Additional data file 1:

Table S1: summary of B. rapa sequence contigs, constituent BAC associations, and targeting of homologous regions of A. thaliana based on BLASTZ matches. Table S2: location of sequence contigs on the B. rapa chromosomes according to a combination of genetic map position, FISH results, physical map contig, and positional information from A. thaliana counterparts. Table S3: statistics of microsynteny in the synteny blocks identified by a genome comparison of B. rapa and A. thaliana. Table S4: identification of sister blocks produced by the same polyploidy events in the Br genome based on At-At and At-Br relationships. Table S5: identification of sister blocks produced by the same polyploidy events in the Bo genome. Table S6: sources of genomic and transcript sequences used in this study.

Format: PDF Size: 369KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional data file 2:

Figure S1: comparison of homologous block end-point distances between 410 B. rapa sequence contigs and their Arabidopsis counterpart regions, indicating a genome shrinkage of approximately 30% in B. rapa. Figure S2: abundance of different transposable element types in the B. rapa genome. Figure S3: comparison of Brassica 'A' genome structures between B. rapa and B. napus. Genome blocks were defined based on 24 AK genome building blocks. The genome structure of Bna was obtained from the reports of Parkin et al. [23] and Schranz et al. [37]. Regions characterized by significant rearrangements (pink box) or insertions/deletions (gray box) between genomes are highlighted by colored boxes. Scale bars on the margins indicate megabase-pairs (Mbp) for Br or centi-Morgans (cM) for Bna. Blocks with the opposite orientation relative to AK are indicated by a gray upward-pointing arrow on the right side of the block. Figure S4: dot plot of B. rapa compared with itself. Each dot in the dot plot represents a reciprocal best BLASTP match between gene pairs at a cutoff value of <E^-20. Red dots show the regions of synteny identified by DiagHunter.

Format: PDF Size: 130KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional data file 3:

The data provided include two worksheets. Gene correspondence data for the 227 synteny blocks identified by DiagHunter are provided in the worksheet entitled 'blocks.' The synteny quality of the blocks is included in the worksheet named 'quality'; tandem duplicated genes were considered to be single homologs. The quality of synteny was defined as described in the Materials and methods.

Format: ZIP Size: 243KB Download file

Additional data file 4:

This dataset indicates the block order, orientation, and color-coding used for each AK block. The synteny-defined block boundaries on the Br chromosomes identified by DiagHunter were defined according to the At locus name described by Schranz et al. [37]. Supporting data, including gene correspondences in all synteny blocks, are included in the worksheet 'At-Br matches in synteny blocks'. Mapping of AK blocks to the Br chromosomes, including block boundaries and orientation, is provided in the worksheet 'AK blocks to Br'. A summary table and graph of AK mapping to the Br chromosomes is provided in the worksheet 'Br chr. chart'.

Format: ZIP Size: 580KB Download file