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Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

Figure 1

Significant hybridization differences are due to structural variation.

(A) The B73 and Mo17 sequences for a portion of the 9,009 locus (sequenced by [28]) were aligned using Vista [71] which displays the percent identity as a sliding window of 100 bp (y-axis is 50% to 100% identity). The location of genes annotated by Brunner et al. [28] (indicated by light blue sequences in the alignment) and repeat elements (the color-coded track right above the alignments; pink indicates retrotransposons and orange indicates transposons) are shown above the VISTA alignment. The log2(Mo17 signal/B73 signal) is shown for each probe in this region. The red probes exhibit significantly different (q<0.0001) signal in B73 and Mo17. The blue line indicates a segment with altered hybridization that was identified using DNAcopy. There are also data tracks that display the repeat annotation and B73/Mo17 similarity for each probe. Note that these annotations are based on the genome-wide analysis, not detailed analyses of these regions. In (B) we present the annotation, alignment and CGH data for a portion of the 9008 loci (sequence and annotated by Brunner et al., [28]).

Figure 1

doi: https://doi.org/10.1371/journal.pgen.1000734.g001