Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)
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- 作者：Pablo F Cavagnaro (1) (2)
Douglas A Senalik (1) (3)
Luming Yang (1)
Philipp W Simon (1) (3)
Timothy T Harkins (4)
Chinnappa D Kodira (5)
Sanwen Huang (6)
Yiqun Weng (1) (3) - 刊名：BMC Genomics
- 出版年：2010
- 出版时间：December 2010
- 年：2010
- 卷：11
- 期：1
- 全文大小：707KB
- 参考文献：1. Tautz D: Hypervariability of simple sequences as a general source for polymorphic DNA markers. / Nucleic Acids Res 1989, 17: 6463鈥?470. CrossRef
2. Gur-Arie R, Cohen CJ, Eitan Y, Shelef L, Hallerman EM, Kashi Y: Simple sequence repeats in Escherichia coli : abundance, distribution, composition, and polymorphism. / Genome Res 2000, 10: 62鈥?1.
3. Toth G, Gaspari Z, Jurka J: Microsatellites in different eukaryotic genomes: survey and analysis. / Genome Res 2000, 10: 967鈥?81. CrossRef
4. Morgante M, Olivieri AM: PCR-amplified microsatellites as markers in plant genetics. / Plant J 1993, 3: 175鈥?82. CrossRef
5. Powell W, Morgante M, Andre C, Henfey M, Vogel J, Tingy S, Rafalsky A: The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. / Mol Breed 1996, 2: 225鈥?38. CrossRef
6. McCouch SR, Teytelman L, Xu YB, Lobos KB, Clare K, Walton M, Fu BY, Maghirang R, Li ZK, Xing YZ, Zhang QF, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L: Development and mapping of 2240 new SSR markers for rice ( Oryza sativa L.). / DNA Res 2002, 9: 199鈥?07. CrossRef
7. Somers DJ, Isaac P, Edwards K: A high-density microsatellite consensus map for bread wheat ( Triticum aestivum L.). / Theor Appl Genet 2004, 109: 1105鈥?114. CrossRef
8. Innan H, Terauchi R, Miyashita NT: Microsatellite polymorphism in natural populations of the wild plant Arabidopsis thaliana . / Genetics 1997, 146: 1441鈥?452.
9. Bowers JE, Meredith CP: The parentage of a classic wine grape, Cabernet Sauvignon . / Nat Genet 1997, 16: 84鈥?7. CrossRef
10. Garza JC, Slatkin M, Freimer NB: Microsatellite allele frequencies in humans and chimpanzees, with implications for constraints on allele size. / Mol Biol Evol 1995, 12: 594鈥?03.
11. MacHugh DE, Shriver MD, Loftus RT, Cunningham P, Bradley DG: Microsatellite DNA variation and the evolution, domestication and phylogeography of taurine and Zebu cattle ( Bos taurus and Bos indicus ). / Genetics 1997, 146: 1071鈥?086.
12. Kashi Y, King D, Soller M: Simple sequence repeats as a source of quantitative genetic variation. / Trends Genet 1997, 13: 74鈥?8. CrossRef
13. Santi L, Wang Y, Stile MR, Berendzen K, Wanke D, Roig C, Pozzi C, Muller K, Muller J, Rohde W, Salamini F: The GA octodinucleotide repeat binding factor BBR participates in the transcriptional regulation of the homeobox gene Bkn3 . / Plant J 2003, 34: 813鈥?26. CrossRef
14. Saveliev A, Everett C, Sharpe T, Webster Z, Festenstein R: DNA triplet repeats mediate heterochromatin-protein-1-sensitive variegated gene silencing. / Nature 2003, 422: 909鈥?13. CrossRef
15. Bates G, Lehrach H: Trinucleotide repeat expansions and human genetic disease. / BioEssays 1994, 16: 277鈥?84. CrossRef
16. Wooster R, Cleton-Jansen AM, Collins N, Mangion J, Cornelis RS, Cooper CS, Gusterson BA, Ponder BAJ, von Deimling A, Wiestler OD, / et al.: Instability of short tandem repeats (microsatellites) in human cancer. / Nat Genet 1994, 6: 152鈥?56. CrossRef
17. Li YC, Korol AB, Fahima T, Beiles A, Nevo E: Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. / Mol Ecol 2002, 11: 2453鈥?465. CrossRef
18. Subramanian S, Mishra RK, Singh L: Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions. / Genome Biol 2003, 4: R13. CrossRef
19. Morgante M, Hanafey M, Powell W: Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. / Nat Genet 2002, 30: 194鈥?00. CrossRef
20. Varshney RK, Graner A, Sorrells ME: Genic microsatellite markers in plants: features and applications. / Trend Biotech 2005, 23: 48鈥?5. CrossRef
21. Whitaker TW, Davis GN: / Cucurbits: botany, cultivation, and utilization. Interscience Publishers, New York; 1962.
22. Jeffrey C: A review of the Cucurbitaceae. / Bot J Linnean Soc 1980, 81: 233鈥?47. CrossRef
23. Renner SS, Schaefer H, Kocyan A: Phylogenetics of Cucumis (Cucurbitaceae): cucumber ( C. sativus ) belongs in an Asian/Australian clade far from melon ( C. melo ). / BMC Evol Biol 2007, 7: 58. CrossRef
24. Sebastian P, Schaefer H, Telford IR, Renner SS: Phylogenetic relationships among domesticated and wild species of Cucumis (Cucurbitaceae): The sister species of melon is from Australia. / Proc Natl Acad Sci USA 2010, 107: 14269鈥?4273. CrossRef
25. Knerr LD, Staub JE, Holder DJ, May BP: Genetic diversity in Cucumis sativus L. assessed by variation at 18 allozyme coding loci. / Theor Appl Genet 1989, 78: 119鈥?28. CrossRef
26. Dijkhuizen A, Kennard WC, Havey MJ, Staub JE: RFLP variation and genetic relationships in cultivated cucumber. / Euphytica 1996, 90: 79鈥?9.
27. Horejsi T, Staub JE: Genetic variation in cucumber ( Cucumis sativus L.) as assessed by random amplified polymorphic DNA. / Genet Res Crop Evol 1999, 46: 337鈥?50. CrossRef
28. Meglic V, Staub JE: Inheritance and linkage relationships of allozyme and morphological loci in cucumber ( Cucumis sativus L.). / Theor Appl Genet 1996, 92: 865鈥?72. CrossRef
29. Kennard WC, Poetter K, Dijkhuizen A, Meglic V, Staub J, Havey M: Linkages among RFLP, RAPD, isozyme, disease resistance, and morphological markers in narrow and wide crosses of cucumber. / Theor Appl Genet 1994, 89: 42鈥?8.
30. Serquen FC, Bacher J, Staub JE: Mapping and QTL analysis of a narrow cross in cucumber ( Cucumis sativus L.) using random amplified polymorphic DNA markers. / Mol Breed 1997, 3: 257鈥?68. CrossRef
31. Park YH, Sensoy S, Wye C, Antonise R, Peleman J, Havey MJ: A genetic map of cucumber composed of RAPDs, RFLPs, AFLPs, and loci conditioning resistance to papaya ringspot and zucchini yellow mosaic viruses. / Genome 2000, 43: 1003鈥?010. CrossRef
32. Danin-Poleg Y, Reis N, Tzuri G, Katzir : Development and characterization of microsatellite markers in Cucumis . / Theor Appl Genet 2001, 102: 61鈥?2. CrossRef
33. Kong Q, Xiang C, Yu Z: Development of EST-SSRs in Cucumis sativus from sequence database. / Mol Ecol Notes 2006, 6: 1234鈥?236. CrossRef
34. Watcharawongpaiboon N, Chunwongse J: Development and characterization of microsatellite markers from an enriched genomic library of cucumber ( Cucumis sativus ). / Plant Breed 2008, 127: 74鈥?1.
35. Bradeen JM, Staub JE, Wye C, Antonise R, Peleman J: Towards an expanded and integrated linkage map of cucumber ( Cucumis sativus L.). / Genome 2001, 44: 111鈥?19. CrossRef
36. Robbins MD, Casler MD, Staub JE: Pyramiding QTL for multiple lateral branching in cucumber using inbred backcross lines. / Mol Breed 2008, 22: 131鈥?39. CrossRef
37. Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, Lucas WJ, Wang X, Xie B, Ni P, Ren Y, Zhu H, / et al.: The genome of the cucumber, Cucumis sativus L. / Nat Genet 2009, 41: 1275鈥?281. CrossRef
38. Ren Y, Zhang ZH, Liu JH, Staub JE, Han YH, Cheng ZC, Li XF, Lu JY, Miao H, Kang HX, Xie BY, Gu XF, Wang XW, Du YC, Jin WW, Huang SW: An integrated genetic and cytogenetic map of the cucumber genome. / PLoS One 2009, 4: e5795. CrossRef
39. Han YH, Zhang ZH, Liu CX, Liu JH, Huang SW, Jiang JM, Jin WW: Centromere repositioning in cucurbit species: Implication of the genomic impact from centromere activation and inactivation. / Proc Natl Acad Sci USA 2009, 106: 14937鈥?4941. CrossRef
40. Weng Y: Genetic diversity among Cucumis metuliferus populations revealed by cucumber microsatellites. / HortSci 2010, 45: 214鈥?19.
41. Weng Y, Johnson S, Staub JE, Huang S: An extended inter-varietal microsatellite linkage map of cucumber, Cucumis sativus L. / HortSci 2010, 45: 882鈥?86.
42. Zhang SP, Miao H, Gu XF, Yang YH, Xie BY, Wang XW, Huang SW, Du YC, Sun RF: Genetic mapping of the scab resistance gene Ccu in cucumber. / J Amer Soc Hort Sci 2010, 135: 53鈥?8.
43. Lister R, Gregory BD, Ecker JR: Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. / Curr Opin Plant Biol 2009, 12: 107鈥?18. CrossRef
44. Arumuganathan K, Earle ED: Estimation of nuclear DNA amounts of plants by flow cytometry. / Plant Mol Biol Rep 1991, 9: 229鈥?41. CrossRef
45. Schl枚tterer C, Tautz D: Slippage synthesis of simple sequence DNA. / Nucleic Acids Res 1992, 20: 211鈥?15. CrossRef
46. IRGSP (International Rice Genome Sequencing Project): The map-based sequence of the rice genome. / Nature 2005, 436: 793鈥?00. CrossRef
47. Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, / et al.: The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). / Science 2006, 313: 1596鈥?04. CrossRef
48. Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, / et al.: The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. / Nature 2007, 449: 463鈥?67. CrossRef
49. Price HJ, Dillon SL, Hodnett G, Rooney WL, Ross L, / et al.: Genome evolution in the genus Sorghum (Poaceae). / Ann Bot 2005, 95: 219鈥?27. CrossRef
50. Huo N, Lazo GR, Vogel JP, You FM, Ma Y, Hayden DM, Coleman-Derr D, Hill TA, Dvorak J, Anderson OD, Luo MC, Gu YQ: The nuclear genome of Brachypodium distachyon : analysis of BAC end sequences. / Funct Integr Genomics 2008, 8: 135鈥?7. CrossRef
51. Mun JH, Kim DJ, Choi HK, Gish J, Debell茅 F, Mudge J, Denny R, Endr茅 G, Saurat O, Dudez AM, Kiss GB, Roe B, Young ND, Cook DR: Distribution of microsatellites in the genome of Medicago truncatula : a resource of genetic markers that integrate genetic and physical maps. / Genetics 2006, 172: 2541鈥?555. CrossRef
52. Leclercq S, Rivals E, Jarne P: Detecting microsatellites within genomes: significant variation among algorithms. / BMC Bioinformatics 2007, 8: 125. CrossRef
53. Weber JL: Informativeness of human (dC-dA)n.(dG-dT)n polymorphisms. / Genomics 1990, 7: 524鈥?30. CrossRef
54. Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R: Computational and experimental characterization of physically clustered simple sequence repeats in plants. / Genetics 2000, 156: 847鈥?54.
55. Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S: Computational and experimental analysis of microsatellites in rice ( Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. / Genome Res 2001, 11: 1441鈥?452. CrossRef
56. Peng JH, Lapitan NL: Characterization of EST derived microsatellites in the wheat genome and development of eSSR markers. / Funct Integr Genomics 2005, 5: 80鈥?6. CrossRef
57. Weng Y, Azhaguvel P, Michels GJ Jr, Rudd JC: Cross-species transferability of microsatellite markers from six aphid (Hemiptera: Aphididae) species and their use for evaluating biotypic diversity in two cereal aphids. / Insect Mol Biol 2007, 16: 613鈥?22.
58. Sia EA, Jinks-Robertson S, Petes T: Genetic control of microsatellite stability. / Mutat Res 1997, 383: 61鈥?0.
59. Eisen JA: Mechanistic basis for microsatellite instability. In / Microsatellites - evolution and application. Edited by: Goldstein DB, Schl枚tterer C. Oxford University Press, Oxford; 1999.
60. Ellegren H: Heterogeneous mutation processes in human microsatellite DNA sequences. / Nat Genet 2000, 24: 400鈥?02. CrossRef
61. Wierdl M, Dominska M, Petes TD: Microsatellite instability in yeast: dependence on the length of the microsatellite. / Genetics 1997, 146: 769鈥?79.
62. Jones AG, Rosenqvist G, Berglund A, Avise JC: Clustered microsatellite mutations in the pipefish Syngnathus typhle . / Genetics 1999, 152: 1057鈥?063.
63. Primmer CR, Saino N, M酶ller AP, Ellegren H: Unravelling the process of microsatellite evolution through analysis of germline mutations in barn swallows. / Mol Biol Evol 1998, 15: 1047鈥?054.
64. Schl枚tterer C, Ritter R, Harr B, Brem G: High mutation rate of a long microsatellite allele in Drosophila melanogaster provides evidence for allele-specific mutation rates. / Mol Biol Evol 1998, 15: 1269鈥?274.
65. Kruglyak SR, Durrett T, Schug MD, Aquadro CF: Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations. / Proc Natl Acad Sci USA 1998, 95: 10774鈥?0778. CrossRef
66. Ellegren H, Primmer CR, Sheldon BC: Microsatellite 'evolution': directionality or bias? / Nat Genet 1995, 11: 360鈥?62. CrossRef
67. Ellegren H, Moore S, Robinson N, Byrne K, Ward W, Sheldon BC: Microsatellite evolution - a reciprocal study of repeat lengths at homologous loci in cattle and sheep. / Mol Biol Evol 1997, 14: 854鈥?60.
68. Fitzsimmons NN, Moritz C, Moore SS: Conservation and dynamics of microsatellite loci over 300 million years of marine turtle evolution. / Mol Biol Evol 1995, 12: 432鈥?40.
69. Li Z, Huang S, Liu S, Pan J, Zhang Z, Tao Q, Shi Q, Jia Z, Zhang W, Chen H, Si L, Zhu L, Cai R: Molecular isolation of the M gene suggests that a conserved-residue conversion induces the formation of bisexual flowers in cucumber plants. / Genetics 2009, 182: 1381鈥?385. CrossRef
70. Wang H, Moore MJ, Soltis PS, Bell CD, Brockington SF, Alexandre R, Davis CC, Latvis M, Manchester SR, Soltis DE: Rosid radiation and the rapid rise of angiosperm-dominated forests. / Proc Natl Acad Sci USA 2009, 106: 3853鈥?858. CrossRef
71. Quackenbush J, Cho J, Lee D, Liang F, Holt I, Karamycheva S, Parvizi B, Pertea G, Sultana R, White J: The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. / Nucleic Acids Res 2001, 29: 159鈥?4. CrossRef
72. Guo SG, Zheng Y, Joung JG, Liu SQ, Zhang ZH, Crasta OR, Sobral BW, Xu Y, Huang SW, Fei ZJ: Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. / BMC Genomics 2010, 11: 384. CrossRef
73. Thiel T, Michalek W, Varshney RK, Graner A: Exploiting EST databases for the development and characterization of gene derived SSR markers in barley ( Hordeum vulgare L.). / Theor Appl Genet 2003, 106: 411鈥?22.
74. Rozen S, Skaletsky H: Primer3 on the www for general users and for biologist programmers. In / Bioinformatics Methods and Protocols: Methods in Molecular Biology. Edited by: Krawetz S, Misener S. Humana Press, Totowa, NJ; 2000:365鈥?86.
75. Murray MG, Thompson WF: Rapid isolation of high molecular weight DNA. / Nucleic Acids Res 1980, 8: 4321鈥?325. CrossRef
76. Weng Y, Li W, Devkota RN, Rudd JC: Microsatellite markers associated with two Aegilops tauschii -derived greenbug resistance loci in wheat. / Theor Appl Genet 2005, 110: 462鈥?69. CrossRef - 作者单位：Pablo F Cavagnaro (1) (2)
Douglas A Senalik (1) (3)
Luming Yang (1)
Philipp W Simon (1) (3)
Timothy T Harkins (4)
Chinnappa D Kodira (5)
Sanwen Huang (6)
Yiqun Weng (1) (3)
1. Horticulture Department, University of Wisconsin, 53706, Madison, WI, USA
2. INTA La Consulta, and CONICET, Mendoza, Argentina
3. USDA ARS Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, 53706, Madison, WI, USA
4. Roche Applied Sciences, 46250, Indianapolis, IN, USA
5. 454 Life Sciences, 06405, Branford, CT, USA
6. Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
文摘
Background Cucumber, Cucumis sativus L. is an important vegetable crop worldwide. Until very recently, cucumber genetic and genomic resources, especially molecular markers, have been very limited, impeding progress of cucumber breeding efforts. Microsatellites are short tandemly repeated DNA sequences, which are frequently favored as genetic markers due to their high level of polymorphism and codominant inheritance. Data from previously characterized genomes has shown that these repeats vary in frequency, motif sequence, and genomic location across taxa. During the last year, the genomes of two cucumber genotypes were sequenced including the Chinese fresh market type inbred line '9930' and the North American pickling type inbred line 'Gy14'. These sequences provide a powerful tool for developing markers in a large scale. In this study, we surveyed and characterized the distribution and frequency of perfect microsatellites in 203 Mbp assembled Gy14 DNA sequences, representing 55% of its nuclear genome, and in cucumber EST sequences. Similar analyses were performed in genomic and EST data from seven other plant species, and the results were compared with those of cucumber. Results A total of 112,073 perfect repeats were detected in the Gy14 cucumber genome sequence, accounting for 0.9% of the assembled Gy14 genome, with an overall density of 551.9 SSRs/Mbp. While tetranucleotides were the most frequent microsatellites in genomic DNA sequence, dinucleotide repeats, which had more repeat units than any other SSR type, had the highest cumulative sequence length. Coding regions (ESTs) of the cucumber genome had fewer microsatellites compared to its genomic sequence, with trinucleotides predominating in EST sequences. AAG was the most frequent repeat in cucumber ESTs. Overall, AT-rich motifs prevailed in both genomic and EST data. Compared to the other species examined, cucumber genomic sequence had the highest density of SSRs (although comparable to the density of poplar, grapevine and rice), and was richest in AT dinucleotides. Using an electronic PCR strategy, we investigated the polymorphism between 9930 and Gy14 at 1,006 SSR loci, and found unexpectedly high degree of polymorphism (48.3%) between the two genotypes. The level of polymorphism seems to be positively associated with the number of repeat units in the microsatellite. The in silico PCR results were validated empirically in 660 of the 1,006 SSR loci. In addition, primer sequences for more than 83,000 newly-discovered cucumber microsatellites, and their exact positions in the Gy14 genome assembly were made publicly available. Conclusions The cucumber genome is rich in microsatellites; AT and AAG are the most abundant repeat motifs in genomic and EST sequences of cucumber, respectively. Considering all the species investigated, some commonalities were noted, especially within the monocot and dicot groups, although the distribution of motifs and the frequency of certain repeats were characteristic of the species examined. The large number of SSR markers developed from this study should be a significant contribution to the cucurbit research community.