Patterns of tandem repetition in plant whole genome assemblies

Molecular Genetics and Genomics

Volumn 281, Issue 6, 2009, Pages 579-590

  Navajas Pérez, Rafael ^a   Paterson, Andrew H ^a  

^a UNIVERSITY OF GEORGIA   (United States)

Author keywords

Tandem repeats; Whole genome assemblies

Indexed keywords

DINUCLEOTIDE; ELEMENT; MONOMER; REPETITIVE DNA; PLANT DNA;

ARABIDOPSIS; ARTICLE; ASPEN; CENTROMERE; CHLAMYDOMONAS REINHARDTII; COMPARATIVE GENOMIC HYBRIDIZATION; DATA BASE; DINUCLEOTIDE REPEAT; DNA MICROARRAY; GENE NUMBER; GENE SEQUENCE; GENE TECHNOLOGY; GRAPE; GREEN ALGA; MOSS; NONHUMAN; NUCLEOTIDE REPEAT; PAPAYA; PHYSCOMITRELLA; PHYSCOMITRELLA PATENS; PLANT GENOME; PRIORITY JOURNAL; RICE; SORGHUM; TANDEM REPEAT; TELOMERE; ANIMAL; BRYOPSIDA; GENETIC MARKER; GENETICS; PLANT GENE;

ARABIDOPSIS THALIANA; BRYOPHYTA; CARICA PAPAYA; CHLAMYDOMONAS REINHARDTII; CHLOROPHYTA; DICOTYLEDONEAE; LILIOPSIDA; PHYSCOMITRELLA PATENS; VITIS;

ANIMALS; ARABIDOPSIS; BRYOPSIDA; CARICA; CHLAMYDOMONAS REINHARDTII; DNA, PLANT; GENES, PLANT; GENETIC MARKERS; GENOME, PLANT; ORYZA SATIVA; POPULUS; REPETITIVE SEQUENCES, NUCLEIC ACID; SORGHUM; TANDEM REPEAT SEQUENCES; VITIS;

EID: 67449132039     PISSN: 16174615     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00438-009-0433-y     Document Type: Article

References (73)

1. MS Akkaya RC Shoemaker JE Specht AA Bhagwat PB Cregan 1995 Integration of simple sequence repeat DNA markers into a soybean linkage map Crop Sci 35 1439 1445
2. Arabidopsis thaliana Genome Initiative (2001) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815
3. L Aragón-Alcaide T Miller T Schwarzacher S Reader G Moore 1996 A cereal centromeric sequence Chromosoma 105 261 268
4. R Batistoni G Pesole S Marracci I Nardi 1995 A tandemly repeated DNA family originated from SINE-related elements in the European plethodontid salamanders (Amphibia, Urodela) J Mol Evol 40 608 615
5. JL Bennetzen 2002 Mechanisms and rates of genome expansion and contraction in flowering plants Genetica 115 29 36
6. G Benson 1999 Tandem repeats finder: a program to analyze DNA sequences Nucl Acids Res 2 573 580
7. CM Bergman H Quesneville 2007 Discovering and detecting transposable elements in genome sequences Brief Bioinform 8 382 392
8. RW Blakesley NF Hansen JC Mullikin PJ Thomas JC McDowell B Maskeri AC Young B Benjamin SY Brooks BI Coleman J Gupta SL Ho EM Karlins QL Maduro S Stantripop C Tsurgeon JL Vogt MA Walker CA Masiello X Guan NISC Comparative Sequencing Program GG Bouffard ED Green 2004 An intermediate grade of finished genomic sequence suitable for comparative analyses Genome Res 14 2235 2244
9. JP Camacho TF Sharbel LW Beukeboom 2000 B-chromosome evolution Philos Trans R Soc Lond B Biol Sci 355 163 178
10. L Cardle L Ramsay D Milbourne M Macaulay D Marshall R Waugh 2000 Computational and experimental characterization of physically clustered simple sequence repeats in plants Genetics 156 847 854
11. R de la Herrán N Cuñado N Navajas-Pérez JL Santos C Ruiz Rejón MA Garrido-Ramos M Ruiz Rejón 2005 The controversial telomeres of lily plants Cytogenet Genome Res 109 144 147
12. M Delseny 2003 Towards an accurate sequence of the rice genome Curr Opin Plant Biol 6 101 105
13. A Depeiges C Goubely A Lenoir S Cocherel G Picard M Raynal F Grellet M Delseny 1995 Identification of the most represented repeated motifs in Arabidopsis thaliana microsatellite loci Theor Appl Genetics 91 160 168
14. F Dong JT Miller SA Jackson GL Wang PC Ronald J Jiang 1998 Rice (Oryza sativa) centromeric regions consist of complex DNA Proc Natl Acad Sci USA 95 8135 8140
15. JR Elder BJ Turner 1995 Concerted evolution of repetitive DNA sequences in eukaryotes Q Rev Biol 70 297 320
16. J-Y Fann A Kovarik V Hemleben NI Tsirekidze TG Beridze 2001 Molecular and structural evolution of Citrus satellite DNA Theor Appl Genet 103 1068 1073
17. DJ Fitzgerald GL Dryden EC Bronson JS Williams JN Anderson 1994 Conserved patterns of bending in satellite and nucleosome positioning DNA J Biol Chem 269 21303 21314
18. RB Flavell MD Bennett JB Smith DB Smith 1974 Genome size and proportion of repeated nucleotide-sequence DNA in plants Biochem Genet 12 257 269
19. S Hagemann B Scheer D Schweizer 1993 Repetitive sequences in the genome of Anemone blanda: identification of tandem arrays and of dispersed repeats Chromosoma 102 312 324
20. S Henikoff K Ahmad HS Malik 2001 The centromere paradox: stable inheritance with rapidly evolving DNA Science 293 1098 1102
21. International Rice Genome Sequencing Project 2005 The map-based sequence of the rice genome Nature 436 793 800
22. O Jaillon JM Aury B Noel A Policriti C Clepet A Casagrande N Choisne S Aubourg N Vitulo C Jubin A Vezzi F Legeai P Hugueney C Dasilva D Horner E Mica D Jublot J Poulain C Bruyère A Billault B Segurens M Gouyvenoux E Ugarte F Cattonaro V Anthouard V Vico C Del Fabbro M Alaux G Di Gaspero V Dumas N Felice S Paillard I Juman M Moroldo S Scalabrin A Canaguier I Le Clainche G Malacrida E Durand G Pesole V Laucou P Chatelet D Merdinoglu M Delledonne M Pezzotti A Lecharny C Scarpelli F Artiguenave ME Pè G Valle M Morgante M Caboche AF Adam-Blondon J Weissenbach F Quétier P Wincker French-Italian Public Consortium for Grapevine Genome Characterization 2007 The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla Nature 449 463 467
23. A Kamm I Galasso T Schmidt JS Heslop-Harrison 1995 Analysis of a repetitive DNA family from Arabidopsis arenosa and relationships between Arabidopsis species Plant Mol Biol 27 853 862
24. R Kapila S Das PS Srivastava M Lakshmikumaran 1996 A novel species-specific tandem repeat DNA family from Sinapis arvensis: detection of telomere-like sequences Genome 39 758 766
25. VV Kapitonov GP Holmquist J Jurka 1998 L1 repeat is a basic unit of heterochromatin satellites in cetaceans Mol Biol Evol 15 611 612
26. Kipling D (1995) The telomere. Oxford University Press, Oxford
27. M Koornneef P Fransz H de Jong 2003 Cytogenetic tools for Arabidopsis thaliana Chromosom Res 11 183 194
28. SE Kubis T Schmidt JS Heslop-Harrison 1998 Repetitive DNA elements as a major component of plant genomes Ann Botany 82 45 55
29. M La Rota RV Kantety JK Yu ME Sorrells 2005 Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley BMC Genomics 6 23
30. W Li A Godzik 2006 Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences Bioinformatics 22 1658 1659
31. KB Lim H de Jong TJ Yang JY Park SJ Kwon JS Kim MH Lim JA Kim M Jin YM Jin SH Kim YP Lim JW Bang HI Kim BS Park 2005 Characterization of rDNAs and tandem repeats in the heterochromatin of Brassica rapa Mol Cells 19 436 444
32. I López-Flores R de la Herrán MA Garrido-Ramos P Boudry C Ruiz-Rejón M Ruiz-Rejón 2004 The molecular phylogeny of oysters based on a satellite DNA related to transposons Gene 339 181 188
33. K Loridon B Cournoyer C Goubely A Depeiges G Picard 1998 Length polymorphism and allele structure of trinucleotide microsatellites in natural accessions of Arabidopsis thaliana Theor Appl Genet 97 591 604
34. J Macas T Mészáros M Nouzová 2002 PlantSat: a specialized database for plant satellite repeats Bioinformatics 18 28 35
35. M Margulies M Egholm WE Altman S Attiya JS Bader LA Bemben J Berka MS Braverman YJ Chen Z Chen SB Dewell L Du JM Fierro XV Gomes BC Godwin W He S Helgesen CH Ho GP Irzyk SC Jando ML Alenquer TP Jarvie KB Jirage JB Kim JR Knight JR Lanza JH Leamon SM Lefkowitz M Lei J Li KL Lohman H Lu VB Makhijani KE McDade MP McKenna EW Myers E Nickerson JR Nobile R Plant BP Puc MT Ronan GT Roth GJ Sarkis JF Simons JW Simpson M Srinivasan KR Tartaro A Tomasz KA Vogt GA Volkmer SH Wang Y Wang MP Weiner P Yu RF Begley JM Rothberg 2005 Genome sequencing in microfabricated high-density picolitre reactors Nature 437 376 380
36. SS Merchant SE Prochnik O Vallon EH Harris SJ Karpowicz GB Witman A Terry A Salamov LK Fritz-Laylin L Maréchal-Drouard WF Marshall LH Qu DR Nelson AA Sanderfoot MH Spalding VV Kapitonov Q Ren P Ferris E Lindquist H Shapiro SM Lucas J Grimwood J Schmutz P Cardol H Cerutti G Chanfreau CL Chen V Cognat MT Croft R Dent S Dutcher E Fernández H Fukuzawa D González-Ballester D González-Halphen A Hallmann M Hanikenne M Hippler W Inwood K Jabbari M Kalanon R Kuras PA Lefebvre SD Lemaire AV Lobanov M Lohr A Manuell I Meier L Mets M Mittag T Mittelmeier JV Moroney J Moseley C Napoli AM Nedelcu K Niyogi SV Novoselov IT Paulsen G Pazour S Purton JP Ral DM Riaño-Pachón W Riekhof L Rymarquis M Schroda D Stern J Umen R Willows N Wilson SL Zimmer J Allmer J Balk K Bisova CJ Chen M Elias K Gendler C Hauser MR Lamb H Ledford JC Long J Minagawa MD Page J Pan W Pootakham S Roje A Rose E Stahlberg AM Terauchi P Yang S Ball C Bowler CL Dieckmann VN Gladyshev P Green R Jorgensen S Mayfield B Mueller-Roeber S Rajamani RT Sayre P Brokstein I Dubchak D Goodstein L Hornick YW Huang J Jhaveri Y Luo D Martínez WC Ngau B Otillar A Poliakov A Porter L Szajkowski G Werner K Zhou IV Grigoriev DS Rokhsar AR Grossman 2007 The Chlamydomonas genome reveals the evolution of key animal and plant functions Science 318 245 250
37. J Messing AK Bharti WM Karlowski H Gundlach HR Kim Y Yu F Wei G Fuks CA Soderlund KF Mayer RA Wing 2004 Sequence composition and genome organization of maize Proc Natl Acad Sci USA 101 14349 14354
38. N Mestrović M Plohl B Mravinac D Ugarković 1998 Evolution of satellite DNAs from the genus Palorus-experimental evidence for the "library" hypothesis Mol Biol Evol 15 1062 1068
39. I Métais C Aubry B Hamon D Peltier R Jalouzot 1998 Cloning, quantification and characterization of a minisatellite DNA sequence from common bean Phaseolus vulgaris L TAG 97 232 237
40. Miklos GL (1985) Localited highly repetitive DNA sequences in vertebrate and invertebrate genomes. In: McIntryre JR (ed) Molecular evolutionary genetics. Plenum Press, New York, pp 231-241
41. JT Miller SA Jackson S Nasuda BS Gill RA Wing J Jiang 1998 Cloning and characterization of a centromere specific DNA element from Sorghum bicolor Theor Appl Genet 96 832 839
42. R Ming S Hou Y Feng Q Yu A Dionne-Laporte JH Saw P Senin W Wang BV Ly KL Lewis SL Salzberg L Feng MR Jones RL Skelton JE Murray C Chen W Qian J Shen P Du M Eustice E Tong H Tang E Lyons RE Paull TP Michael K Wall DW Rice H Albert ML Wang YJ Zhu M Schatz N Nagarajan RA Acob P Guan A Blas CM Wai CM Ackerman Y Ren C Liu J Wang J Wang JK Na EV Shakirov B Haas J Thimmapuram D Nelson X Wang JE Bowers AR Gschwend AL Delcher R Singh JY Suzuki S Tripathi K Neupane H Wei B Irikura M Paidi N Jiang W Zhang G Presting A Windsor R Navajas-Pérez MJ Torres FA Feltus B Porter Y Li AM Burroughs MC Luo L Liu DA Christopher SM Mount PH Moore T Sugimura J Jiang MA Schuler V Friedman T Mitchell-Olds DE Shippen CW de Pamphilis JD Palmer M Freeling AH Paterson D Gonsalves L Wang M Alam 2008 The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus) Nature 452 991 996
43. M Morgante M Hanafey W Powell 2002 Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes Nat Genet 30 194 200
44. JH Mun DJ Kim HK Choi J Gish F Debellé J Mudge R Denny G Endré O Saurat AM Dudez GB Kiss B Roe ND Young DR Cook 2006 Distribution of microsatellites in the genome of Medicago truncatula: a resource of genetic markers that integrate genetic and physical maps Genetics 172 2541 2555
45. MG Murray DL Peters WF Thompson 1981 Ancient repeated sequences in the pea and mung bean genomes and implications for genome evolution J Mol Evol 17 31 42
46. K Nagaki H Tsujimoto T Sasakuma 1998 A novel repetitive sequence of sugar cane, SCEN family, locating on centromeric regions Chromosom Res 6 295 302
47. N Nagarajan R Navajas-Pérez M Pop M Alam R Ming AH Paterson SL Salzberg 2008 Genome-wide analysis of repetitive elements in papaya Tropical Plant Biol 3-4 191 201
48. R Navajas-Pérez T Schwarzacher R de la Herrán C Ruiz Rejón M Ruiz Rejón MA Garrido-Ramos 2006 The origin and evolution of the variability in a Y-specific satellite-DNA of Rumex acetosa and its relatives Gene 368 61 71
49. T Nunome K Suwabe A Ohyama H Fukuoka 2003 Characterization of trinucleotide microsatellites in eggplant Breed Sci 53 77 83
50. RJ Okagaki RL Phillips 2004 Maize DNA-sequencing strategies and genome organization Genome Biol 5 223
51. AH Paterson JE Bowers R Bruggmann I Dubchak J Grimwood H Gundlach G Haberer U Hellsten T Mitros A Poliakov J Schmutz M Spannagl H Tang X Wang T Wicker AK Bharti J Chapman FA Feltus U Gowik E Lyons C Maher A Narechania B Penning L Zhang NC Carpita M Freeling AR Gingle CT Hash B Keller PE Klein S Kresovich MC McCann R Ming DG Peterson D Ware P Westhoff KFX Mayer J Messing DS Rokhsar 2009 The Sorghum bicolor genome and the diversification of grasses Nature 457 551 556
52. DG Peterson SR Wessler AH Paterson 2002 Efficient capture of unique sequences from eukaryotic genomes Trends Genet 18 547 550
53. ME Petracek PA Lefebvre CD Silflow J Berman 1990 Chlamydomonas telomere sequences are A+T-rich but contain three consecutive G-C base pairs Proc Natl Acad Sci USA 87 8222 8226
54. M Plohl N Mestrović B Bruvo D Ugarković 1998 Similarity of structural features and evolution of satellite DNAs from Palorus subdepressus (Coleoptera) and related species J Mol Evol 46 234 239
55. RL Poole 2007 The TAIR database Methods Mol Biol 406 179 212
56. J Rajagopal S Das DK Khurana PS Srivastava M Lakshmikumaran 1999 Molecular characterization and distribution of a 145-bp tandem repeat family in the genus Populus Genome 42 909 918
57. SA Rensing D Lang AD Zimmer A Terry A Salamov H Shapiro T Nishiyama PF Perroud EA Lindquist Y Kamisugi T Tanahashi K Sakakibara T Fujita K Oishi T Shin-I Y Kuroki A Toyoda Y Suzuki S Hashimoto K Yamaguchi S Sugano Y Kohara A Fujiyama A Anterola S Aoki N Ashton WB Barbazuk E Barker JL Bennetzen R Blankenship SH Cho SK Dutcher M Estelle JA Fawcett H Gundlach K Hanada A Heyl KA Hicks J Hughes M Lohr K Mayer A Melkozernov T Murata DR Nelson B Pils M Prigge B Reiss T Renner S Rombauts PJ Rushton A Sanderfoot G Schween SH Shiu K Stueber FL Theodoulou H Tu Y Van de Peer PJ Verrier E Waters A Wood L Yang D Cove AC Cuming M Hasebe S Lucas BD Mishler R Reski IV Grigoriev RS Quatrano JL Boore 2008 The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants Science 319 64 69
58. C Rizzon L Ponger BS Gaut 2006 Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice PLoS Comput Biol 2 9 e115
59. N Saini J Shultz DA Lightfoot 2008 Re-annotation of the physical map of Glycine max for polyploid-like regions by BAC end sequence driven whole genome shotgun read assembly BMC Genomics 9 323
60. CR Simoens J Gielen M Van Montagu D Inzé 1988 Characterization of highly repetitive sequences of Arabidopsis thaliana Nucleic Acids Res 16 6753 6766
61. MJM Smulders G Bredemeijer W Rus-Kortekaas P Arens B Vosman 1997 Use of short microsatellites from database sequences to generate polymorphisms among Lycopersicon esculentum cultivars and accessions of other Lycopersicon species Theor Appl Genet 97 264 272
62. QJ Song EW Fickus PB Cregan 2002 Characterization of trinucleotide SSR motifs in wheat Theor Appl Genet 104 286 293
63. W Stephan 1989 Tandem-repetitive noncoding DNA: forms and forces Mol Biol Evol 6 198 212
64. GA Tuskan S Difazio S Jansson J Bohlmann I Grigoriev U Hellsten N Putnam S Ralph S Rombauts A Salamov J Schein L Sterck A Aerts RR Bhalerao RP Bhalerao D Blaudez W Boerjan A Brun A Brunner V Busov M Campbell J Carlson M Chalot J Chapman GL Chen D Cooper PM Coutinho J Couturier S Covert Q Cronk R Cunningham J Davis S Degroeve A Déjardin C Depamphilis J Detter B Dirks I Dubchak S Duplessis J Ehlting B Ellis K Gendler D Goodstein M Gribskov J Grimwood A Groover L Gunter B Hamberger B Heinze Y Helariutta B Henrissat D Holligan R Holt W Huang N Islam-Faridi S Jones M Jones-Rhoades R Jorgensen C Joshi J Kangasjärvi J Karlsson C Kelleher R Kirkpatrick M Kirst A Kohler U Kalluri F Larimer J Leebens-Mack JC Leplé P Locascio Y Lou S Lucas F Martin B Montanini C Napoli DR Nelson C Nelson K Nieminen O Nilsson V Pereda G Peter R Philippe G Pilate A Poliakov J Razumovskaya P Richardson C Rinaldi K Ritland P Rouzé D Ryaboy J Schmutz J Schrader B Segerman H Shin A Siddiqui F Sterky A Terry CJ Tsai E Uberbacher P Unneberg J Vahala K Wall S Wessler G Yang T Yin C Douglas M Marra G Sandberg Y Van de Peer D Rokhsar 2006 The genome of black cottonwood, Populus trichocarpa (Torr. & Gray) Science 313 1596 1604
65. S Tutois C Cloix C Cuvillier MC Espagnol J Lafleuriel G Picard S Tourmente 1999 Structural analysis and physical mapping of a pericentromeric region of chromosome 5 of Arabidopsis thaliana Chromosome Res 7 143 156
66. D Ugarković M Plohl 2002 Variation in satellite DNA profiles, causes and effects EMBO J 21 5955 5959
67. M von Stackelberg SA Rensing R Reski 2006 Identification of genic moss SSR markers and a comparative analysis of twenty-four algal and plant gene indices reveal species-specific rather than group-specific characteristics of microsatellites BMC Plant Biol 6 9
68. J Wang C Chen J-K Na Q Yu S Hou RE Paull PH Moore M Alam R Ming 2008 Genome-wide comparative analyses of microsatellites in papaya Tropical Plant Biol 3-4 278 292
69. TY Wu R Wu 1987 A new rice repetitive DNA shows sequence homology to both 5S RNA and tRNA Nucleic Acids Res 15 5913 5923
70. HK Wu MC Chung TY Wu CN Ning R Wu 1991 Localization of specific repetitive DNA sequences in individual rice chromosomes Chromosoma 100 330 338
71. H Yan J Jiang 2007 Rice as a model for centromere and heterochromatin research Chromosom Res 15 77 84
72. X Zhao X Ding Y Ji D Stelly AH Paterson 1998 Macromolecular organization and genetic mapping of a recently-amplified tandem repeat family (B77) in cotton Plant Mol Biol 38 1031 1042
73. MS Zwick MN Islam-Faridi HB Zhang GL Hodnett MI Gomez JS Kim HJ Price DM Stelly 2000 Distribution and sequence analysis of the centromere-associated repetitive element CEN38 of Sorghum bicolor (Poaceae) Am J Bot 12 1757 1764