Large-scale polymorphism of heterochromatic repeats in the DNA of Arabidopsis thaliana.
BACKGROUND
The composition of the individual eukaryote's genome and its variation within a species remain poorly defined. Even for a sequenced genome such as that of the model plant Arabidopsis thaliana accession Col-0, the large arrays of heterochromatic repeats are incompletely sequenced, with gaps of uncertain size persisting in them.


RESULTS
Using geographically separate populations of A. thaliana, we assayed variation in the heterochromatic repeat arrays using two independent methods and identified significant polymorphism among them, with variation by as much as a factor of two in the centromeric 180 bp repeat, in the 45S rDNA arrays and in the Athila retroelements. In the accession with highest genome size as measured by flow cytometry, Loh-0, we found more than a two-fold increase in 5S RNA gene copies relative to Col-0; results from fluorescence in situ hybridization with 5S probes were consistent with the existence of size polymorphism between Loh-0 and Col-0 at the 5S loci. Comparative genomic hybridization results of Loh-0 and Col-0 did not support contiguous variation in copy number of protein-coding genes on the scale needed to explain their observed genome size difference. We developed a computational data model to test whether the variation we measured in the repeat fractions could account for the different genome sizes determined with flow cytometry, and found that this proposed relationship could account for about 50% of the variance in genome size among the accessions.


CONCLUSIONS
Our analyses are consistent with substantial repeat number polymorphism for 5S and 45S ribosomal genes among accession of A. thaliana. Differences are also suggested for centromeric and pericentromeric repeats. Our analysis also points to the difficulties in measuring the repeated fraction of the genome and suggests that independent validation of genome size should be sought in addition to flow cytometric measurements.
Davison
Jerry
J
University of Washington, Department of Biology, Box 355325, Seattle, WA 98195-5325, USA. ox@u.washington.edu
Tyagi
Anand
A
Comai
Luca
L
D017360:Arabidopsis / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics*; D017343:Genes, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D006570:Heterochromatin / Q000235:genetics*; D018895:Microsatellite Repeats; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D013698:Templates, Genetic
D018744:DNA, Plant; D006570:Heterochromatin
Plant Cell. 1999 Nov;11(11):2099-112
10559437
Plant Physiol. 2003 Jun;132(2):461-8
12805579
Hum Mol Genet. 1999 Feb;8(2):205-15
9931328
Science. 2007 Jun 8;316(5830):1497-502
17540862
Plant Cell Rep. 2004 Nov;23(5):263-71
15368076
Genome Res. 2000 May;10(5):679-90
10810091
Nature. 2006 Feb 16;439(7078):851-5
16482158
Cell Biophys. 1990 Dec;17(3):257-67
1714351
Plant J. 2006 Oct;48(2):307-19
16995901
Trends Genet. 2000 Sep;16(9):418-20
10973072
Genetics. 1987 Oct;117(2):285-95
17246404
Plant J. 2001 Aug;27(4):285-96
11532174
Genome Res. 1997 Nov;7(11):1045-53
9371740
Nature. 2004 Dec 9;432(7018):695-716
15592404
Genome Res. 2006 Aug;16(8):949-61
16809666
Jpn J Genet. 1994 Aug;69(4):361-70
7545957
Plant J. 1996 Feb;9(2):259-72
8820610
Nucleic Acids Res. 2003 Jul 15;31(14):e73
12853650
Ann Bot. 2003 Apr;91(5):547-57
12646499
Science. 2004 Jul 23;305(5683):525-8
15273396
Gene. 1992 Mar 15;112(2):225-8
1348233
Plant J. 1995 Feb;7(2):273-86
19764126
Hereditas. 1975;79(2):293-300
1141006
Ann Bot. 2005 Jan;95(1):201-6
15596467
Int J Urol. 2005 Nov;12(11):984-9
16351655
Plant J. 1998 Mar;13(6):867-76
9681023
Genome Res. 2000 May;10(5):597-610
10810082
Biotechniques. 2003 Feb;34(2):374-8
12613259
Genetica. 2002 May;115(1):29-36
12188046
Ann Bot. 2004 Mar;93(3):317-21
14724121
Nat Rev Genet. 2004 May;5(5):345-54
15143317
Genome Res. 2003 Feb;13(2):195-205
12566397
Bioinformatics. 2005 Mar15;21(6):821-2
15531610
Cytogenet Cell Genet. 1998;82(3-4):192-4
9858814
DNA Res. 2000 Dec 31;7(6):315-21
11214966
Chromosome Res. 2003;11(3):227-40
12769290
Chromosome Res. 2003;11(3):217-26
12769289
Cytometry. 1984 Jul;5(4):355-63
6468176
Nature. 2000 Dec 14;408(6814):796-815
11130711
PLoS Biol. 2004 Jul;2(7):E207
15252450
Curr Biol. 2006 Jul 11;16(13):1322-8
16824920
BMC Bioinformatics. 2005;6:62
15780134
DNA Res. 2001 Dec 31;8(6):285-90
11853315
DNA Res. 2002 Aug 31;9(4):117-21
12240833
Biochem Genet. 1984 Oct;22(9-10):923-30
6517855