Advertisement

< Back to Article

Following Tetraploidy in Maize, a Short Deletion Mechanism Removed Genes Preferentially from One of the Two Homeologs

Figure 4

Distribution of runs: Runs of lost genes, or runs of genes retained.

x-axis: length of the run, in genes. y-axis: number of runs. Black bars represent observed data. The white circles within the gray bars represent the median number of runs of that length observed from 1,000 simulations. The gray bars mark the limits within which the values of 95% from the simulations fell. Panels A–D refer to runs of deletions. Panels E and F refer to runs of genes retained from the maize lineage tetraploidy. (A) Observed and distributions of deletion runs in the over-fractionated homeologous regions including all deletion data, and simulated distributions assuming genes are lost solely through a 1 gene deletion mechanism. (B) Observed distributions of deletion runs in the over-fractionated homeologous regions with deletions longer than nine genes removed as likely segmental transpositions, and simulated distributions assuming genes are lost solely through a 1 gene deletion mechanism. (C) Observed and simulated distributions of deletions in the under-fractionated homeologous regions, assuming genes are lost solely through a 1 gene deletion mechanism. (D) Observed and simulated distributions of deletion runs in the over-fractionated homeologous regions, using a model where 80% of deletions are single gene, 15% remove two adjacent genes, and 5% of deletions remove three genes in a row, best fit ratio determined by a genetic algorithm. (E) Observed runs of genes retained in both homeologs and simulated distributions assuming genes are lost solely through a 1 gene deletion mechanism. (F) Observed runs of genes retained in both homeologs compared to the simulated expectation assuming 80% single-gene deletions, 15% two-gene, and 5% three-gene.

Figure 4

doi: https://doi.org/10.1371/journal.pbio.1000409.g004