Supplemental Data

Files in this Data Supplement:

• Supplemental Figure 1 - Schematic representation of the divergence time of shared genes between the B73, Mo17 and McC haplotypes at the bz1 locus. The divergence time in Myr (Millions of years) was determined for exons based on synonymous substitutions and for introns based on all substitutions but no Indels. The closest related haplotypes per gene are indicated and the divergence time or the average value, when the relationship extends over neighboring genes, is noted. For more details see Supplemental Table 7.
• Supplemental Figure 2 - Histogram of intergenic distances (bp) between shared and non-shared genes in loci 9002, 9008, 9009 bz1 and adh1.
• Supplemental Table 1 - Position of allelic and non-shared LTR-retrotransposons in loci 9002, 9008,9009, adh1 and bz1.
• Supplemental Table 2 - Characterization of the predicted genes at each analyzed locus. The highest Blast hit, its E-value and the corresponding accession number is listed for each FGENESH prediction. A Blast hit is considered as full length if all predicted exons are homologous to a known gene or protein from the database or as incomplete in all other cases. The gene position of each predicted maize gene is listed for each inbred sequence as well as the chromosomal location of its rice ortholog (rice chromosome, PAC clone accession number and location on PAC clone). The number of corn ESTs (blast score >120) and MPSS tags (>2 ppm) identified per gene are listed in the last two columns.
• Supplemental Table 3 - Estimated insertion timepoints of retrotransposons shared between B73 and Mo17. K: nucleotide differences between the LTRs, SE(K): standard error of K; TD: estimated insertion timepoint in Myr (Millions of years); SE(TD): standard error of TD in Myr (Millions of years). The average between B73 and Mo17 was assigned to each shared element. (* highly mutated parts at the 5' ends of the B73 LTRs were excluded from the estimation)
• Supplemental Table 4 - Estimated insertion timepoints of LTR-retrotransposons unique to either B73 or Mo17. K: nucleotide differences between the LTRs, SE(K): standard error of K; TD: estimated insertion timepoint in Myr (Millions of years); SE(TD): standard error of TD in Myr (Millions of years).
• Supplemental Table 5 - Fraction of genic and non-genic sequences in shared and non-shared sequences per locus. Grey boxes represent the percentage of the genic or non-genic portion in the allelic and non-shared fraction at each locus, respectively. The sequences from the three inbreds at the bz1 locus are only divided into genic and non-genic sequences.
• Supplemental Table 6 - Summary of the number of MITEs identified at loci 9002, 9008 and 9009 in B73 and Mo17. Elements are classified based on the target site duplication (Stowaway family: TA; Tourist family: TAA, TAC, TGA, TTA, TCA).
• Supplemental Table 7 - Genetic distances of the 9 shared genes between the B73, Mo17 and McC haplotypes at the bz1 locus, calculated separately for exons (synonymous substitutions) and introns (all substitutions but no Indel). Time of divergence TD (Millions of years, Myr) is estimated by a molecular clock for genes based on synonymous base substitutions per site per year for the adh1 and adh2 genes in grasses (Gaut et al., 1996). K: nucleotide divergence, SE(K) standard error of K, TD: estimated time of divergence, SE(TD) standard error of the estimated divergence time.
• Supplemental Table 8 - Rice homologs of the genes at the bz locus on maize chromosome 9S. The closest rice homolog was identified by tblastn against the rice sequence (http://www.ncbi.nlm.nih.gov/BLAST/Genome/PlantBlast.shtml?4). The corresponding rice PAC clone and its chromosomal location are listed in columns 2 to 4.
• Supplemental Table 9 - Shared and non-shared genes at loci 9002, 9008, 9009 bz1 and adh1 with identified corn ESTs and/or corn Lynx MPSS tags. Only ESTs with a blastn score of 120 or higher and MPSS tags of at least 2 ppm are considered.