The origins of Arabidopsis
duplications
supplementary material to accompany T.J. Vision, D.G.
Brown & S.D. Tanksley (2000) Science 290:2114-2117.
Here, we present raw data and results from our analysis of the history of
genomic duplications in Arabidopsis thaliana.
Sequences and positions of protein-coding genes on chromosomes 2 and 4 were
obtained on 12/17/1999 from the TIGR and MIPS ftp sites:
ftp://ftp.tigr.org/pub/data/a_thaliana/chromosomeII and
ftp://warthog.mips.biochem.mpg.de/pub/cress/chrIV/ESSAseq.
Accession numbers of sequences and tiling path data for chromosomes 1, 3 and
5 were obtained from The Arabidopsis Information Resource
(http://www.arabidopsis.org) and from Genbank [D. A. Benson, et al., Nucleic
Acids Res. 28, 15 (2000)] on 4/30/2000.
According to TAIR in April 2000, these data represent 80-90% of the full
genome sequence.
Please see the published paper for methodological details of the analysis and
an explanation of the results.
Tables are ASCII text and images are GIFs. Left click to view and right
click to save.
Raw data for chromosomes 2 and 4
Raw data for chromosomes 1, 3 and 5
Genome-wide patterns of sequence similarity
- BLASTP
results for all pairs of genes
- Positions of
cORFs in whole genome matrix
- Positions
of cORFs on each chromosome
- Matching pairs of
cORFs
- Figures showing matches between all pairs of chromosomes: 1v1, 1v2, 1v3, 1v4, 1v5, 2v2, 2v3, 2v4, 2v5, 3v3, 3v4, 3v5, 4v4, 4v5, 5v5
- Figure
showing matches among all chromosomes
The figures show the
positions of cORFs with high-scoring BLAST matches (the relative positions
within the chromosomes are marked on the axes). The two colors indicate
the transcriptional orientation of the cORFs. Red indicates that both
genes are oriented in parallel, blue that they are oriented in opposite
directions. The reference direction is arbitrary, but blocks are largely
composed of runs of one color since a change in color between adjacent matches
within a block suggests an inversion. The relative strength of the match is
shown by color instensity; brighter matches are of higher rank than duller ones.
Blocks of duplication
Genscan output and Clustal alignments for areas of interest are
available upon request.
Todd J. Vision, Department of Biology, University of North Carolina at Chapel Hill
Daniel G. Brown, Department of Computer Science, University of Waterloo
Steven D. Tanksley, Department of Plant Biology, Cornell University
Please send comments and questions to Todd Vision
Last modified 8 Jul 2002 by Todd Vision
