Bacterial Artificial Chromosomes (BACs) derived from the B chromosome, based on homology with the B specific sequence, were subcloned and sequenced. Analysis of DNA sequence data indicated the presence of 23 common retroelements, as well as novel sequences of B chromosome origin. Generally, where the same retrotransposon type was observed in both A and B chromosomes, there were more copies per unit of sequence in the B centromeric region (the major site of B repeat) than in the A centromere, except for Huck-1. Based on previous estimates of the age of the major burst of transposition into the maize genome, the oldest retrotransposons (Ji-6 and Tekay, ∼5.0 and 5.2 million years ago, respectively) were found in the B centromere region only, while the next two oldest (Huck-1 and Opie-1) were found in both the A and B sequences. Phylogenetic analysis of Opie retroelements from both A and B centromeres indicated that some of the B Opie centromeric sequences share a more recent common ancestor with A Opie retroelements than they do with other B Opie centromeric sequences. These results imply that the supernumerary maize B chromosome has coexisted with the A chromosomes during that period of transposition. They also support the hypothesis that the B chromosome had its origins from A chromosome elements, or that alternative origins, such as being donated to the maize genome in a wide species cross, preceded six million years ago, because the spectrum of retrotransposons in the two chromosomes is quite similar.   

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-transcription 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, chromosome 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 kilobase-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).
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