Identification and diversity of functional centromere satellites in the wild rice species Oryza brachyantha

Chromosome Research

Volumn 21, Issue 8, 2013, Pages 725-737

  Yi, Chuandeng ^a   Zhang, Wenli ^b   Dai, Xibin ^a   Li, Xing ^a   Gong, Zhiyun ^a   Zhou, Yong ^a   Liang, Guohua ^a   Gu, Minghong ^a  

^a YANGZHOU UNIVERSITY   (China)

^b NANJING AGRICULTURAL UNIVERSITY   (China)

Author keywords

centromere; Oryza brachyantha; repetitive DNA; satellite DNA

Indexed keywords

ARTICLE; CENTROMERE; CHROMOSOMAL LOCALIZATION; IMMUNOHISTOCHEMISTRY; NONHUMAN; ORYZA; ORYZA BRACHYANTHA; PRIORITY JOURNAL; RETROPOSON; RICE; SEQUENCE ALIGNMENT;

BASE SEQUENCE; CENTROMERE; CHROMOSOMES, PLANT; DNA, PLANT; DNA, SATELLITE; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOME, PLANT; IN SITU HYBRIDIZATION, FLUORESCENCE; MOLECULAR SEQUENCE DATA; POACEAE; RETROELEMENTS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; TANDEM REPEAT SEQUENCES;

EID: 84891798659     PISSN: 09673849     EISSN: 15736849     Source Type: Journal    
DOI: 10.1007/s10577-013-9374-8     Document Type: Article

References (54)

1. Aggarwal RK, Brar DS, Khush GS (1997) Two new genomes in the Oryza complex identified on the basis of molecular divergence analysis using total genomic DNA hybridization. Mol Gen Genet 254:1-12
2. Alfenito MR, Birchler JA (1993) Molecular characterization of a maize B chromosome centric sequence. Genetics 135:589-597
3. Ammiraju JS, Lu F, Sanyal A, Yu Y, Song X, Jiang N, Pontaroli AC, Rambo T, Currie J, Collura K, Talag J, Fan C, Goicoechea JL, Zuccolo A, Chen J, Bennetzen JL, Chen M, Jackson S, Wing RA (2008) Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. Plant Cell 20:3191-3209
4. Amor DJ, Kalitsis P, Sumer H, Choo KH (2004) Building the centromere: from foundation proteins to 3D organization. Trends Cell Biol 14:359-368
5. Bao W, Zhang W, Yang Q, Zhang Y, Han B, Gu M, Xue Y, Cheng Z (2006) Diversity of centromeric repeats in two closely related wild rice species, Oryza officinalis and Oryza rhizomatis. Mol Genet Genom 275:421-430
6. Bennetzen JL (2007) Patterns in grass genome evolution. Curr Opin Plant Biol 10:176-181
7. Brandes A, Thompson H, Dean C, Heslop-Harrison JS (1997) Multiple repetitive DNA sequences in the paracentromeric regions of Arabidopsis thaliana L. Chromosom Res 5:238-246
8. Brar DS, Khush GS (1997) Alien introgression in rice. Plant Mol Biol 35:35-47
9. Cheng Z, Buell CR, Wing RA, Jiang J (2002a) Resolution of fluorescence in-situ hybridization mapping on rice mitotic prometaphase chromosomes, meiotic pachytene chromosomes and extended DNA fibers. Chromosom Res 10:379-387
10. Cheng Z, Dong F, Langdon T, Ouyang S, Buell CR, Gu M, Blattner FR, Jiang J (2002b) Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14:1691-1704
11. Choo KH, Vissel B, Nagy A, Earle E, Kalitsis P (1991) A survey of the genomic distribution of alpha satellite DNA on all the human chromosomes, and derivation of a new consensus sequence. Nucleic Acids Res 19:1179-1182
12. Clarke L (1990) Centromeres of budding and fission yeasts. Trends Genet 6:150-154
13. Clarke L (1998) Centromeres: proteins, protein complexes, and repeated domains at centromeres of simple eukaryotes. Curr Opin Genet Dev 8:212-218
14. Devos KM, Gale MD (1997) Comparative genetics in the grasses. Plant Mol Biol 35:3-15
15. Dong F, Miller JT, Jackson SA, Wang GL, Ronald PC, Jiang J (1998) Rice (Oryza sativa) centromeric regions consist of complex DNA. Proc Natl Acad Sci U S A 95:8135-8140
16. Gao D, Gill N, Kim HR, Walling JG, Zhang W, Fan C, Yu Y, Ma J, SanMiguel P, Jiang N, Cheng Z, Wing RA, Jiang J, Jackson SA (2009) A lineage-specific centromere retrotransposon in Oryza brachyantha. Plant J 60:820-831
17. Ge S, Sang T, Lu BR, Hong DY (1999) Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proc Natl Acad Sci U S A 96:14400-14405
18. Hall AE, Keith KC, Hall SE, Copenhaver GP, Preuss D (2004) The rapidly evolving field of plant centromeres. Curr Opin Plant Biol 7:108-114
19. Hall SE, Kettler G, Preuss D (2003) Centromere satellites from Arabidopsis populations: maintenance of conserved and variable domains. Genome Res 13:195-205
20. Harrington JJ, Van Bokkelen G, Mays RW, Gustashaw K, Willard HF (1997) Formation of de novo centromeres and construction of first-generation human artificial microchromosomes. Nat Genet 15:345-355
21. Harrison GE, Heslop-Harrison JS (1995) Centromeric repetitive DNA sequences in the genus Brassica. Theor Appl Genet 90:157-165
22. Hass BL, Pires JC, Porter R, Phillips RL, Jackson SA (2003) Comparative genetics at the gene and chromosome levels between rice (Oryza sativa) and wildrice (Zizania palustris). Theor Appl Genet 107:773-782
23. Henikoff S, Ahmad K, Malik HS (2001) The centromere paradox: stable inheritance with rapidly evolving DNA. Science 293:1098-1102
24. Jackson SA, Wang ML, Goodman HM, Jiang J (1998) Application of fiber-FISH in physical mapping of Arabidopsis thaliana. Genome 41:566-572
25. Jiang J, Birchler JA, Parrott WA, Dawe RK (2003) A molecular view of plant centromeres. Trends Plant Sci 8:570-575
26. Jiang J, Gill BS, Wang GL, Ronald PC, Ward DC (1995) Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes. Proc Natl Acad Sci U S A 92:4487-4491
27. Kang TJ, Yang MS (2004) Rapid and reliable extraction of genomic DNA from various wild-type and transgenic plants. BMC Biotechnol 4:20
28. Le MH, Duricka D, Karpen GH (1995) Islands of complex DNA are widespread in Drosophila centric heterochromatin. Genetics 141:283-303
29. Lee HR, Zhang W, Langdon T, Jin W, Yan H, Cheng Z, Jiang J (2005) Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species. Proc Natl Acad Sci U S A 102:11793-11798
30. Lu F, Ammiraju JS, Sanyal A, Zhang S, Song R, Chen J, Li G, Sui Y, Song X, Cheng Z, de Oliveira AC, Bennetzen JL, Jackson SA, Wing RA, Chen M (2009) Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci U S A 106:2071-2076
31. Martinez-Zapater JM, Estelle MA, Somerville CR (1986) A highly repeated DNA sequence in Arabidopsis thaliana. Mol Gen Genet 204:417-423
32. Murata M (2002) Telomeres and Centromeres in Plants. Current Genom 3:527-538
33. Murphy TD, Karpen GH (1995) Localization of centromere function in a Drosophila minichromosome. Cell 82:599-609
34. Nagaki K, Cheng Z, Ouyang S, Talbert PB, Kim M, Jones KM, Henikoff S, Buell CR, Jiang J (2004) Sequencing of a rice centromere uncovers active genes. Nat Genet 36:138-145
35. Nagaki K, Song J, Stupar RM, Parokonny AS, Yuan Q, Ouyang S, Liu J, Hsiao J, Jones KM, Dawe RK, Buell CR, Jiang J (2003) Molecular and cytological analyses of large tracks of centromeric DNA reveal the structure and evolutionary dynamics of maize centromeres. Genetics 163:759-770
36. Palmer D, Kevany M, Mackworth-Young C, Batchelor R, Lombardi G, Lechler R (1991) Generation and characterization of an HLA-DR alpha-specific monoclonal antibody using L-cell transfectants expressing human and mouse class II major histocompatibility dimers. Immunogenetics 33:12-17
37. Peterson, D.G.; Tomkins, J.P.; Frisch, D.A.; Wing, R.A.; and Paterson, A.H. (2000). Construction of plant bacterial artificial chromosome (BAC) libraries: An illustrated guide. Journal of Agricultural Genomics 5: www.ncgr.org/research/jag
38. Round EK, Flowers SK, Richards EJ (1997) Arabidopsis thaliana centromere regions: genetic map positions and repetitive DNA structure. Genome Res 7:1045-1053
39. Singer MF (1982) Highly repeated sequences in mammalian genomes. Int Rev Cytol 76:67-112
40. Sullivan KF, Hechenberger M, Masri K (1994) Human CENP-A contains a histone H3 related histone fold domain that is required for targeting to the centromere. J Cell Biol 127:581-592
41. Talbert PB, Bryson TD, Henikoff S (2004) Adaptive evolution of centromere proteins in plants and animals. J Biol 3:18
42. Talbert PB, Masuelli R, Tyagi AP, Comai L, Henikoff S (2002) Centromeric localization and adaptive evolution of an Arabidopsis histone H3 variant. Plant Cell 14:1053-1066
43. Tang H, Bowers JE, Wang X, Ming R, Alam M, Paterson AH (2008) Synteny and collinearity in plant genomes. Science 320:486-488
44. Tyler-Smith C, Oakey RJ, Larin Z, Fisher RB, Crocker M, Affara NA, Ferguson-Smith MA, Muenke M, Zuffardi O, Jobling MA (1993) Localization of DNA sequences required for human centromere function through an analysis of rearranged Y chromosomes. Nat Genet 5:368-375
45. Vafa O, Sullivan KF (1997) Chromatin containing CENP-A and alpha-satellite DNA is a major component of the inner kinetochore plate. Curr Biol 7:897-900
46. Vaughan DA, Morishima H, Kadowaki K (2003) Diversity in the Oryza genus. Curr Opin Plant Biol 6:139-146
47. Warburton PE, Cooke CA, Bourassa S, Vafa O, Sullivan BA, Stetten G, Gimelli G, Warburton D, Tyler-Smith C, Sullivan KF, Poirier GG, Earnshaw WC (1997) Immunolocalization of CENP-A suggests a distinct nucleosome structure at the inner kinetochore plate of active centromeres. Curr Biol 7:901-904
48. Willard HF, Waye JS (1987) Chromosome-specific subsets of human alpha satellite DNA: analysis of sequence divergence within and between chromosomal subsets and evidence for an ancestral pentameric repeat. J Mol Evol 25:207-214
49. Wolfgruber TK, Sharma A, Schneider KL, Albert PS, Koo DH, Shi J, Gao Z, Han F, Lee H, Xu R, Allison J, Birchler JA, Jiang J, Dawe RK, Presting GG (2009) Maize centromere structure and evolution: sequence analysis of centromeres 2 and 5 reveals dynamic Loci shaped primarily by retrotransposons. PLoS Genet 5:e1000743
50. Yi CD, Gong ZY, Liang GH, Wang FH, Tang SZ, Gu MH (2007) Isolation and characterization of the centromeric BAC clones from differnet genomes in genus Oryza. HEREDITAS (Beijing) 29:851-858
51. Zhang D, Yang Q, Bao W, Zhang Y, Han B, Xue Y, Cheng Z (2005a) Molecular cytogenetic characterization of the Antirrhinum majus genome. Genetics 169:325-335
52. Zhang, W. (2005). Functional Analysis of Centromeric Elements of Two Diploid Genomes BB and FF in Oryza Genus. [D].Beijing:Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
53. Zhang W, Yi C, Bao W, Liu B, Cui J, Yu H, Cao X, Gu M, Liu M, Cheng Z (2005b) The transcribed 165-bp CentO satellite is the major functional centromeric element in the wild rice species Oryza punctata. Plant Physiol 139:306-315
54. 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