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The salmonid genome contains an ancient whole genome duplication and consequently contains many duplicate regions [ 41].
During the analysis of LD patterns, we will differentiate between LD within the duplicate regions and LD between paralogous windows of the original and duplicated blocks (from here on, we refer to the latter as LD between duplicates).
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.
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.
In the DeFFS, index entries of inodes support variable-sized blocks in order to increase the manageability and flexibility of duplicate regions.
The age estimates varied from 866 to 2,131 ybp, with the duplicate regions intermediate at 1,506 ybp.
Similar(27)
The issue is how to identify and eliminate the duplicate region efficiently.
The important design issues supporting duplicate elimination are how to manage data blocks and how to detect duplicate region.
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.
We further explored this duplicate region by comparing the sequences in the three genomic assemblies.
Examination of the distributions of retrotransposed and duplicated pseudogenes, segmentally duplicated regions and tandemly duplicated genes suggest that pseudogenes are not disproportionately associated with segmentally duplicated regions or clusters of tandemly replicated genes (Additional file 4).
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