Sequence organization and evolutionary dynamics of Brachypodium-specific centromere retrotransposons

Chromosome Research

Volumn 21, Issue 5, 2013, Pages 507-521

  Qi, L L ^a   Wu, J J ^b   Friebe, B ^c   Qian, C ^c   Gu, Y Q ^d   Fu, D L ^b   Gill, B S ^c  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b SHANDONG AGRICULTURAL UNIVERSITY   (China)

^c KANSAS STATE UNIVERSITY   (United States)

^d WESTERN REGIONAL RESEARCH CENTER   (United States)

Author keywords

Brachypodium distachyon; Centromere retrotransposons; Evolution

Indexed keywords

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; BARLEY; BRACHYPODIUM; CENTROMERE; CHROMOSOME SATELLITE; FLUORESCENCE IN SITU HYBRIDIZATION; LONG TERMINAL REPEAT; MAIZE; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENOME; PRIORITY JOURNAL; RETROPOSON; RICE; RYE; SEQUENCE ANALYSIS; WHEAT;

BACTERIA (MICROORGANISMS); BRACHYPODIUM; BRACHYPODIUM DISTACHYON; HORDEUM; POACEAE; POOIDEAE; SECALE CEREALE; TRITICEAE; TRITICUM AESTIVUM; ZEA MAYS;

BASE SEQUENCE; BRACHYPODIUM; CENTROMERE; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, PLANT; EVOLUTION, MOLECULAR; GENE ORDER; GENOME, PLANT; IN SITU HYBRIDIZATION, FLUORESCENCE; RETROELEMENTS; SEQUENCE ALIGNMENT; TERMINAL REPEAT SEQUENCES;

EID: 84884289213     PISSN: 09673849     EISSN: 15736849     Source Type: Journal    
DOI: 10.1007/s10577-013-9378-4     Document Type: Article

References (51)

1. Abbo S, Dunford RP, Foote T, Reader SM, Flavell RB, Moore G (1995) Organization of retroelement and stem-loop repeat families in the genomes and nuclei of cereals. Chromosome Res 3:5-15
2. Ananiev EV, Phillips RL, Rines HW (1998) Chromosome-specific molecular organization of maize (Zea mays L.) centromeric regions. Proc Natl Acad Sci USA 95:13073-13078
3. Aragón-Alcaide L, Miller T, Schwatzacher T, Reader S, Moore G (1996) A cereal centromeric sequence. Chromosoma 105:261-268
4. Bolot S, Abrouk M, Masood-Quraishi U, Stein N, Messing J, Feuillet C, Salse J (2009) The 'inner circle' of the cereal genomes. Curr Opin Plant Bio 12:119-125
5. Buchmann JP, Matsumoto T, Stein N, Keller B, Wicker T (2012) Inter-species sequence comparison of Brachypodium reveals how transposon activity corrodes genome colinearity. Plant J 71:550-556
6. Cheng Z, Dong F, Langdon T, Ouyang S, Buell CR, Gu MH, Blattner FR, Jiang J (2002) Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14:1691-1704
7. Choulet F, Wicker T, Rustenholz C et al (2010) Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell 22:1686-1701
8. Copenhaver GP, Nickel K, Kuromori T, Benito MI, Kaul S et al (1999) Genetic definition and sequence analysis of Arabidopsis centromeres. Science 286:2468-2474
9. Dong F, Miller T, Jacson SA, Wang GL, Ronald PC, Jinag J (1998) Rice (Oryza sativa) centromeric regions consist of complex DNA. Proc Natl Acad Sci USA 95:8135-8140
10. Du J, Tian Z, Hans CS, Laten HM, Cannon SB, Jackson SA, Shoemaker RC, Ma J (2010) Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison. Plant J 63:584-598
11. Francki MG (2001) Identification of Bilby, a diverged centromeric Ty1-copia retrotransposon family from cereal rye (Secale cereale L.). Genome 44:266-274
12. Gao D, Gill N, Kim HR, Walling JG, Zhang W, Fan C, Yu Y, Ma J, SanMigue P, Jiang N et al (2009) A lineage-specific centromere retrotransposon in Oryza brachyantha. Plant J 60:820-831
13. Hall SE, Kettler G, Preuss D (2003) Centromere satellites from Arabidopsis populations: maintenance of conserved and variable domains. Genome Res 13:195-205
14. Henikoff S, Ahmad K, Malik HS (2001) The centromere paradox: stable inheritance with rapidly evolving DNA. Science 203:1098-1102
15. Hudakova S, Michalek W, Presting GG, Ten Hoopen R, Dos Santos K, Jasencakova Z, Schubert I (2001) Sequence organization of barley centromeres. Nucleic Acids Res 29:5029-5035
16. Huo N, Gu YQ, Lazo GR, Vogel JP, Coleman-Derr D, Luo MC, Thilmony R, Garvin DF, Anderson OD (2006) Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics. Genome 49:1099-1108
17. Jiang J, Nasuda S, Dong F, Scherrer CW, Woo SS, Wing RA, Gill BS, Ward DC (1996) A conserved repetitive DNA element located in the centromeres of cereal chromosomes. Proc Natl Acad Sci USA 93:14210-14213
18. Jiang J, Birchler JA, Parrott WA, Dawe RK (2003) A molecular view of plant centromeres. Trends Plant Sci 8:570-575
19. Jin WW, Melo JR, Nagaki K, Talbert PB, Henikoff S, Dawe RK, Jiang J (2004) Maize centromeres: organization and functional adaptation in the genetic background of oat. Plant Cell 16:571-581
20. Jin WW, Lamb JC, Vega JM, Dawe RK, Birchler JA, Jiang J (2005) Molecular and functional dissection of the maize B chromosome centromere. Plant Cell 17:1412-1423
21. Kulikova O, Geurts R, Lamine M et al (2004) Satellite repeats in the functional centromere and pericentromeric heterochromatin of Medicago truncatula. Chromosoma 113:276-283
22. Kumekawa N, Ohtsubo E, Ohtsubo H (1999) Identification and phylogenetic analysis of gypsy-type retrotransposons in the plant kingdom. Genes Genet Syst 74:299-307
23. Kumekawa N, Ohmido N, Fukui K, Ohtsubo E, Ohtsubo H (2001) A new gypsy-type retrotransposon, RIRE7: preferential insertion into the tandem repeat sequence TrsD in pericentromeric heterochromatin regions of rice chromosomes. Mol Genet Genomics 265:480-488
24. Lamb JC, Yu W, Han F, Birchler JA (2008) Plant centromeres. Genome Dyn 4:95-107
25. Lee HR, Zhang W, Langdon T, Jin WW, Yan H, Cheng Z, Jiang J (2005) Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species. Proc Natl Acad Sci USA 102:11793-11798
26. Li B, Choulet F, Heng Y et al (2013) Wheat centromeric retrotransposons: the new ones take a major role in centromeric structure. Plant J 73:952-965
27. Lim K-B, Yang T-J, Hwang Y-J et al (2007) Characterization of the centromere and peri-centromere retrotransposons in Brassica rapa and their distribution in related Brassica species. Plant J 49:173-183
28. Liu Z, Yue W, Li D et al (2008) Structure and dynamics of retrotransposons at wheat centromeres and pericentromeres. Chromosoma 117:445-456
29. Ma J, Bennetzen JL (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci USA 101:12404-12410
30. Ma J, Wing R, Bennetzen JL, Jackson SA (2007) Evolutionary history and positional shift of a rice centromere. Genetics 177:1217-1220
31. Miller JT, Dong F, Jackson SA, Song J, Jiang J (1998) Retrotransposon-related DNA sequences in the centromeres of grass chromosomes. Genetics 150:1615-1623
32. Nagaki K, Song J, Stupar RM et al (2003a) Molecular and cytological analyses of large tracks of centromeric DNA reveal the structure and evolutionary dynamics of maize centromeres. Genetics 163:759-770
33. Nagaki K, Talbert PB, Zhong CX, Dawe RK, Henikoff S, Jiang J (2003b) Chromatin immunoprecipitation reveals that the 180-bp satellite repeat is the key functional DNA element of Arabidopsis thaliana centromeres. Genetics 163:1221-1225
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, Neumann P, Zhang D, Ouyang S, Buell CR, Cheng Z, Jiang J (2005) Structure, divergence, and distribution of the CRR centromeric retrotransposon family in rice. Mol Biol Evol 22:845-855
36. Presting GG, Malysheva L, Fuchs J, Schubert I (1998) A Ty3-gypsy retrotransposon-like sequence localizes to the centromeric regions of cereal chromosomes. Plant J 16:721-728
37. Price AL, Jones NC, Pevzner PA (2005) De novo identification of repeat families in large genomes. Bioinformatics 21(Suppl 1):i351-i358
38. Qi LL, Friebe B, Zhang P, Gill BS (2009) A molecular-cytogenetic method for locating genes to pericentromeric regions facilitates a genome-wide comparison of synteny between the centromeric regions of wheat and rice. Genetics 183:1235-1247
39. Qi LL, Friebe B, Wu J, Gu Y, Qian C, Gill BS (2010) The compact Brachypodium genome conserves centromeric regions of a common ancestor with wheat and rice. Funct Integr Genomics 10:477-492
40. Round EK, Flowers SK, Richards EJ (1997) Arabidopsis thaliana centromere regions: genetic map positions and repetitive DNA structure. Genome Res 91:1007-1019
41. Šafář J, Bartoš J, Janda J et al (2004) Dissecting large and complex genomes: flow sorting and BAC cloning of individual chromosomes from bread wheat. Plant J 39:960-968
42. Sharma A, Presting GG (2008) Centromeric retrotransposon lineages predate the maize/rice divergence and differ in abundance and activity. Mol Genet Genomics 279:133-147
43. Tek AL, Kashihara K, Murata M, Nagaki K (2010) Functional centromeres in soybean include two distinct tandem repeats and a retrotransposon. Chromosome Res 18:337-347
44. The International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nuture 463:763-768
45. Weber B, Schmidt T (2009) Nested Ty3-gypsy retrotransposons of a single Betaprocumbens centromere contain a putative chromodomain. Chromsome Res 17:379-396
46. Wen R, Moore G, Shaw PJ (2012) Centromeres cluster de novo at the beginning of meiosis in Brachypodium distachyon. PLoS One 7:e44681
47. Wu J, Fujisawa M, Tian Z et al (2009) Comparative analysis of complete orthologous centromeres from two subspecies of rice reveals rapid variation of centromere organization and structure. Plant J 60:805-819
48. Zhang P, Li WL, Fellers J, Friebe B, Gill BS (2004a) BAC-FISH in wheat identifies chromosome landmarks consisting of different types of transposable elements. Chromosoma 112:288-299
49. Zhang Y, Huang Y, Zhang L et al (2004b) Structural features of the rice chromosome 4 centromere. Nucleic Acids Res 32:2023-2030
50. Zhao X, Wang H (2007) LTR-FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res 35(Web Server issue):W265-W268
51. Zhong CX, Marshall JB, Topp C et al (2002) Centromeric retroelements and satellites interact with maize kinetochore protein CENH3. Plant Cell 14:2825-2836