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

Figure 3

Determining which maize homeologous genes were deleted following tetraploidy.

(A) Cartoon of a GEvo blastn comparison graphic depicting a 13-gene stretch of sorghum with the two orthologous regions of maize. Sorghum nucleotides were masked except those in official gene models or genes shared between sorghum and maize (SI1); maize DNA was masked for repeat sequences. Blastn high scoring pairs (hits) are colored orange if they are Sb-Zm1 and purple if they are Sb-Zm2. Colored lines indicate orthology. The code B021BB2DDDB10B abbreviates these data, where B = both genes remain, 0 = gene missing in syntenous Zm positions (these are discarded), 1 = the gene on Zm1 remains alone because its homeolog was deleted, 2 = the gene on Zm2 remains alone because its homeolog was deleted, and D = local duplicates of an arbitrary mother gene leftmost in the cluster (D's are discarded). Therefore, the essential code for this 13-gene Sb stretch reduces to B21BB2B1B. The circle indicates a Zm1 gene that has some completely and some partially deleted exons; we noted these partially fractionated genes for further research, but we counted them as present (B). The brackets enclose clusters of tandemly duplicated genes in both Sb and Zm2. The arrow indicates a single gene in Sb hitting a reverse tandem duplication in maize; maize genes like this one were counted as present. Please use http://genomevolution.org/r/37e to reproduce on-the-fly the Sb2 region blast experiment, the region containing Sb02g030760-Sb02g030950 drawn above. (B) Using the same color code of the panel above, these are two exemplary small regions from the total of 37 regions comprising our syntenic dataset. The regions exemplifying fractionation bias (AL3–7) and no bias (AL3–8) are color-coded in such a way that the number of gene deletions suffered by Zm homeolog 1 versus Zm homeolog 2 is easy to count. A 1∶1 (p = 0.5) ratio of these deletions computes to not biased. p≤0.1 is weak support and ≤0.05 is strong support that these deletions significantly deviate from this 1∶1 null hypothesis.

Figure 3

doi: https://doi.org/10.1371/journal.pbio.1000409.g003