As illustrated in Figure 5, reads generated from a duplicated region containing a single base change align to both regions.
Genes that had the majority of their sequence in a duplicated region were considered duplicated genes.
Within the SlbZIP family, a total of 40 SlbZIP genes are located in the segmental duplicate regions in the tomato genome, suggesting that the segment chromosomal duplications contribute greatly to the expansion of the tomato SlbZIP family.
The duplicate region experienced fractionation during evolution leading to Brassicaceae and Solanaceae lineages, resulting in scattered bCRK-I orthologs with little conserved synteny, whereas in grasses the tandem duplicate region was lost.
The chromosome distribution and the genetic analysis reveal that 58 ZmbZIP genes are located in the segmental duplicate regions in the maize genome, suggesting that the segment chromosomal duplications contribute greatly to the expansion of the maize bZIP family.
The portion of the genome that exists in duplicate regions serves as a baseline for evaluating whether genes in a given gene family have been lost or retained at a rate higher than expected for the genome as a whole.
For example, Gm04.2, Gm04.1, and Gm04.3 located in different duplicate regions of the same chromosome, all have two introns flanked by three exons.
Sites called as heterozygotes within a single strain could be due to infection by multiple wAna genomes, a duplicated region differing in one duplicate by a mutation, or a false variant call from sequencing error.
2, were located in duplicate regions (Table 1).
Additionally, the chimpanzee BRCA1 locus contains an 8 Kb deletion in the partially duplicated 5' region.
This added to the credibility of the analysis by showing that the approach finds actual associations in that the duplicated regions possibly share appreciable sequence similarity.
