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Gm12S *Gm15S Gm20N Gm05N Gm12N Gm06S Gm07S Gm17N *Gm08N *Gm16S Annu. Rev. Plant Biol. 2012.63:283-305. Downloaded from www.annualreviews.org by University of Minnesota - Twin Cities - Wilson Library on 05/07/12. For personal use only. Glycine max genome *Gm05S *Gm13N *Gm07N *Gm19N Gm09N *Gm13S Gm15N *Gm20S Gm10S *Gm10N *Gm14N Gm14S *Gm17S Gm02S *Gm11N *Gm02N Gm01S *Gm01N Gm03S *Gm09S *Gm03N Gm16N Gm19S Gm18S Gm06N Gm11S Gm08S Gm04N *Gm04S *Gm18N 3S 7N 7S *5N 5S *1N 1S 2N *6N *6S *8S *4S 8N *2S 3N 4N Medicago truncatula genome 292 Young·Bharti
Annu. Rev. Plant Biol. 2012.63:283-305. Downloaded from www.annualreviews.org by University of Minnesota - Twin Cities - Wilson Library on 05/07/12. For personal use only. the earlier work of Hougaard et al. (35) by focusing on ∼126 cross-species ESTs mapped in Arachis and compared with available Mt and Lj sequences. They found that most synteny blocks align to a single region in either genome, an important observation because it implies that a previously predicted papilionoid WGD event (see below) predated the divergence of Arachis from galegoids and phaseoloids, and so occurred very early in the evolution of the subfamily. In Muchero et al. (61), more than 10,000 SNPs were discovered within available EST databases of cowpea (V. unguiculata) and then used in map construction leading to 928 positioned cowpea loci through the use of a medium-throughput Illumina GoldenGate assay system. Comparison with Gm revealed 85% macrosynteny, while macrosynteny with the more distantly related Mt was still high at 82%. In a similar study, McClean et al. (56) examined >300 gene-based Phaseolus loci coming from EST and BAC-end sequence data and compared them with the Gm reference genome sequence, discovering 55 synteny blocks on 35 of Gm’s 40 chromosome arms. Syntenic blocks averaged 32 centimorgans in length in Phaseolus, a genetic distance that corresponded to an average physical distance of 4.9 Mb in Gm. Using this set of synteny blocks as reference points, they could tentatively position another 15,000 Phaseolus gene sequences solely based on the Gm genome sequence. Side-by-side comparison of sequenced genomes is the most powerful way to learn about genome histories. In such comparisons it becomes possible to estimate the fraction of shared genes, the size distribution of synteny blocks, or differences between genomes in gene density or organization. Going a step further, one can examine genome rearrangements at the macroscale, whether they are shared or lineage specific, or drill down to the base-pair level to dissect the fine structure of conserved colinear genes. Ultimately, as more sequenced species are added to the analysis, we begin to see the actual step-by-step changes that distinguish one genome from another. One of the first sequence-based comparisons in legumes was between Mt and Gm. Focusing on a genome region surrounding a nematoderesistance gene in Gm (rhg1) on chromosome Gm18, Mudge et al. (62) found that 75% of genes were colinear between Mt and Gm in a region spanning ∼150 genes, including a remarkable stretch where 33 of 35 genes (94%) were conserved and colinear, a phenomenon they termed hypersynteny. Cannon et al. (15) later carried out a genome-scale sequence comparison based on the partially completed Mt and Lj genomes available at the time. In the case of one large synteny block between Mt05N and Lj02S, they found that 58 of 94 genes (62%) existed as colinear orthologous pairs between the syntenic segments. Indeed, synteny between Mt and Lj was found to extend nearly genomewide, despite a time span of 40–50 Mya since speciation. Figure 1 shows an updated dot-plot comparison of Mt and Lj based on versions of the genomes available in mid-2011 (Reference 100 and ftp://ftp.kazusa.or. jp/pub/lotus/lotus_r2.5/pseudomolecule). ←−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−− Figure 2 Whole-genome dot-plot of the cool-season legume Medicago truncatula (Mt) ssp. truncatula Jemalong-A17 (horizontal axis) and the warm-season legume Glycine max (Gm) var. Williams 82 (vertical axis). The pericentromeric regions of Gm chromosomes have been removed for this analysis. An asterisk next to a chromosome number indicates reverse complement. Chromosome arms have been rearranged so that the synteny blocks line up along the center diagonal, which makes the comparison easier to visualize. The presence of two synteny diagonals for almost every Mt region indicates an additional recent whole-genome duplication (
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