A comparative study of retrotransposons in the centromeric regions of A and B chromosomes of maize

Cytogenetic and Genome Research

Volumn 110, Issue 1-4, 2005, Pages 203-208

  Theuri, J ^a   Phelps Durr, T ^a,b   Mathews, S ^a,c   Birchler, J ^a  

^a UNIVERSITY OF MISSOURI   (United States)

^b Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^c HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOSOME; BACTERIAL ARTIFICIAL CHROMOSOME; CENTROMERE; COMPARATIVE STUDY; DNA SEQUENCE; DNA TRANSPOSITION; GENE SEQUENCE; GENOME; MAIZE; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT CHROMOSOME; PRIORITY JOURNAL; RETROPOSON; SEQUENCE HOMOLOGY; SUPERNUMERARY CHROMOSOME;

CENTROMERE; CHROMOSOME MAPPING; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, PLANT; DNA TRANSPOSABLE ELEMENTS; RETROELEMENTS; ZEA MAYS;

ZEA MAYS;

EID: 23844443813     PISSN: 14248581     EISSN: None     Source Type: Journal    
DOI: 10.1159/000084953     Document Type: Article

References (35)

1. Alfenito MR, Birchler JA: Molecular characterization of a maize B chromosome centric sequence. Genetics 135:589-597 (1993).
2. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, LipMan DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402 (1997).
3. Ananiev EV, Phillips RL, Rines HW: Chromosome-specific molecular organization of maize (Zea mays L.) centromeric regions. Proc Natl Acad Sci USA 95:13073-13078 (1998).
4. Bennetzen JL, Kellogg EA: Do plants have a one-way ticket to genomic obesity? Plant Cell 9:1509-1514 (1997).
5. Birren B, Mancino V, Shizuya H: Bacterial Artificial Chromosomes, in Green ED, Birren B, Klapholz S, Myers RM, Pieter H (eds): Genome Analysis, pp 214-295 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor 1999).
6. Boeke JD, Corces VG: Transcription and reverse-tran-scription of retrotransposons. Annu Rev Microbiol 43:403-434 (1989).
7. Carlson WR: The B-chromosome of maize. CRC Crit Rev Plant Sci 3:201-226 (1986).
8. Dhar MK, Friebe B, Koul AK, Gill BS: Origin of an apparent B chromosome by mutation, chromo some fragmentation and specific DNA sequence amplification. Chromosoma 111:332-340 (2002).
9. Felsenstein J: Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791 (1985).
10. Gaut BS, Doebley JF: DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci USA 94:6809-6814 (1997).
11. Gaut BS, D'Ennequin MLT, Peek AS, Sawkins MC: Maize as a model for the evolution of plant nuclear genomes, in Ayala FJ, Fitch WM, Clegg MT (eds): Variation and Evolution in Plants and Microorganisms, pp 187-210 (National Academy Press, Washington DC 2000).
12. Henikoff S, Ahmad K, Malik HS: The centromere paradox: stable inheritance with rapidly evolving DNA. Science 293:1098-1102 (2001).
13. Hilton H, Gaut BS: Speciation and domestication of maize and its wild relatives: evidence from the globulin-1 gene. Genetics 150:863-872 (1998).
14. Jones N, Houben A: B chromosomes in plants: escapees from the A chromosome genome? Trends Plant Sci 8:417-423 (2003).
15. Kaszas E, Birchler JA: Misdivision analysis of centromere structure in maize. EMBO J 15:5246-5255 (1996).
16. Kaszas E, Birchler JA: Meiotic transmission rates correlate with physical features of rearranged centromeres in maize. Genetics 150:1683-1692 (1998).
17. Kidwell MG, Lisch D: Transposable elements as sources of variation in plants and animals. Proc Natl Acad Sci USA 94:7704-7711 (1997).
18. Kumar A, Bennetzen JL: Plant retrotransposons. Annu Rev Genet 33:479-532 (1999).
19. Kunze R, Saedler H, Lonnig WE: Plant transposable elements. Adv Bot Res 27:331-470 (1997).
20. Lamb JC, Birchler JA: The role of DNA sequence in centromere formation. Genome Biol 4:214 (2003).
21. Nagaki K, Song J, Stupar RM, Parokonny AS, Yuan Q, Ouyang S, Liu J, Hsiao J, Jones KM, Dawe RK, Buell CR, Jiang J: Molecular and cytological analyses of large tracks of centromeric DNA reveal the structure and evolutionary dynamics of maize centromeres. Genetics 163:759-770 (2003).
22. Page BT, Wanous MK, Birchler JA: Characterization of a maize chromosome 4 centromeric sequence: evidence for an evolutionary relationship with the B chromosome centromere. Genetics 159:291-302 (2001).
23. Puertas MJ: Nature and evolution of B chromosomes in plants: A non-coding but information-rich part of plant genomes. Cytogenet Genome Res 96:198-205 (2002).
24. SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL: The paleontology of intergene retrotransposons of maize. Nat Genet 20:43-45 (1998).
25. Schmidt T: LINEs, SINEs, and repetitive DNA: non-LTR retrotransposons in plant genomes. Plant Mol Biol 40:903-910 (1999).
26. Shizuya H, Birren B, Kim UJ, Mancini V, Slepak T, et al: Cloning and stable maintenance of 300 kilo-base-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci USA 89:8794-8797 (1992).
27. Stark EA, Connerton I, Bennet ST, Barnes SR, Parker JS, Forster JW: Molecular analysis of the structure of the maize B chromosome. Chromosome Res 4:15-23 (1996).
28. Swofford DL: PAUP *. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4 (Sinauer Associates, Sunderland MA 2002).
29. Tavaré S: Some probabilistic and statistical problems on the analysis of DNA sequences. Lec Math Life Sci 17:57-86 (1986).
30. Thompson JD, Higgins DG, Gibson TJ: ClustalW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position, specific gap penalties, and weight matrix choice. Nucleic Acids Res 22:4673-4680 (1994).
31. Tikhonov AP, SanMiguel PJ, Nakajima Y, Gorenstein NM, Bennetzen JL, Avramova Z: Colinearity and its exceptions in orthogolous adh regions of maize and sorghum. Proc Natl Acad Sci USA 96:7409-7414 (1999).
32. Woo SS, Jiang J, Gill BS, Paterson AH, Wing RA: Construction and characterization of a bacterial artificial chromosome library of Sorghum bicolor. Nucleic Acids Res 22:4922-4931 (1994).
33. Xiong Y, Eickbush TH: Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J 9:3353-3362 (1990).
34. Yuan Q, Hill J, Moffat K, Hsiao J, Cheng Z, et al: Genome sequencing of a 239-kb region of rice chromosome 10L reveals a high frequency of gene duplication and a large chloroplast DNA insertion. Mol Genet Genomics 267:713-720 (2002).
35. Zhong CX, Marshall JB, Topp C, Mroczek R, Kato A, Nagaki K, Birchler JA, Jiang J, Dawe RK: Centromeric retroelements and satellites interact with maize kinetochore protein CENH3. Plant Cell 14:2825-2836 (2002).