Figure 1

The pipeline of the marker candidate algorithm. In the first step, EST collections of selected species are compared with the proteome of the reference species in order to estimate the copy number. Sequences with one or two homologs in the Arabidopsis proteome are considered because Arabidopsis has undergone a recent whole genome duplication whereas legumes have not. EST sequences passing this criterion are compared to L. japonicus and M. truncatula genomic sequences in order to score the presence and length of introns. Sequences with the same Arabidopsis reference are then aligned and primers are designed using this alignment as input. For this purpose, the PriFi software [13] is used.