Arabidopsis Positional History Dataset

Information includes chromosome start/stop, strand, duplicate state (parent=P, duplicate=AT number, or interrupter=I), TAIR9 gene description, the chromosomal position for each outgroup (-, S, G, FN, FB, F), the numerical synteny value for each chromosomal position (1=S except for grape, where 2=S; 0.2=FB or FN, 0.1=G or -, and 0=F), total synteny value (the average of all synteny values for all outgroups), whether or not the gene had any exons (TAIR9 data), TAIR8 chromosome start/stop, functional gene space, the difference between gene space and functional gene space. Functional gene space, CNS data, GO terms, and homeolog data is from Version 2 as annotated by S. Subramaniam in this lab, unpublished. The CNS data was originally from TAIR8 but has been merged with TAIR9. Following this are TAIR9 GEvo link, and best hit data in A. lyrata and poplar for all transposed genes

Gene list showing synteny, methylation and GC content for 4 monocot species.

(XLSX)</p

Plot of the GC content of all genes at the 3^rd position of each codon for the first 50 codons (GC3-50).

The GC3-50 content of genes showed a very different distribution among the monocot grasses tested vs the eudicots tested. The eudicots appeared to have a relatively normal distribution of GC3-50 content, with Arabidopsis, peach and grape having median content of approximately 46% but poplar and tomato showing lower medians of 40% and 34% respectively. The grasses had irregular distributions of GC3-50 content, containing a class of genes with a modal GC3-50 content of 90–94%, and another class with a mode near 40% with many genes falling in between the two clusters. AT- Arabidopsis thaliana, PT- Populus trichocarpa, PP- Prunus persica, SL- Solanum lycopersicum, VV- Vitis vinifera, BD- Brachypodiuum distachyon, OS- Oryza sativa, SB- Sorghum bicolor, ZM- Zea mays.</p

Number of genes from 9 species found to be in a syntenic location in other species.

Number of genes from 9 species found to be in a syntenic location in other species. AT- Arabidopsis thaliana, PT- Populus trichocarpa, PP- Prunus persica, SL- Solanum lycopersicum, VV- Vitis vinifera, BD- Brachypodiuum distachyon, OS- Oryza sativa, SB- Sorghum bicolor, ZM- Zea mays.</p

Sorghum to rice synteny.

Dots indicate syntenic gene pairs conserved in gene order between the two species. Syntenic segments were identified as stretches of 7 or more genes conserved in order between the two genomes. The x-axis represents 52,424 rice genes and the y-axis represents 47,205 sorghum genes.</p

Average methylation levels at CG, CHG and CHH sites by gene copy number as determined by number of within genome BLAST hits.

Average methylation levels at CG, CHG and CHH sites by gene copy number as determined by number of within genome BLAST hits.</p

Correlation between methylation levels for three different methylation types and the GC3-50 content for genes from nine species.

Correlation between methylation levels for three different methylation types and the GC3-50 content for genes from nine species.</p

Gene Ontology (GO) terms associated with syntenic and non-syntenic genes.

(XLSX)</p

Figures showing dot plots of synteny, GC3 content for syntenic and non-syntenic genes, and copy number vs GC3 content for all 9 species.

(DOCX)</p

Gene list showing synteny, methylation and GC content for 5 dicot species.

(XLSX)</p