As much as 15 percent of human genes are duplicated with segmental duplications covering 5.2 percent of the genome [37].
Indeed, the Brachypodium genome shows six major chromosomal duplications covering 92.1% of the genome, which represent ancestral whole-genome duplications, and so detection of paralogs is likely to be a major factor in detecting more than one gene from blast searches [ 7].
This understanding had to be revised after a series of genome-wide analyses using SNP-microarrays and comparative genome hybridization analyses as well as in in silico comparisons of genomes from different individuals, which revealed more than 1400 deletions or duplications covering 12% of the "healthy" human genome sequence [ 92, 96– 101].
For mapping of the Marf group, male large duplications (∼1 2 Mb) covering the X chromosome (Haelterman et al., 2014) were crossed with female y,w mut*,P{neoFRT}19A isogenized flies that were balanced with FM7c,Kr-GAL4,UAS-GFP Kr > GFM7c,Kr-GAL4,UAS-GFP Kr
This duplicated rice segment was the largest of five segmental duplications between Os01 and Os05 covering 354 duplicated gene pairs indicated by grey connecting lines (os01_05_5, Figure 4a, Table S1 of Additional file 1).
Five major duplications were also identified, covering 28% of the genome and involving the following chromosome-to-chromosome relationships: o1-o2-o10 (yellow), o6-o11 (green), o3-o6 (purple), o7-o8 (brown), o5-o8 (red).
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(A ) For mapping of Marf, the lethality of all Marf alleles were rescued by large duplication Dp(1 Y dx5,y/C(1)M5 (4C11;6D8 + 1A1 1B4) covering the Marf locus.
Gene duplication was classified into two groups: low-stringency duplication (protein pairs with ≥ 30% identity and covering ≥ 70% protein length) and high-stringency duplication (protein pairs with ≥ 50% identity and covering ≥ 90% protein length) [ 34].
