Bacterial artificial chromosome (BAC) sequence assembly generated 410 Br sequence contigs (sequences composed of more than one BAC sequence) covering 65.8 Mbp (Tables S1 and S2 in Additional data file 1). These sequence contigs span 75.3 Mbp of the At genome, representing 92.2% of the total At euchromatic region (Figure 1 and Table 1). A total of 43.9 Mbp remain as uncovered gaps: among these, 6.4 Mbp are attributable to euchromatin gaps, and the remaining 37.5 Mbp to pericentromeric heterochromatin gaps.

The genome coverage of the gene-rich Br sequences was estimated by representation in two different datasets: expressed sequence tag (EST) sequences and conserved single-copy genes. Based on a BLAT analysis of 32,395 Br unigenes (a set of ESTs that appear to arise from the same transcription locus) against the sequence contigs, the proportion of hits recovered under stringent conditions (see Materials and methods) was 29.2%. This result was largely consistent with the proportion of rosid-conserved single-copy genes showing matches to Br sequences. A TBLASTN comparison of 1,070 At-Medicago truncatula (Mt) conserved single-copy genes against Br sequences revealed a 24.3% match. Both methods indicate approximately 30% coverage of euchromatin in the dataset analyzed; thus, the euchromatic region of Br is estimated to be approximately 220 Mbp, 42% of the whole genome given that the genome size of Br is 529 Mbp 30.

Gene annotation was carried out using our specialized Br annotation pipeline. Gene prediction of the Br sequence data using a variety of ab initio, similarity-based, and EST/full-length cDNA-based methods resulted in the construction of 15,762 gene models. Taken together with the genome coverage of Br sequences, the overall number of protein-coding genes in the Br genome is at least 52,000 to 53,000, which is higher than those of other plant genomes sequenced thus far, including At 7, rice (Oryza sativa (Os)) 8, poplar (Populus trichocarpa (Pt)) 9, grape 10, papaya 11, and sorghum 12. However, the estimated total number of genes in the Br genome is only twice that of At. Details of the annotation are available online at the URL cited in the 'Data used in this study' section in the Materials and methods.

The gene structure and density statistics are shown in Table 2. The base composition of Br and At genes is very similar. The average length of Br genes (ATG to stop codon) is 73% that of At genes. This is consistent with previous reports on Bo 192026. This difference appears to be due to one less exon per gene and shorter exon and intron lengths in Br. The average gene density of 1 per 4.2 kilobase-pairs (kbp) in Br is slightly lower than that in At (1 per 3.8 kbp). Thus, the At/Br ratio of gene density is 0.90, indicating slightly less compact organization of Br euchromatin than At euchromatin. Moreover, the distance between the homologous block endpoints in Br and At has an R² of 0.63 with a dAt/dBr slope of 1.36 (Figure S1 in Additional data file 2). This result indicates that gene-containing regions in At occupy approximately 30 to 40% more space than their Br counterparts. Based on these data and the results mentioned above, we postulate that the euchromatic genome of Br has shrunken by approximately 30% compared to its syntenic At counterpart. Most of the genome shrinkage in Br could be explained by the deletion of roughly one-third of the redundant proteome as well as TEs in the euchromatic Br genome. Only 14% of the Br genes were tandem duplicates compared with 27% of At genes in a 100-kbp window interval. In addition, only 45 nucleotide binding site-encoding genes were identified in Br, suggesting that the total number of nucleotide binding site-encoding genes in the Br genome is likely to be almost the same as that in At (approximately 200) 3132. A database search revealed that a total of 12,802 (81%) of the predicted Br genes have similarity (<E^-10) to proteins in the non-redundant nucleotide database of the National Center for Biotechnology Information (NCBI); 2,960 (19%) are Br unique genes. To assess the putative function of the genes that recorded no hits to non-redundant proteins, we assigned functional categories to the Br unique genes using gene ontology analysis; however, this analysis could not identify a putative function for approximately 85% of the Br unique genes. Thus, we can conclude that 16% of the proteome of Br has acquired a novel function since the Br-At divergence.

Repetitive sequence analysis revealed that 6% of euchromatic Br sequences are composed of TEs, a twofold greater amount than identified in the counterpart At euchromatic genome, presumably due to a greater number of LTRs and long interspersed elements (Table 3). In addition, low complexity repetitive sequences are relatively abundant in the Br euchromatic region, indicating Br-specific expansion of repetitive sequences. The distribution of repetitive sequences and TEs along the chromosomes was not uneven (Figure S2 in Additional data file 2). It has previously been reported, based on partial draft genome shotgun sequences, that Bo (approximately 696 Mbp) has a significantly higher proportion of both class I and class II TEs sequences than At 33. Taken together with these previous reports 3435, TEs appear to be partly responsible for genome expansion in the Brassica lineage, and these TEs appear to accumulate predominantly in the heterochromatic regions of Br.

To identify syntenic regions in the Br and At genomes, we compared the whole proteome between the two genomes using BLASTP analysis, and putative synteny blocks were plotted using DiagHunter and GenoPix2D programs 36. The non-redundant chromosome-ordered genome sequence in the Br build was 62.5 Mbp. An additional 3.2 Mbp had not yet been assigned to chromosomes and was therefore not used for synteny analysis. We examined the synteny blocks at three different levels: whole genome (Figure 2a), large-scale synteny blocks in chromosome-to-chromosome windows (Figure 2b; Additional data file 3), and microsynteny <2.5 Mbp (the synteny can be viewed at the URL cited in the 'Data used in this study' section in the Materials and methods). Although the Br genome build was partial and incomplete with only approximately 30% of euchromatin represented and some misordered contigs present, the level of synteny between the genomes was prominent and distinct. The DiagHunter program detected 227 highly homologous syntenic blocks with 72% of the sequenced and anchored Br sequence assigned to synteny blocks in At and 72% of At euchromatic sequence assigned to synteny blocks in Br when multiple blocks overlapping the same region were counted (Figure 2a). Considering the history of frequent genome duplication events in Brassicaceae, this result strongly indicates the presence of secondary or tertiary blocks resulting from WGT.

The Br and At genomes share a minimum of 20 large-scale synteny blocks with substantial microsynteny; these synteny blocks extend the length of whole chromosome arms. At shows synteny of chromosome arms with multiple chromosome blocks of Br, apparently corresponding to triplicated remnants (Figure 2b). At1S (short arm), At2L (long arm), At4L, and At5 have three long-range synteny counterparts in three independent Br chromosomes. However, At1L and At3 have only one or two synteny blocks in the Br genome. Moreover, some genome regions of At, including a smaller section of At2S and At4S, show no significant synteny with Br counterparts, indicating chromosome-level deletion of triplicated segments. Incidentally, Br shows synteny with a major single chromosome along almost the entire length (A1, A2, A4, and A10) or fragments of multiple At chromosomes in a complicated mosaic pattern, indicating frequent recombination of Br chromosomes. Notable regions of synteny are shown in Figure 2b, and are At1S-A6/A8/A9, At1L-A7, At2L-A3/A4/A5, At3S-A3/A5, At3L-A7/A9, At4L-A1/A3/A8, and At5-A2/A3/A10 (synteny view available at the URL cited in the 'Data used in this study' section in the Materials and methods. Additional synteny blocks scattered throughout genome regions, probably due to recombination, were also identified.

Within individual synteny blocks, microsynteny (conservation of gene content and order) was considerable. The average degree of proteome conservation for all predicted synteny blocks was 52 ± 13% in the blocks (Table S3 in Additional data file 1). This value is almost the same as that of the Mt-Lotus japonicus comparison in which an ancient WGD event at a similar time period (Ks 0.7 to 0.9) as the Br-At WGD but earlier speciation (Ks 0.6) than Br-At was detected 18. The underestimated value reported here presumably reflects significant gene loss and rearrangement after WGT in the Br lineage resulting in genome shrinkage, based on the fact that deletion events in syntenic blocks of the Br genome were twofold more frequent than in the At genome. Genes without corresponding homologs in syntenic regions contributed to 15 ± 7% of all genes from Br but 33 ± 13% from At (Table S3 in Additional data file 1; Additional data file 3). Genes encoding proteins involved in transcription or signal transduction were not found to be significantly more retained in syntenic blocks than those encoding proteins classified as having other functions. Further genome sequencing will help resolve the synteny in the uncovered and/or the scattered genome regions.

Comparison of the genomes of Br and At allows insight into the origin and evolution of the Brassica 'A' genome. Previous comparative mapping studies have identified a putative ancestral karyotype (AK) comprising 24 building blocks on 8 chromosomes from which the current Arabidopsis and Brassica genomes have evolved via fusion/fission, rearrangement, and deletion of chromosomes followed by polyploidy 23373839. According to the At-AK relationship and pair information of Br-At synteny blocks, we defined conserved genome building blocks of AK on the Br genome build (Figure 3; Additional data file 4). The pattern of block boundaries on Br chromosomes was similar to that reported pattern for Bna 'A' genome components, albeit more complicated (Figure S3 in Additional data file 2). Most of the block boundaries were conserved between Br and the 'A' genome components of Bna with the exception of several insertions/deletions; this is presumably due to limited sequence and marker information. In addition, inversion or serial mismatched block boundaries were found on A2, A7 and A9, respectively, suggesting recombination of homologous counterpart regions between the 'A' and 'C' genomes in Bna.

An examination of the Br genome from the perspective of ancestral blocks reveals that three copies of the genome are present, as predicted from the WGT (Figure 3). Although there are several discontinuous matches due to gaps between syntenic blocks, almost 50% of the ancestral blocks were triplicated in the Br genome, while others occurred only once or twice, indicating loss of blocks during genome rearrangement. Blocks D, G, and M could not be found on the Br genome. The Br genome is highly rearranged relative to At compared with AK. Block R was localized together with block W in triplicate regions (A2, A3, and A10). However, in At5, blocks R and W were separated on the short arm and long arm, respectively 3839. Similarly, blocks E and N were adjacent and triplicated in Br but separated in At. Meanwhile, blocks K and L, which are fused in AK but split in different chromosomes of At, were adjacent (A6) or separated (A9) on the same chromosomes of Br. However, we did not determine precisely which copy of the replicated AK block family corresponds to the Br BACs because of the possibility that Br sequences in the polyploid genome were not accurately positioned. Because several genetic markers originate from duplicate or triplicate regions of the Br genome, the true location of the BACs could correspond to any of the amplified bands, which could result in inaccurate mapping of the BAC sequence. In this case, the resulting assignment of the BAC to an incorrect linkage group on a specific AK block family member would also be flawed; however, we found that almost all BAC sequences showed excellent correspondence to the correct family of AK blocks. Further analysis, including chromosome painting and additional genome sequencing, will allow determination of the precise location of AK blocks in the Br genome.

To deduce the approximate time point of polyploidy and speciation, we compared the distribution of synonymous substitution (Ks) in homologous sequences identified by a reciprocal best BLAST hit search between Br and the completely annotated sequences of At, Pt, Mt, and Os. As shown in Figure 4a-c, Br shares a single ancient duplication event (1R) with Os, Pt, and Mt as illustrated by single peaks at Ks modes of 2.5 to 2.6, 2.2 to 2.3, and 1.8 to 1.9, respectively, indicating successive splitting of the Br lineage from monocots and eurosid I during the early and late Cretaceous period around 60 to 120 MYA, depending on the neutral substitution rate used 40. The age distributions of At and Br yield clear peaks corresponding to 2R at Ks = 1.7 to 1.8 and 1.8 to 1.9, respectively, lower than that of the Br-Pt comparison but similar to that of the Br-Mt comparison (Figure 4e, f). This suggests that an ancient burst of gene duplications due to the 2R event in At and Br must have occurred almost immediately after divergence between eurosid I and eurosid II. Taken together with recent studies of the Pt 9 and Mt genomes 18, we conclude that genome duplication in rosids occurred independently after the split from the last common rosid ancestor, and that most polyploidy events (2R, 3R, and 4R) in Brassicaceae postdate the eurosid I (Pt and Mt)-eurosid II (At and Br) divergence.

The Ks distribution for At and Br orthologs displayed two peaks at Ks = 0.3 to 0.4 and 2.0 to 2.1, corresponding to shared duplication events (3R and 2R) and speciation between the genomes at around 13 to 17 MYA (Figure 4d). As reported before, the oldest duplication (1R) could not be seen in the Ks distributions in both genomes. Surprisingly, a comparison of the Ks mode for the paralogs in At and Br identified remarkable differences in the duplicated genes retained in the two genomes. Furthermore, the At genome has two clear peaks for 3R (mode Ks = 0.6 to 0.7) and 2R (mode Ks = 1.7 to 1.8). However, in the Br genome, two peaks representing 4R (mode Ks = 0.2 to 0.3) and 2R (mode Ks = 1.8 to 1.9) are evident, but the 3R peak has collapsed (Figure 4e, f). The difference between the distributions for Br-Br versus Br-At (P = 1.65E^-8) was significantly higher than that for At-At versus Br-At (P = 0.001). Taken together, these findings suggest that duplicated genes produced by the 3R event were widely lost in the triplicated Br genome.

Because we used approximately 30% of the euchromatic sequence of Br, we could have underestimated the 3R event due to biased sampling. To test this possibility, we analyzed the Ks distribution using ESTs. The age distribution of Br based on approximately 120,000 ESTs showed a pattern essentially identical to that obtained using the genome sequence data, illustrating loss of the 3R peak (Figure 5a). The additional peak for Ks = 0.10 to 0.15 may represent a very recent segmental duplication event. Loss of the 3R event appears to be specific to Br amongst Brassica genomes (Figure 5b-f); a Bo-Bo comparison yielded a Ks distribution different to that of Br-Br, with a clear peak corresponding to 3R (mode Ks = 0.85 to 0.90). A similar pattern was observed in the Bna-Bna comparison with underestimation of the peaks for 3R. However, note that the Ks modes for ortholog comparison between Br and Bo, Bo and Bna, and Br and Bna showed very similar Ks distribution with the two peaks for 4R and 2R at similar Ks modes as those in Br-Br paralog analyses, but loss of a peak for 3R. In particular, when the interval of Ks for the Br-Bo comparison was magnified, one additional peak, lying slightly below that for 4R at Ks = 0.34 to 0.36, was identified at Ks = 0.22 to 0.24; this indicates the genome split at around 8 MYA (Figure 5g).

Detection of a peak reflecting 3R in the Bo and Bna genomes but absence of this peak in the Br genome and between the other Brassica genomes strongly supports the hypothesis that duplicated genes from the 3R event were lost in the Br genome due to gradual deletion or suppression, presumably due to functional redundancy in the polyploid genome. To further explore this hypothesis, we compared the degree of conservation of duplicated genes in the sister blocks resulting from 3R and 4R. We found that 33 and 18 sister block pairs were selected for in the 3R and 4R events in the Br genome, respectively (Table S4 in Additional data file 1). The degree of conservation of duplicated genes for 4R was 44%, almost the same as that of the triplicated FLC region 20, but only 20% for 3R, a value approximately twofold lower than that of Bo based on calculations from published data 19. This suggests greater deletion of duplicated genes in Br than Bo (Table 4; Tables S4 and S5 in Additional data file 1).

Investigation of crop genomes not only offers information that can be used for agricultural improvement, but also provides opportunities to understand angiosperm biology and evolution. As of 2009, the genome sequences of only five economically important crop plants (rice, poplar, grape, papaya, and sorghum) have been published 89101112, and whole genome sequencing projects are currently underway for only a few selected crop species. One hurdle faced when sequencing a crop genome is genome obesity due to polyploidy and repetitive DNA 41. Therefore, a stepwise approach is required to obtain genome-wide information from crop genomes, and strategies for targeting gene-rich fractions are required. In combination with EST sequencing, two approaches - methylation filtration 42 and Cot-based cloning and sequencing 43 - were developed to capture euchromatic regions. Although both methods enrich for gene-rich fractions, they can exclude transcriptionally suppressed regions or euchromatic regions with abundant interspersed repetitive sequences (tandem repeats). We applied a novel gene space targeting method by allocating BAC clones to a closely related model genome based on BAC end sequence (BES) matches; this approach has not previously been reported in a genome sequencing project. This method has several advantages. First, gene-rich fractions of the crop genome can be obtained successfully in silico without additional experiments. We collected approximately 30% of the euchromatic region of B. rapa in this study. If a greater overlap between the clones and target region is allowed, and additional information in the form of genetic maps and physical contigs is used, the gene-rich fraction recovered is likely to increase significantly. Second, clone-by-clone strategies used in genome sequencing can benefit directly from this method because of selection of gene-rich seed BACs as well as the alignment of sequence scaffolds. Quick selection of a sufficient number of gene-rich seed BACs and directed ordering of the sequence scaffold will likely accelerate clone-based whole genome sequencing at reduced cost. The BAC clones selected in this study can be used as seed BACs for the ongoing clone-by-clone genome sequencing of Br 2728. Third, this analysis allows investigation of syntenic relationships between wild and crop genomes, thereby informing our understanding of crop evolution. Integration of genomes based on sequence level comparisons can offer a platform for the correlation between specific genes and phenotypes, which is important for further improvement of crops. We anticipate that application of our method will accelerate knowledge spreading from nodal model species to closely related taxa. For example, genome sequencing of other Brassica crops, particularly the construction of sequence assemblies and scaffolds of Bna, can benefit from the information obtained from the Br genome; this holds true even for next-generation sequencing. Thus, we anticipate that this study will make a significant contribution to structural and comparative genomic studies of crop species.

A large-scale comparison of Br genomic sequences and the whole euchromatic region of At demonstrated extensive synteny between the genomes, and provided clear evidence of a recent WGT event in the Brassica lineage. Our results significantly expand on previous observations of synteny between At and Br based on comparative genetic mapping 23 and small-scale comparisons of homologous regions 20 by deciphering the start-end points of macrosynteny blocks and elucidating the fine-scale details of microsynteny within the syntenic regions more accurately. Even though the Br sequencing project is still underway and the sequences used in this study are incomplete, the scale of synteny between the two genomes at both the macro- and micro-levels is significant. As the Br sequencing project moves forward, the availability of nearly complete coverage of the euchromatin will enable more precise definition of syntenic blocks between At and Br, which can be used to reconstruct ancestral chromosome sequences of Brassica.

Despite the WGT event, the total number of genes in the Br genome was estimated to be approximately 53,000, which is only a twofold increase compared with that of At. The usual fate of a duplicate-gene pair in a polyploid genome is nonfunctionalization or the deletion of one copy 444546. The reduction in the overall number of genes in the triplicated Br genome can be regarded as a result of a process that restores the diploid state, thereby counterbalancing genome obesity. This process seemed to be driven by the deletion of redundant genome components at the level of both the chromosome and the gene. A genome-wide synteny comparison between Br and At revealed that some of the triplicated copies of Br segments were lost or reconstructed. In addition, microsynteny analysis also indicated a relatively shrunken genome throughout the entire euchromatic region of the Br genome, with the Br gene space occupying a fraction 30% smaller than that of At due to a higher frequency of deletion events in the Br genome. A previous study reported that in the At genome, genes with regulatory functions, such as those encoding transcription factors or genes involved in signal transduction, were retained significantly more often than genes with other molecular functions 5. However, we did not find differential retention of genes according to molecular function, which suggests random deletion of redundant genes in triplicated regions of the Br genome before functional diversification.

Several mechanisms responsible for post-polyploid changes have been proposed. These include chromosome rearrangements caused by unequal crossing-over, homologous recombination, translocation, or other cytogenetic events 47484950. A tandem array with high sequence similarity would be a good candidate for deletion, because it is more likely to recombine and less likely to have a severe phenotype when one redundant gene is deleted. Fewer tandem duplicate genes in the Br genome may, therefore, be attributable to an increase in the rate of deletion. Incidentally, because polyploidy itself is a form of genomic 'disturbance,' it might induce a cellular response such as epigenetic silencing by hypermethylation, which may be especially relevant to genome evolution 48. As a result, the epigenetic response itself may accelerate the rate of mutation, thereby causing rapid genomic change as seen in Br. In addition, polyploidy could increase transposable element activity, causing the deletion of genes or even chromosome segments. Illegitimate recombination of TEs has been demonstrated to have the ability to remove large blocks of DNA in Arabidopsis, rice, 1549 and wheat 51. We speculate that the twofold increase in transposon accumulation in the triplicated euchromatic regions of Br compared to the euchromatic counterpart regions of At might be correlated with the deletion of duplicated genes.

Multiple rounds of polyploidy are thought to have occurred during angiosperm evolution, although the number and timing of polyploidy events vary between plant groups 552. Thus, most modern plant genomes harbor evidence of multiple rounds of past polyploidization. The genome evolution of Brassicaceae has been inferred mainly from studying Arabidopsis. There is evidence from several studies for one round of genome duplication after the eudicot divergence and additional rounds of polyploidization following the divergence of Arabidopsis from its common ancestor with cotton 5. In this study, we refined inferences of the number and timing of polyploidy events, and we now discuss the impact of these events on the structure and evolution of the Brassica 'A' genome (Figure 6). Ks estimates suggest that the Brassica genome shared two genome duplication events (2R and 3R) with Arabidopsis postdating the eurosid I (Pt and Mt) and eurosid II (At and Br) divergence. The third polyploidy event (4R) was a Brassica lineage-specific whole genome triplication after the split of Brassica from the common ancestor of Brassica and Arabidopsis. The 227 synteny blocks identified between Br and At can serve as a basis for reconstruction of the ancestral genome and chromosomes of the Br-At ancestor, although a more complete genome sequence and additional evidence are still required. The mapping of ancestral chromosome building blocks to the Br genome strongly suggests that the Br genome evolved from a pre-triplicated ancestor with a unique organization of the retracted AK, which was different from that of At, by chromosomal rearrangement shortly after 3R but prior to 4R. This event might have resulted in the divergence of the Arabidopsis and Brassica lineages.

More importantly, differential gene loss following 4R in the Brassica genome might be responsible for the diversification of the genome, based on the finding that significantly more genes duplicated as a result of 3R have been lost in Br than in Bo. However, it is not clear if duplicated genes from the 3R event that were retained in Bo have diverged functionally. It appears that the split between Br and Bo happened rapidly (0.1 Ks interval) compared to the At-Brassica split (0.3 Ks interval), perhaps due to differential retention of duplicated genes and genome recombination in the ancestral Brassica genome. These observations, along with the independent accumulation of repetitive sequences, may have facilitated speciation within the tribe Brassiceae, which contains approximately 240 highly diverse species. Further analysis and cross-comparisons of diploid and allopolyploid genomes of Brassica will enhance our understanding of the fate of duplicated genes in the Brassica genome. It appears that, as a counterbalance to genome obesity, there was higher selection pressure on redundant genes in the triplicated Brassica ancestor, accelerating gene loss in this triplicated ancestor compared to the Arabidopsis-Brassica common ancestor. Alternatively, differences in the life cycles of Brassica progenitors might have resulted in the differential deletion of duplicated genes in Brassica genomes. Moreover, artificial selection after domestication could also have had an impact on differentiation of diploid Brassica genomes. Taken together, the available evidence suggests that genome duplication and chromosomal diploidization are ongoing processes collectively driving the evolution of Brassica genomes.

We previously published an efficient and novel clone selection method based on in silico BES matches to a model genome, which we named the comparative tiling method 29. To select gene-rich Br BAC clones covering the entire At euchromatic regions, a total of 92,000 BESs were allocated to At chromosomes by using BLASTZ at a cutoff of <E^-6 with both end matches at 30 to 500 kbp intervals. A total of 4,647 BAC clones were allocated to 92 Mbp of At euchromatic regions and 589 minimally overlapping BAC clones (292 overlapping clones with an average of 41 kbp overlaps and 297 singleton clones) were finally selected and sequenced using an ABI 3730xl sequencer. The minimal sequence goal was five phase 2 (fully oriented and ordered sequence with some small gaps and low quality sequences) contigs, but 18 clones (3%) were sequenced as phase 1 due to large repetitive sequences (Table S1 in Additional data file 1). To anchor clones, a combination of sequence-based genetic mapping 53, fingerprint contig data 54, and fluorescent in situ hybridization (FISH) was used (Table S2 in Additional data file 1). The sequence contig assembly was created based on overlapping sequences. BAC sequences were assembled into big sequence contigs by first comparing paired BES matches and BAC sequences sharing overlapping positions on the target At chromosomes using Pipmaker 55. Then, sequence contigs were assembled based on overlapping sequences using Phred/Phrap/Consed programs 565758. The location of sequence contigs or BAC singletons was determined primarily by genetic marker anchors with fingerprint contig information, paired BES, and FISH results providing additional information about local contig and BAC ordering. Pseudochromosome sequences were created by connecting sequence assemblies with 10-kbp additions of anonymous sequences. All the Br sequences used in this study are available at NCBI and the URL cited below in the 'Data used in this study' section and relevant reference sequence sources are listed in Table S6 in Additional data file 1.

The sequence coverage of the Br genome by BACs was estimated by calculating the proportions of Br EST unigenes and conserved single-copy rosid genes with strong matches. For EST comparisons, we considered unigenes to have a genome match if more than 90% of unigenes matched with at least 95% identity in a BLAT 59 analysis. For the single-copy rosid gene comparison, we created a list of 1,070 single-copy At and Mt genes not included in the Br EST collections. They were considered to have a genome match in Br if at least 50% of the gene matched in a TBLASTN 60 search at a cutoff of <E^-100. The assembled sequences were masked using RepeatMasker 61 using a dataset combining the plant repeat element database of the Munich Information Center for Protein Sequence (MIPS) 62 and our specialized database of Br repetitive sequences. Gene model prediction was performed using EVidenceModeler 63. Putative exons and open reading frames were predicted ab initio using FGENESH 64 and AUGUSTUS 65 programs with the parameters trained using the Br matrix. To predict consensus gene structures, Br ESTs plus full-length cDNAs, plant transcripts, and plant protein sequences were aligned to the predicted genes using PASA 66 and AAT 67 packages. The predicted genes and evidence sequences were then assembled according to the weight of each evidence type using EVidenceModeler. The highest scoring set of connected exons, introns, and noncoding regions was selected as a consensus gene model. Proteins encoded by gene models were searched against the Pfam database 68 and automatically assigned a putative name based on conserved domain hits or similarity with previously identified proteins. Annotated gene models were also searched against a database of plant transposon-encoded proteins 69. Predicted proteins with a top match to transposon-encoded proteins were excluded from the annotation and gene counts.

Syntenic regions of the genomes of Br and At were identified by a proteome comparison based on BLASTP 60 analysis. The entire proteomes of the two genomes were compared, and only the top reciprocal BLASTP matches per chromosome pair were selected (minimum of 50% alignment coverage at a cutoff of <E^-20). We chose to perform a BLASTP similarity search because it is inherently more sensitive than BLASTN 60. Moreover, the BLASTP hit matrix contains fewer BLAST hits that are due to repetitive nucleotide sequences. Chromosome scale synteny blocks were inferred by visual inspection of dot-plots using DiagHunter with parameters as described in Cannon et al. 36. Gene orientation, insertions/deletions, and inversions were considered, and at least four genes with the same respective orientations in both genomes were required to establish a primary candidate synteny block. To distinguish highly homologous real synteny blocks from false positives due to multiple rounds of polyploidy followed by genome rearrangement, we manually checked all the primary candidate blocks. Previous studies reported that the degree of gene conservation between At and the Brassica genome in several selected syntenic regions was >50%. Based on this result, 227 blocks showing a gene conservation index of >50% (twice the number of conserved matches divided by the total number of non-redundant genes in the blocks; tandem duplicated genes were collapsed to a single homolog) were selected as real syntenic regions. For microsynteny analysis, we manually broke the blocks if At homologs of independent Br sequences in the syntenic blocks were separated by more than 10 kbp. The synteny display is available online at the URL cited in the 'Data used in this study' section.

The timing of duplication events and the divergence of homologous segments was estimated by calculating the number of synonymous substitutions per synonymous site (Ks) between homologous genes. For the model genome comparisons, annotated gene models were used, whereas for the comparison between the Brassica genomes, ESTs were analyzed, even though they are error-prone. One drawback associated with the analysis of paralogs derived from ESTs is that multiple entries for the same gene can be included in the dataset, leading to overestimation of redundant Ks measures 5. However, it is reasonable to assume that redundant Ks measures are randomly distributed among all the Ks values; thus. the effect of redundancy is likely to have been neutral. Before comparing the Ks distribution for EST paralogs and genome sequences of Br, we carefully checked the patterns of Ks in the EST data; we did not find any significantly overestimated bulges or peaks. To identify orthologs and paralogs, the protein sequences of the gene models or ESTs were aligned using the all-against-all alignment and the resulting alignment was used as a reference to align the nucleotide sequences. After removing gaps, the Ks values from pairwise alignments of homologous sequences were determined using the maximum likelihood method implemented in the CODEML 70 program of the PAML 71 package under the F3×4 model, similar to the analysis described by Blanc et al. 25. We compared the mode rather than the mean of Ks distributions, because the mode is not affected by bias due to incorrectly defined homolog pairs, which is partly responsible for unexpected overestimation of Ks. Only gene pairs with a Ks estimate of <5 were considered for further evaluation and their Ks age distribution was calculated using the interval 0.02 to 0.1. Divergence time calculations were based on the neutral substitution rate of 1.5 × 10^-8 substitutions per site per year for chalcone synthase (Chs) and alcohol dehydrogenase (Adh) 40.

Because Br BAC clones were selected to minimally overlap the target At region, self comparison of Br sequences using the DiagHunter program found few duplicated regions (Figure S4 in Additional data file 2). Instead, we manually identified sister blocks of duplication events by using synteny group information between Br and At. Br sequence blocks were defined as putative sister blocks of 3R if two different sequence blocks showed high synteny with respect to At regions known to be duplicated remnants of 3R 72, whereas independent Br sequence blocks sharing the same syntenic relationship with a single At region were selected as sister blocks of 4R. For additional validation, we compared the Ks distribution modes between the paralog gene pairs in the sister blocks.

All the data used in this study can be accessed online at 73.