and its comparison with that of Nicotiana tabacum: the role of RNA editing in generating divergence in the process of plant speciation. Mol Biol Evol 19:1602–1612

    Article  CAS  PubMed  Google Scholar 

  109. Schroeder H, Hoeltken AM, Fladung M (2011) Differentiation of Populus species using chloroplast single nucleotide polymorphism (SNP) markers - essential for comprehensible and reliable poplar breeding. Plant Biol 14:374–381

    Article  PubMed  CAS  Google Scholar 

  110. Sanguinetti CJ, Dias Neto E, Simpson AJG (1994) Rapid silver staining and recovery of PCR products separated on polyacrylamide gels. Biotechniques 17:915–919

    Google Scholar 

  111. Rahman MH, Jaquish B, Khasa PD (2000) Optimization of PCR protocol in microsatellite analysis with silver and SYBR® stains. Plant Mol Biol Rep 18:339–348

    Article  CAS  Google Scholar 

  112. Guicking D et al (2008) Single nucleotide sequence analysis: a cost- and time-effective protocol for the analysis of microsatellite- and indel-rich chloroplast DNA regions. Mol Ecol Resour 8:62–65

    Article  CAS  PubMed  Google Scholar 

  113. Noh EW et al (2011) Plastid genes psaM and ndhB are differentially degraded between hard and soft pines. In: 4th IUFRO conference on the breeding and genetic resources of five-needle pines, Book of Abstracts. Institute of Monitoring of Climatic and Ecological Systems SB RAS (IMCES), Tomsk, Russia, p 33

    Google Scholar 

  114. Jo YD et al (2011) Complete sequencing and comparative analyses of the pepper (Capsicum annuum L.) plastome revealed high frequency of tandem repeats and large insertion/deletions on pepper plastome. Plant Cell Rep 30:217–229

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We thank Irena Nanista, Bianca Widmar, Ingrid Gerstl, and Renate Slunsky for technical assistance in the laboratory over the years. Funding for projects was by the European Commission—research project RAP—Realising Ash’ Potential, QLK5-2001-00631; Jubiläumsfond der Stadt Wien (Migrationsforschung); and the Austrian Science Funds (P 22716-B16 Gentianella).

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Heinze, B., Koziel-Monte, A., Jahn, D. (2014). Analysis of Variation in Chloroplast DNA Sequences. In: Besse, P. (eds) Molecular Plant Taxonomy. Methods in Molecular Biology, vol 1115. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-767-9_5

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