Genome-wide analysis of plastome sequence variation and development of plastidial CAPS markers in common potato and related Solanum species
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Bryan GJ, McNicoll J, Ramsay G, Meyer RC, De Jong WS (1999) Polymorphic simple sequence repeat markers in chloroplast genomes of Solanaceous plants. Theor Appl Genet 99(5):859–867
Butler JM, Reeder DJ (2001) Detection of DNA polymorphisms using PCR-RFLP and capillary electrophoresis. Methods Mol Biol 163:49–56
Camadro EL, Carputo D, Peloquin SJ (2004) Substitutes for genome differentiation in tuber-bearing Solanum: interspecific pollen-pistil incompatibility, nuclear-cytoplasmic male sterility, and endosperm. Theor Appl Genet 109(7):1369–1376
Cardi T, Bastia T, Monti L, Earle ED (1999) Organelle DNA and male fertility variation in Solanum spp. and interspecific somatic hybrids. Theor Appl Genet 99(5):819–828
Chung H-J, Jung JD, Park H-W, Kim J-H, Cha HW, Min SR, Jeong W-J, Liu JR (2006) The complete chloroplast genome sequences of Solanum tuberosum and comparative analysis with Solanaceae species identified the presence of a 241-bp deletion in cultivated potato chloroplast DNA sequence. Plant Cell Rep 25(12):1369–1379
Daniell H, Lee S-B, Grevich J, Saski C, Quesada-Vargas T, Guda C, Tomkins J, Jansen R (2006) Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes. Theor Appl Genet 112(8):1503–1518
Dumolin-Lapègue S, Pemonge M-H, Petit RJ (1997) An enlarged set of consensus primers for the study of organelle DNA in plants. Mol Ecol 6(4):393–397
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 Res 9(3):673–690
Gargano D, Craig W, Lenzi P, Scotti N, Grillo S, Cardi T (2003) Stable plastid transformation of potato cv. Desiree with a gene involved in fatty acid desaturation. In Proceedings of the XLVII Italian Society of Agricultural Genetics—SIGA Annual Congress, Verona, Italy. www.siga.unina.it/SIGA2003/2005_2030.htm
Gargano D, Vezzi A, Scotti N, Gray JC, Valle G, Grillo S, Cardi T (2005) The complete nucleotide sequence genome of potato (Solanum tuberosum cv. Désirée) chloroplast DNA. In Proceedings of the 2nd Solanaceae Genome Workshop 2005, Ischia, Italy, p 107
Hawkes JG (1990) The Potato: evolution, biodiversity and genetic resources. Belhaven Press, London, UK
Hawkes JG (1994) Origins of cultivated potatoes and species relationships. In: Bradshaw JE, Mackay GR (eds) Potato genetics. CAB International, Cambridge, pp 3–42
Hollingsworth PM, Forrest LL, Spouge JL, Hajibabaei M, Ratnasingham S, van der Bank M, Chase MW, Cowan RS, Erickson DL, Fazekas AJ, Graham SW, James KE, Kim K-J, Kress WJ, Schneider H, van AlphenStahl J, Barrett SCH, van den Berg C, Bogarin D, Burgess KS, Cameron KM, Carine M, Chacon J, Clark A, Clarkson JJ, Conrad F, Devey DS, Ford CS, Hedderson TAJ, Hollingsworth ML, Husband BC, Kelly LJ, Kesanakurti PR, Kim JS, Kim Y-D, Lahaye R, Lee H-L, Long DG, Madrinan S, Maurin O, Meusnier I, Newmaster SG, Park C-W, Percy DM, Petersen G, Richardson JE, Salazar GA, Savolainen V, Seberg O, Wilkinson MJ, Yi D-K, Little DP (2009) A DNA barcode for land plants. Proc Natl Acad Sci USA 106(31):12794–12797
Horning ME, Cronn RC (2006) Length polymorphism scanning is an efficient approach for revealing chloroplast DNA variation. Genome 49(2):134–142
Hosaka K (2002) Distribution of the 241 bp deletion of chloroplast DNA in wild potato species. Am J Potato Res 79(2):119–123
Ingvarsson PK, Ribstein S, Taylor DR (2003) Molecular evolution of insertions and deletion in the chloroplast genome of silene. Mol Biol Evol 20(11):1737–1740
Kahlau S, Aspinall S, Gray JC, Bock R (2006) Sequence of the tomato chloroplast DNA and evolutionary comparison of solanaceous plastid genomes. J Mol Evol 63(2):194–207
Kelchner SA (2000) The evolution of non-coding chloroplast DNA and its application in plant systematics. Ann Missouri Bot Gard 87(4):482–498
Kim K-J, Lee H-L (2005) Widespread occurrence of small inversions in the chloroplast genomes of land plants. Mol Cells 19(1):104–113
Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH (2005) Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci USA 102(23):8369–8374
Martyrosyan EV, Ryzhova NN, Kochieva EZ (2007) Polymorphism of chloroplast microsatellite DNA loci in Russian potato cultivars. Genetika 43(11):1325–1327
Masood MS, Nishikawa T, Fukuoka S, Njenga PK, Tsudzuki T, Kadowaki K (2004) The complete nucleotide sequence of wild rice (Oryza nivara) chloroplast genome: first genome wide comparative sequence analysis of wild and cultivated rice. Gene 340(1):133–139
Nguyen TT, Nugent G, Cardi T, Dix PJ (2005) Generation of homoplasmic plastid transformants of a commercial cultivar of potato (Solanum tuberosum L.). Plant Sci 168(6):1495–1500
Olmstead RG, Palmer JD (1994) Chloroplast DNA systematics: a review of methods and data analysis. Am J Bot 81(9):1205–1224
Orczyk W, Przetakiewicz J, Nadolska-Orczyk A (2003) Somatic hybrids of Solanum tuberosum–application to genetics and breeding. Plant Cell Tiss Organ Cult 74(1):1–13
Perl A, Aviv D, Galun E (1991) Nuclear-organelle interaction in Solanum: interspecific cybridizations and their correlation with a plastome dendrogram. Mol Gen Genet 228(1–2):193–200
Powell W, Morgante M, McDevitt R, Vendramin GG, Rafalski JA (1995) Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines. Proc Natl Acad Sci USA 92(17):7759–7763
Provan J, Powell W, Dewar H, Bryan G, Machray GC, Waugh R (1999) An extreme cytoplasmic bottleneck in the modern European cultivated potato (Solanum tuberosum) is not reflected in decreased levels of nuclear diversity. Proc R Soc Lond B 266(1419):633–639
Provan J, Powell W, Hollingsworth PM (2001) Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends Ecol Evol 16(3):142–147
Schmitz-Linneweber C, Regel R, Du TG, Hupfer H, Herrmann RG, Maier RM (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(9):1602–1612
Schwartz S, Elnitski L, Li M, Weirauch M, Riemer C, Smit A, Program NCS, Green ED, Hardison RC, Miller W (2003) MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences. Nucl Acids Res 31(13):3518–3524
Scotti N, Monti L, Cardi T (2003) Organelle DNA variation in parental Solanum spp. genotypes and nuclear-cytoplasmic interactions in Solanum tuberosum (+) S. commersonii somatic hybrid-backcross progeny. Theor Appl Genet 108(1):87–94
Shaw J, Lickey EB, Beck JT, Farmer SB, Liu W, Miller J, Siripun KC, Winder CT, Schilling EE, Small RL (2005) The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am J Bot 92(1):142–166
Shaw J, Lickey EB, Schilling EE, Small RL (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(3):275–288
Sidorov VA, Kasten D, Pang S-Z, Hajdukiewicz PTJ, Staub JM, Nehra NS (1999) Stable chloroplast transformation in potato: use of green fluorescent protein as a plastid marker. Plant J 19(2):209–216
Simmons MP, Ochoterena H (2000) Gaps as characters in sequence-based phylogenetic analyses. Syst Biol 49(2):369–381
Small RL, Ryburn JA, Cronn RC, Seelanan T, Wendel JF (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(9):1301–1315
Spooner DM (2009) DNA barcoding will frequently fail in complicated groups: an example in wild potatoes. Am J Bot 96(6):1177–1189
Spooner DM, Castillo RT (1997) Reexamination of series relationships of South American wild potatoes (Solanaceae: Solanum sect. Petota): evidence from chloroplast DNA restriction site variation. Am J Bot 84(5):671–685
Tian S, Luo LC, Ge S, Zhang ZY (2008) Clear genetic structure of Pinus kwangtungensis (Pinaceae) revealed by a plastid DNA fragment with a novel minisatellite. Ann Bot 102(1):69–78
Timme RE, Kuehl JV, Boore JL, Jansen RK (2007) A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats. Am J Bot 94(3):302–312
Valkov VT, Scotti N, Kahlau S, MacLean D, Grillo S, Gray JC, Bock R, Cardi T (2009) Genome-wide analysis of plastid gene expression in potato leaf chloroplasts and tuber amyloplasts: transcriptional and posttranscriptional control. Plant Physiol 150(4):2030–2044
Valkov VT, Gargano D, Manna C, Formisano G, Dix PJ, Gray JC, Scotti N, Cardi T (2011) High efficiency plastid transformation in potato and regulation of transgene expression in leaves and tubers by alternative 5′ and 3′ regulatory sequences. Transgenic Res 20(1):137–151
Verma D, Daniell H (2007) Chloroplast vector systems for biotechnology applications. Plant Physiol 145(4):1129–1143
Waugh R, Glendinning DR, Duncan N, Powell W (1990) Chloroplast DNA variation in European potato cultivars. Potato Res 33(4):505–513
Wilkinson L, Hill MA, Vang E (1992) SYSTAT: statistics. Version 5.2 ed. SYSTAT Inc, Evanston
Yamane K, Yano K, Kawahara T (2006) Pattern and rate of indel evolution inferred from whole chloroplast intergenic regions in sugarcane, maize and rice. DNA Res 13(5):197–204