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Repetitive Sequences in the Potato and Related Genomes

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The Potato Genome

Part of the book series: Compendium of Plant Genomes ((CPG))

Abstract

Repetitive sequence elements refer to sequences which are repeated a number of times in the genome and are generally composed of either the interspersed elements or tandem repeats, which may be coding or non-coding. Solanum genomes, like that of potato and tomato, are exceptionally rich in repetitive elements and have evolved by the multidirectional activities of the repetitive elements. Interspersed elements, in particular, have contributed to the evolution of Solanum genomes, not only by their amplification in the genome, but also by their association with different genes. The genomic proximity of interspersed elements to genes may influence the expression patterns, development of alternative functions, emergence of new genes or elimination of existing genes. Long terminal repeat (LTR) retrotransposons represent the most abundant class of repetitive elements among all the repeats and they are also considered the progenitors of some genes and other types of repeats such as microsatellites. Centromeric, telomeric, minisatellites and microsatellites constitute tandem repeats, which are abundant in the Solanum genomes. The patterns of occurrence and abundance of repeats vary among different species of Solanum, although a careful analysis reveals a number of perceptible evolutionary trends. Tandem repeats, particularly microsatellites, have frequently been exploited for the development of molecular markers for diverse applications in potato. The present chapter deals with the occurrence and distribution of different categories of repetitive elements in potato and the related Solanum genomes.

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References

  • Abad JP, de Pablos B, Agudo M, Molina I, Giovinazzo G, Martin Gallardo A, Villasante A (2004) Genomic and cytological analysis of the Y chromosome of Drosophila melanogaster: telomere-derived sequences at internal regions. Chromosoma 113:295–304

    Article  CAS  PubMed  Google Scholar 

  • Alfenito MR, Birchler JA (1993) Molecular characterization of a maize B chromosome centric sequence. Genetics 135:589–597

    CAS  PubMed  PubMed Central  Google Scholar 

  • Araujo PG, Casacuberts JM, Costa APP, Hashimoto RY, Grandbastien MA, Van Sluys MA (2001) Retrolyc1 subfamilies defined by different U3 LTR regulatory regions in the Lycopersicon genus. Mol Genet Genomics 266:35–41

    Article  CAS  PubMed  Google Scholar 

  • Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218

    Article  CAS  Google Scholar 

  • Ashkenazi V, Chani E, Lavi U, Levy D, Hillel J, Veilleux RE (2001) Development of microsatellite markers in potato and their use in phylogenetic and fingerprinting analyses. Genome 44:50–62

    Article  CAS  PubMed  Google Scholar 

  • Baucom RS, Estill JC, Chaparro C, Upshaw N, Jogi A, Deragon JM, Westerman RP, Sanmiguel PJ, Bennetzen JL (2009) Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome. PLoS Genet 5:e1000732

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Becker J, Heun M (1995) Mapping of digested and undigested random amplified microsatellite polymorphisms in barley. Genome 38:991–998

    Google Scholar 

  • Bennetzen JL (2000) Transposable element contributions to plant gene and genome evolution. Plant Mol Biol 42:251–269

    Article  CAS  PubMed  Google Scholar 

  • Bennetzen JL, Ma J, Devos KM (2005) Mechanisms of recent genome size variation in flowering plants. Ann Bot (Lond.) 95:127–132

    Article  CAS  Google Scholar 

  • Bennetzen JL, Wang H (2014) The contributions of transposable elements to the structure, function and evolution of plant genomes. Ann Rev Plant Biol 65:505–530

    Article  CAS  Google Scholar 

  • Boeke JD (1997) LINEs and Alus—The poly A connection. Nat Genet 16:6–7

    Article  CAS  PubMed  Google Scholar 

  • Bolzan AD (2012) Chromosomal aberrations involving telomeres and interstitial telomeric sequences. Mutagenesis 27:1–15

    Article  CAS  PubMed  Google Scholar 

  • Bornet B, Goraguer F, Joly G, Branchard M (2002) Genetic diversity in European and Argentinian cultivated potatoes (Solanum tuberosum subsp. tubersosum) detected by inter-simple sequence repeats (ISSRs). Genome 45:481–484

    Google Scholar 

  • Bureau TE, Wessler SR (1992) Tourist: a large family of small inverted repeat elements frequently associated with maize genes. Plant Cell 4:1283–1294

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bureau TE, Wessler SR (1994) Stowaway: A new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants. Plant Cell 6:907–916

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Casa AM, Brouwer C, Nagel A, Wang L, Zhang Q, Kresovich S, Wessler SR (2000) The MITE family Heartbreaker (Hbr): molecular markers in maize. Proc Natl Acad Sci 97:10083–10089

    Google Scholar 

  • Chang RY, O’Donoughue LS, Bureau TE (2001) Inter-MITE polymorphisms (IMP): a high throughput transposon-based genome mapping and fingerprinting approach. Theor Appl Genet 102:773–781

    Google Scholar 

  • Chani E, Ashkenazi V, Hillel J, Veilleux RE (2002) Microsatellite marker analysis of an anther-derived potato family: skewed segregation and gene centromere mapping. Genome 45:236–242

    Google Scholar 

  • Charlesworth B, Sniegowski P, Stephan W (1994) The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371:215–220

    Google Scholar 

  • Cheng ZJ, Murata M (2003) A centromeric tandem repeat family originating from a part of Ty3/gypsy-retroelement in wheat and its realtives. Genetics 164:665–672

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cifarelli RA, Gallitelli M, Cellini F (1995) Random amplified hybridization microsatellites (RAHM): isolation of a new class of microsatellite-containing DNA clones. Nucleic Acids Res 23:3802–3803

    Google Scholar 

  • Costa APP, Scortecci K, Hashimoto RY, Araujo PG, Grandbastien MA, van Sluys MA (1999) Retrolyc-1, a member of the Tnt1 retrotransposon super-family in the Lycopersicon peruvianum genome. Genetica 197:65–72

    Article  Google Scholar 

  • Dewannieux M, Esnault C, Heidmann T (2003) LINE-mediated retrotransposition of marked Alu sequences. Nat Genet 35:41–48

    Article  CAS  PubMed  Google Scholar 

  • Dong F, Song J, Naess SK, Helgeson JP, Gebhardt C, Jiang J (2000) Development and applications of a set of chromosome-specific cytogenetic DNA markers in potato. Theor Appl Genet 101:1001–1007

    Article  CAS  Google Scholar 

  • Edwards D, Coghill J, Batley J, Holdsworth M, Edwards KJ  (2002) Amplification and detection of transposon insertion flanking sequences using fluorescent MuAFLP. Biotechniques 32:1090–1097

    Google Scholar 

  • Ender A, Schwenk K, Stadler T, Streit B, Schierwater B (1996) RAPD identification of microsatellites in Daphnia. Mol Ecol 5:437–441

    Google Scholar 

  • Feingold S, Lloyd J, Norero N, Bonierbale M, Lorenzen J (2005) Mapping and characterization of new EST-derived microsatellites for potato (Solanum tuberosum L.). Theor Appl Genet 111:456–466

    Google Scholar 

  • Frello S, Orgaard M, Jacobsen N, Heslop-Harrison JS (2004) The genomic organization adn evolutionary distribution of a tandemly repeated DNA sequence family in the genus Crocus (Iridiaceae). Hereditas 141:81–88

    Article  CAS  PubMed  Google Scholar 

  • Frey M, Stettner C, Gierl A (1998) A general method for gene isolation in tagging approaches: amplification of insertion mutagenised sites (AIMS). Plant J 13:717–721

    Google Scholar 

  • Ganal MW, Lapitan NLV, Tanksley SD (1988) A molecular and cytogenetic survey of major repeated DNA sequences in tomato (Lycopersicon esculentum). Mol Gen Genet 213:262–268

    Article  CAS  Google Scholar 

  • Gebhardt C, Eberle B, Leonards-Schippers C, Walkemeier B, Salamini F (1995) Isolation, characterization and RFLP linkage mapping of a DNA repeat family of Solanum spegazzinii by which chromosome ends can be localized on the genetic map of potato. Genet Res 65:1–10

    Google Scholar 

  • Ghislain M, Spooner DM, Rodriguez F, Villamon F, Nunez J, Vasquez C, Waugh R, Bonierbale M (2004) Selection of highly informative and user-friendly microsatellites (SSRs) for genotyping of cultivated potato. Theor Appl Genet 108:881–890

    Google Scholar 

  • Ghislain M, Nunez J, del Rosarion Herrera M, Pignataro J, Guzman F, Bonierbale M, Spooner DM (2009) Robust and highly informative microsatellite-based genetic identity kit for potato. Mol Breed 23:377–388

    Article  CAS  Google Scholar 

  • Gong Z, Wu Y, Koblízková A, Torres GA, Wang K, Iovene M, Neumann P, Zhang W, Novak P, Buell CR, Macas J, Jiang J (2012) Repeatless and repeat-based centromeres in potato: implications for centromere evolution. Plant Cell 24:3559–3574

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gorji AM, Poczai P, Polgar Z, Taller J (2011) Efficiency of Arbitrarily Amplified Dominant Markers (SCOT, ISSR and RAPD) for Diagnostic Fingerprinting in Tetraploid Potato. Am J Potato Res 88:226–237

    Google Scholar 

  • Grandbastien MA, Spielmann A, Caboche M (1989) Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature 337:376–380

    Google Scholar 

  • Grandbastien MA, Audeon C, Bonnivard E, Casacuberta JM, Chalhoub B, Costa APP, Le QH, Melayah D, Petit M, Poncet C, Tam SM, van Sluys MA, Mhiri C (2005) Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae. Cytogenet Genome Res 110:229–241

    Google Scholar 

  • Grover A, Sharma PC (2011) Is spatial occurrence of microsatellites in the genome a determinant of their function and dynamics contributing to genome evolution? Curr Sci 100:859–869

    CAS  Google Scholar 

  • Grover A, Sharma PC (2012) Tandem repetitions in transcriptomes of some Solanaceae species. Am J Mol Biol 2:140–152

    Article  CAS  Google Scholar 

  • Grover A, Aishwarya V, Sharma PC (2007) Biased distribution of microsatellite motifs in the rice genome. Mol Genet Genomics 277:469–480

    Article  CAS  PubMed  Google Scholar 

  • Grover A, Ramesh B, Sharma PC (2009) Development of microsatellite markers in potato and their transferability in some members of Solanaceae. Physiol Mol Biol Plants 15:343–358

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Grover A, Gupta SM, Pandey P, Singh S, Ahmed Z (2012) Random genomic scans at microsatellite loci for genetic diversity estimation in cold adapted Lepidium latifolium. Plant Genet Resour-Characterization Utilization 10:224–231

    Article  CAS  Google Scholar 

  • Hayden MJ, Sharp PJ (2001) Sequence-tagged microsatellite profiling (STMP): a rapid technique for developing SSR markers. Nucleic Acids Res 29:e43

    Google Scholar 

  • He L, Liu J, Torres GA, Zhang H, Jiang J, Xie C (2013) Interstitial telomeric repeats are enriched in the centromeres of chromosomes in Solanum species. Chromosome Res 21:5–13

    Article  CAS  PubMed  Google Scholar 

  • Huang KC, Yang HC, Li KT, Liu LY, Charng YC (2012) Ds transposon is biased towards providing splice donor sites for exonization in transgenic tobacco. Plant Mol Biol 79:509–519

    Article  CAS  PubMed  Google Scholar 

  • Jacobs JME, van Eck HJ, Arens P, Verkerk-Bakker B, te Lintel Hekkert B, Bastiaanssen HJM, El-Kharbotly A, Pereira A, Jacobsen E, Stiekema WJ (1995) A genetic map of potato (Solanum tuberosum) integrating molecular markers, including transposons, and classical markers. Theor Appl Genet 91:289–300

    Article  CAS  PubMed  Google Scholar 

  • Jin WW, Lamb JC, Vega JM, Dawe RK, Birchler JA, Jiang JM (2005) Molecular and functional dissection of the maize B centromere. Plant Cell 17:1412–1423

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jiang J, Birchler JB, Parrott WA, Dawe RK (2003) A molecular view of plant centromeres. Trends Plant Sci 8:570–575

    Article  CAS  PubMed  Google Scholar 

  • Jiang N, Gao D, Xiao H, van der Knaap E (2009) Genome organization of the tomato sun locus and characterization of the unusual retrotransposon Rider. Plant J 60:181–193

    Article  CAS  PubMed  Google Scholar 

  • Kajikawa M, Okada N (2002) LINEs mobilize SINEs in the eel through a shared 39 sequence. Cell 111:433–444

    Article  CAS  PubMed  Google Scholar 

  • Kalendar R, Grob T, Regina M, Suoniemi A, Schulman A (1999) IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theor Appl Genet 98:704–711

    Google Scholar 

  • Kawchuk LM, Lynch DM, Thomas J, Penner B, Sillito D, Kulcsar F (1996) Characterization of Solanum tuberosum simple sequence repeats and application to potato cultiwar identification. Am Potato J 73:325–335

    Google Scholar 

  • Kriedt RA, Cruz GMQ, Bonatto SL, Freitas LB (2014) Novel transposable elements in solanaceae: evolutionary relationships among Tnt1-related sequences in wild petunia species. Plant Mol Biol 32:142

    Article  CAS  Google Scholar 

  • Komarova NY, Grabe T, Huigen DJ, Hemleben V, Volkov RA (2004) Organization, differential expression and methylation of rDNA in artificial Solanum allopolyploids. Plant Mol Biol 56:439–463

    Article  CAS  PubMed  Google Scholar 

  • Korandova M, Krucek T, Vrbova K, Frydrychova RC (2014) Distribution of TTAGG-specific telomerase activity in insects. Chromosome Res 22:495–503

    Article  CAS  PubMed  Google Scholar 

  • Kumar A, Bennetzen JL (1999) Plant Retrotransposons. Annu Rev Genet 33:479–532

    Article  CAS  PubMed  Google Scholar 

  • Langdon T, Seago C, Jones RN, Ougham H, Thomas H, Foster JW, Jenkins G (2000) De novo evolution of satellite DNA on the rye B chromosome. Genetics 154:869–884

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lapitan NLV (1992) Organization and evolution of higher plant nuclear genomes. Genome 35:171–181

    Article  CAS  Google Scholar 

  • Lara-Carbrera SI, Spooner DM (2000) Taxonomy of Mexican diploid potato (Solanum sect Petota) species: Morphological and microsatellite data. United States Department of Agriculture, Agriculture Research Service

    Google Scholar 

  • Lin KW, Yan J (2008) Endings in the middle: current knowledge of interstitial telomeric sequences. Mutat Res 658:95–110

    Article  CAS  PubMed  Google Scholar 

  • Lisch D (2013) How important are transposons for plant evolution? Nat Rev Genet 14:49–61

    Article  CAS  PubMed  Google Scholar 

  • Litt M, Luty JA (1989) A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet 44:397–401

    Google Scholar 

  • Lockton S, Gaut BS (2009) The contribution of transposable elements to expressed coding sequence in Arabidopsis thaliana. J Mol Evol 68:80–89

    Article  CAS  PubMed  Google Scholar 

  • Lunt DH, Hutchinson WF, Carvalho GR (1999) An efficient method for PCR-based isolation of microsatellite arrays (PIMA). Mol Ecol 8:891–893

    Google Scholar 

  • Macas J, Meszaros T, Nouzova M (2002) PlantSat: A specialized database for plant satellite repeats. Bioinformatics 18:28–35

    Article  CAS  PubMed  Google Scholar 

  • Makalowski W (2000) Genomic scrap yard: how genomes utilize all that junk. Gene 259:61–67

    Article  CAS  PubMed  Google Scholar 

  • Malkamaki U, Clark MS, Rita H, Valkonen JPT, Pehu E (1996) Analyses of solanaceous species using repetitive genomic DNA sequences isolated from Solanum brevidens. Plant Sci 117:121–129

    Article  Google Scholar 

  • Manetti ME, Rossi M, Costa APP, Clausen AM, Sluys MAV (2007) Radiation of the TntI retrotransposons superfamily in three Solanaceae genera. BMC Evol Biol 7:34

    Google Scholar 

  • Matioli SR, de Brito RA (1995) Obtaining genetic markers by using double stringency PCR with microsatellites and arbitrary primers. Biotechniques 19:752–756

    Google Scholar 

  • McGregor CE, Greyling M, Warnich L (2000a) The use of simple sequence repeats (SSRs) to identify commercially important potato (Solanum tuberosum L.) cultivars in South Africa. S Afr J Plant Biol 17:177–180

    Article  CAS  Google Scholar 

  • McGregor CE, Lambert CA, Greyling M, Louw JH, Warnich L (2000b) A comparative assessment of DNA fingerprinting techniques (RAPD, ISSR, AFLP and SSR) in potato (Solanum tuberosum L.) germplasm. Euphytica 113:135–144

    Article  CAS  Google Scholar 

  • Mehra M, Gangwar I, Shankar R (2015) A deluge of complex repeats: The Solanum Genome. PLoS ONE 10(8):e0133962

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Melters DP, Bradnam KR, Young HA, Telis N, May MR, Ruby JG, Sebra R, Peluso P, Eid J, Rank D, Garcia JF, DeRisi JL, Smith T, Tobias C, Ross-Ibarra J, Korf I, Chan SWL (2013) Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. Genome Biol 14:R10

    Article  PubMed  PubMed Central  Google Scholar 

  • Mendez-Lago M, Wild J, Whitehead SL, Tracey A, de Pablos B, Rogers J, Szybalski W, Villasante A (2009) Novel sequencing strategy for repetitive DNA in a Drosophila BAC clone reveals that the centromeric region of the Y chromosome evolved from a telomere. Nucleic Acids Res 37:2264–2273

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Meyer W, Mitchell TG, Freedman EZ, Vilgalys R (1993) Hybridization probes for conventional DNA fingerprinting used as single primers in the polymerase chain reaction to distinguish strains of Cryptococcus neoformans. J Clin Microbiol 31:2274–2280

    Google Scholar 

  • Milbourne D, Meyer R, Bradshaw JE, Baird E, Bonar N, Provan J, Powell W, Waugh R (1997) Comparison of PCR based marker systems for the analysis of genetic relationships in cultivated potato. Mol Breed 3:127–136

    Article  CAS  Google Scholar 

  • Milbourne D, Meyer RC, Collins AJ, Ramsay LD, Gebhardt C, Waugh R (1998) Isolation, characterization and mapping of simple sequence repeat loci in potato. Mol Gen Genet 259:233–245

    Article  CAS  PubMed  Google Scholar 

  • Min WK, Han JH, Kang WH, Lee HR, Kim BD (2008) Reverse random amplified microsatellite polymorphism reveals enhanced polymorphisms in the 3′ end of simple sequence repeats in the pepper genome. Mol Cells 26:250–257

    Google Scholar 

  • Momose M, Abe Y, Ozeki Y (2010) Miniature inverted-repeat transposable elements of stowaway are active in potato. Genetics 186:59–66

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moniz de Sa M, Drouin G (1996) Phylogeny and substitution rates of angiosperm actin genes. Mol Biol Evol 13:1198–1212

    Article  CAS  PubMed  Google Scholar 

  • Morgante M, Vogel JM (1999) Compound microsatellite primers for the detection of genetic polymorphisms. U.S. Patent No. 5:955, 276

    Google Scholar 

  • Muotri AR, Marchetto MC, Coufal NG, Gage FH (2007) The necessary junk: new functions for transposable elements. Hum Mol Genet 2:R159–R167

    Article  CAS  Google Scholar 

  • Nagaki K, Talbert PB, Zhong CX, Dawe RK, Henikoff S, Jiang J (2003) Chromatin immunoprecipitation reveals that the 180-bp satellite repeat is the key functional DNA element of Arabidopsis thaliana centromeres. Genetics 163(3):1221–1225

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nagaki K, Shibata F, Suzuki G, Kanatani A, Ozaki S, Hironaka A, Kashihara K, Murata M (2011) Coexistence of NtCENH3 and two retrotransposons in tobacco centromeres. Chromosome Res 19(5):591–605

    Article  CAS  PubMed  Google Scholar 

  • Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin YC, Scofield DG, Vezzi F, Delhomme N, Giacomello S et al (2013) The Norway spruce genome sequence and conifer genome evolution. Nature 497:579–584

    Article  CAS  PubMed  Google Scholar 

  • Oosumi T, Garlick B, Belknap WR (1995) Identification and characterization of putative transposable DNA elements in solanaceous plants and Caenorhabditis elegans. Proc Natl Acad Sci USA 92:8886–8890

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Osborne BI, Corr CA, Prince JP, Hehl R, Tanksley SD, McCormick S, Baker B (1991) Ac transposition from a TDNA can generate linked and unlinked clusters of insertions in the tomato genome. Genetics 129:833–844

    CAS  PubMed  PubMed Central  Google Scholar 

  • Park KC, Kim NH, Cho YS, Kang KH, Lee JK, Kim NS (2003) Genetic variations of AA genome Oryza species measured by MITE-AFLP. Theor Appl Genet 197:203–209

    Google Scholar 

  • Pasero P, Sjakste N, Blettry C, Got C, Marilley M (1993) Long-range organization and sequence directed curvature of Xenopus laevis satellite 1 DNA. Nucleic Acids Res 21:4703–4710

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Paz RC, Rendina Gonzalez AP, Ferrer MS, Masuelli RW (2015) Short-term hybridization activates Tnt1 and Tto1 copia retrotransposons in wild tuber bearing Solanum species. Plant Biol (Stuttg) 17:860–869

    Article  CAS  Google Scholar 

  • Pehu E, Thomas M, Poutala T, Karp A, Jones MGK (1990) Species-specific sequences in the genus Solanum: identification, characterization, and application to study somatic hybrids of S. brevidens and S. tuberosum. Theor Appl Genet 80:693–698

    Google Scholar 

  • Peters SA, Bargesten JW, Szinay D, van de Belt J, Visser RGF, Bai Y, de Jong H (2012) Structural homology in the Solanaceae: analysis of genomic regions in support of synteny studies in tomato, potato and pepper. Plant J 71:602–614

    Article  CAS  PubMed  Google Scholar 

  • Pozueta-Romero J, Houlne G, Schantz R (1998) Identification of a short interspersed repetitive element in partially spliced transcripts of the bell pepper (Capsicum annuum) PAP gene: New evolutionary and regulatory aspects on plant tRNA-related SINEs. Gene 214:51–58

    Article  CAS  PubMed  Google Scholar 

  • Preiszner J, Takacs I, Bilgin M, Gyorgyey J, Dudits D, Feher A (1994) Organization of a Solatium brevidens repetitive sequence related to the TGRI subtelomeric repeats of Lycopersicon esculentum. Theor Appl Genet 89:1–8

    Google Scholar 

  • Presting GG, Frary A, Pillen K, Tanksley SD (1996) Telomere homologous sequences occur near the centromeres of many tomato chromosomes. Mol Gen Genet 251:526–531

    Article  CAS  PubMed  Google Scholar 

  • Prevost A, Wilkinson MJ (1999) A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theor Appl Genet 98:107–112

    Google Scholar 

  • Provan J, Powell W, Waugh R (1996) Microsatellite analysis of relationships within cultivated potato (Solanum tuberosum). Theor Appl Genet 92:1078–1084

    Article  CAS  PubMed  Google Scholar 

  • Raker CM, Spooner DM (2002) Chilean Tetraploid Cultivated Potato, Solanum tuberosum, is Distinct from the Andean Populations: Microsatellite Data. Crop Sci 42:1451–1458

    Google Scholar 

  • Richardson T, Cato S, Ramser J, Kahl G, Weising K (1995) Hybridization of microsatellites to RAPD: a new source of polymorphic markers. Nucleic Acids Res 23:3798–3799

    Google Scholar 

  • Rokka VM, Clark MS, Knudson DL, Pehu E, Lapitan NLV (1998) Cytological and molecular characterization of repetitive DNA sequences of Solanum brevidens and Solanum tuberosum. Genome 41:487–494

    Google Scholar 

  • Roorkiwal M, Grover A, Sharma PC (2009) Genome-wide analysis of conservation and divergence of microsatellites in rice. Mol Genet Genomics 282:205–215

    Article  CAS  PubMed  Google Scholar 

  • Rossi M, Araujo PG, de Jesus EM, Varani AM, Van Sluys MA (2004) Comparative analysis of Mutator-like transposases in sugarcane. Mol Genet Genomics 272:194–203

    Article  CAS  PubMed  Google Scholar 

  • Rossi MS, Pesce CG, Reig OA, Kornblihtt AR, Zorzopulos J (1993) Retroviral-like features in the monomer of the major satellite DNA from the South American rodents of the genus Ctenomys. DNA Seq 3:379–381

    Article  CAS  PubMed  Google Scholar 

  • Salser W, Bowen S, Browne D, El Adli N, Fedoroff N, Fry K, Heindell H, Paddock G, Poon R, Wallace B, Whitcome P (1976) Investigation of the organization of mammalian chromosomes at the DNA sequence level. Fed Proc 35:23–35

    CAS  PubMed  Google Scholar 

  • Sampath P, Murukarthick J, Izzah NK, Lee J, Choi HI, Shirasawa K, Choi BS, Liu S, Nou IS, Yang TJ (2014) Genome-wide comparative analysis of 20 miniature inverted-repeat transposable element families in Brassica rapa and B. oleracea. PLoS ONE 9:e94499

    Google Scholar 

  • San Miguel P, Bennetzen JL (1998) Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Annals Bot 82:37–44

    Article  CAS  Google Scholar 

  • Schmidt T, Heslop-Harrison JS (1993) Variability and evolution of highly repeated DNA sequences in the genus Beta. Genome 36:1074–1079

    Article  CAS  PubMed  Google Scholar 

  • Schneider K, Douches DS (1997) Assessment of PCR based simple sequence repeats to fingerprint North American potato cultivars. Am Potato J 74:149–160

    Article  CAS  Google Scholar 

  • Schweizer G, Borisjuk N, Borisjuk L, Stafler M, Stelzer T, Schilde L, Hemleben V (1993) Molecular analysis of highly repeated genome fractions in Solanum and their use as markers for the characterization of species and cultivars. Theor Appl Genet 85:801–808

    CAS  PubMed  Google Scholar 

  • Sharma PC, Grover A, Kahl G (2007) Mining microsatellites in eukaryotic genomes. Trends Biotechnol 25:490–498

    Article  CAS  PubMed  Google Scholar 

  • Sharma V, Nandineni MR (2014) Assessment of genetic diversity among Indian potato (Solanum tuberosum L.) collection using microsatellite and retrotransposon based marker systems. Mol Phylogenet Evol 73:10–17

    Article  CAS  PubMed  Google Scholar 

  • Sherman JD, Stack SM (1995) Two-dimensional spreads of synaptonemal complexes from Solanaceous plants. VI. High-resolution recombination nodule map for tomato (Lycopersicon esculentum). Genetics 141:683–708

    CAS  PubMed  PubMed Central  Google Scholar 

  • Singer MF (1982) Highly repeated sequences in mammalian genomes. Int Rev Cytol 76:67–112

    Article  CAS  PubMed  Google Scholar 

  • Smith GP (1976) Evolution of repeated DNA sequences by unequal crossover. Science 191:528–535

    Article  CAS  PubMed  Google Scholar 

  • Sorek R (2007) The birth of new exons: Mechanisms and evolutionary consequences. RNA 13:1603–1608

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Spooner DM, Nunez J, Rodriguez F, Naik PS, Ghislain M (2005) Nuclear and chloroplast DNA reassessment of the origin of Indian potato varieties and its implications for the origin of the early European potato. Theoret Appl Genet 110:1020–1026

    Google Scholar 

  • Spooner DM, Nunez J, Trujillo G, Herrera MR, Guzman F, Ghislain M (2007) Extensive simple sequence repeat genotyping of potato landraces supports a major re-evaluation of their gene pool structure and classification. Proc Natl Acad Sci USA 104:19398–19403

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stadler M, Stelzer T, Borisjuk N, Zanke C, Schilde-Rentschler L, Hemleben V (1995) Distribution of novel and known repeated elements of Solanum and application for the identification of somatic hybrids among Solanum species. Theor Appl Genet 91:1271–1278

    Article  CAS  PubMed  Google Scholar 

  • Staton SE, Bakken BH, Blackman BK, Chapman MA, Kane NC, Tang S, Ungerer MC, Knapp SJ, Rieseberg LH, Burke JM (2012) The sunflower (Helianthus annuus L.) genome reflects a recent history of biased accumulation of transposable elements. Plant J 72(1):142–153

    Article  CAS  PubMed  Google Scholar 

  • Stupar RM, Song J, Tek AL, Cheng Z, Dong F, Jiang J (2002) Highly condensed potato pericentromeric heterochromatin contains rDNA-related tandem repeats. Genetics 162:1435–1444

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tang J, Baldwin SJ, Jacobs JME, van der Linden CG, Voorrips RE, Leunissen JAM, van Eck H, Vosman B (2008) Large-scale identification of polymorphic microsatellites using an in silico approach. BMC Bioinformatics 9:374

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tang X, Datema E, Guzman MO, de Boer JM, van Eck HJ, Bachem CW, Visser RG, de Jong H (2014) Chromosomal organizations of major repeat families on potato (Solanum tuberosum) and further exploring in its sequenced genome. Mol Genet Genomics 289:1307–1319

    Article  CAS  PubMed  Google Scholar 

  • Tanksley SD, Ganal MW, Prince JP, de Vicente MC, Bonierbale MW, Broun P, Fulton TM, Giovannoni JJ, Grandillo S, Martin GB, Messeguer R, Miller JC, Miller L, Paterson AH, Pineda O, Roder MS, Wing RA, Wu W, Young ND (1992) High density molecular linkage maps of the tomato and potato genomes. Genetics 132:1141–1160

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tek AL, Jiang J (2004) The centromeric regions of potato chromosomes contain megabase-sized tandem arrays of telomere-similar sequence. Chromosoma 113:77–83

    Article  CAS  PubMed  Google Scholar 

  • Tek AL, Song J, Macas J, Jiang J (2005) Sobo, a recently amplified satellite repeat of potato, and its implications for the origin of tandemly repeated sequences. Genetics 170:1231–1238

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Temnykh S, DeClerk G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations and genetic marker potential. Genome Res 11:1441–1452

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • The Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–197

    Article  CAS  Google Scholar 

  • The Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641

    Article  CAS  Google Scholar 

  • Torres GA, Gong Z, Iovene M, Hirsch CD, Buell CR, Bryan GJ, Novak P, Macas J, Jiang J (2011) Organization and evolution of subtelomeric satellite repeats in the potato genome. G3 (Bethesda) 1:85–92

    Google Scholar 

  • Treangen TJ, Salzberg SL (2012) Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet 13:36–46

    Article  CAS  Google Scholar 

  • van de Lagemaat LN, Landry JR, Mager DL, Medstrand P (2003) Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions. Trends Genet 19:530–536

    Article  PubMed  CAS  Google Scholar 

  • van den Broeck D, Maes T, Sauer M, Zethof J, De Keukeleire P, D’hauw M, Van Monatgu M, Grates T (1998) Transposon display identifies individual transposable elements in high copy number lines. Plant J 13:121–129

    Google Scholar 

  • Van Os H, Andrzejeweski S, Bakker E, Barrena I, Bryan GJ, Caromel B, Ghareeb B et al (2006) Construction of a 10,000-marker ultradense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genomewide physical map. Genetics 173:1075–1087

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Veilleux RE, Shen LY, Paz MM (1995) Analysis of the genetic composition of anther-derived potato by randomly amplified polymorphic DNA and simple sequence repeats. Genome 38:1153–1162

    Article  CAS  PubMed  Google Scholar 

  • Versalovic J, Schneider M, de Bruijn FJ, Lupski JR (1994) Genomic fingerprinting of bacteria using repetitive sequence based PCR (rep-PCR). Methods Mol Cell Biol 5:25–40

    Google Scholar 

  • Visser RG, Bachem CW, de Boer JM, Bryan GJ, Chakrabati SK, Feingold S, Gromadka R, van Ham RC, Huang S, Jacobs JM, Kuznetsov B (2009) Sequencing the potato genome: outline and first results to come from the elucidation of the sequence of the world’s third most important food crop. Am J Potato Res 86:417

    Google Scholar 

  • Volpe TA, Kidner C, Hall IM, Teng G, Grewal SIS, Martienssen RA (2002) Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297:1833–1837

    Google Scholar 

  • Walsh JB (1987) Persistence of tandem arrays: implications for satellite and simple-sequence DNAs. Genetics 115:553–567

    CAS  PubMed  PubMed Central  Google Scholar 

  • Waugh R, McLean K, Flavell AJ, Pearce, SR, Kumar A, Thomas BB, Powell W (1997) Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Mol Gen Genet 253:687–694

    Google Scholar 

  • Weber JL, May PE (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 44:388–396

    Google Scholar 

  • Weiner AM, Deininger PL, Efstratiadis A (1986) Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu Rev Biochem 55:631–661

    Google Scholar 

  • Wenke T, Dobel T, Sorensen TR, Junghans H, Weisshaar B, Schmidt T (2011) Targeted identification of short interspersed nuclear element families shows their widespread existence and estreme heterogeneity in plant genomes. Plant Cell 23:3117–3128

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8:973–982

    Article  CAS  PubMed  Google Scholar 

  • Wu KS, Jones R, Danneberger L, Scolnik PA (1994) Detection of microsatellite polymorphisms without cloning. Nucleic Acids Res 22:3257–3258

    Google Scholar 

  • Wu F, Tanksley SD (2010) Chromosomal evolution in the plant family Solanaceae. BMC Genom 11:182

    Article  CAS  Google Scholar 

  • Yasui Y, Nasuda S, Matsuoka Y, Kawahara T (2001) The Au family, a novel short interspersed element (SINE) from Aegilops umbellulata. Theor Appl Genet 102:463–470

    Article  CAS  Google Scholar 

  • Yoshioka Y, Matsumoto S, Kojima S, Ohshima K, Okada N, Machida Y (1993) Molecular characterization of a short interspersed repetitive element from tobacco that exhibits sequence homology to specific tRNAs. Proc Natl Acad Sci USA 90:6562–6566

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang H, Koblížková A, Wang K, Gong Z, Oliveira L, Torres GA, Wu Y, Zhang W, Novák P, Buell CR, Macas J, Jiang J (2014) Boom-bust turnovers of megabase-sized centromeric DNA in Solanum species: Rapid evolution of DNA sequences associated with centromeres. Plant Cell 26:1436–1447

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhong CX, Marshall JB, Topp C, Mroczek R, Kato A, Nagaki K, Birchler JA, Jiang J, Dawe RK (2002) Centromeric retroelements and satellites interact with maize kinetochore protein CENH3. Plant Cell 14:2825–2836

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou Z, Bebeli PJ, Somers DJ, Gustafson JP (1997) Direct amplification of minisatellite-region DNA with VNTR core sequences in the genus Oryza. Theor Appl Genet 95:942–949

    Google Scholar 

  • Zhu W, Ouyang S, Iovene M, O’Brien K, Vuong H, Jiang J, Buell CR (2008) Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition. BMC Genom 9:286

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Defence Institute of Bio Energy Research, Defence Research and Development Organization, Ministry of Defence, Government of India, Goraparao, Haldwani, India

    Atul Grover

  2. University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India

    P. C. Sharma

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  1. Atul Grover
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Correspondence to P. C. Sharma .

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  1. ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India

    Swarup Kumar Chakrabarti

  2. Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan, China

    Conghua Xie

  3. ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India

    Jagesh Kumar Tiwari

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Grover, A., Sharma, P.C. (2017). Repetitive Sequences in the Potato and Related Genomes. In: Kumar Chakrabarti, S., Xie, C., Kumar Tiwari, J. (eds) The Potato Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-66135-3_9

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