Copy number variants, small regions of duplication or deletion within the genome, are more common in autism than control subjects (Marshall et al., 2008; Pinto et al., 2010).
The 1q21 region of chromosome 1 is a classic example, given its association with multiple clinical disorders and its complex architecture, with multiple regions of duplication that make complete assembly extremely difficult.
Recently, a study using a large number of MAP isolates provided an example of such a genomic polymorphism including 2 large regions of duplication, termed vGI-17 (containing 63 ORFs) and vGI-18 (containing 109 ORFs), observed in most MAP-C strains but not MAP-S isolates [ 21].
We thank Jean-Michel Ane and Muthusubramanian Venkatashwaran for the Arqua1 strain, helpful discussions and assistance with Medicago experiments, Michelle Graham for early help in identifying regions of duplication between the Gm18 Rhg1 locus and Gm11, and Melissa Mitchum for advice about SCN testing with A. rhizogenes-generated roots and for critical reading of the manuscript.
In regions of duplications, depth-of-coverage shows a statistically significant increase due to recruitment of paralogous reads.
The analysis of duplication-inferred mutations (DIMs) was restricted to intergenic regions of duplications, focusing on the mutational spectrum in regions that are believed to be more neutral with respect to selection forces.
Among 105 SNPs being targeted in their study, 64 SNPs mapped to the intergenic regions of duplications used in our analysis, of which they experimentally verified 11 as PSVs.
In the more proximal region of the duplication (genes F, H and I), gene pairs appear to be less influenced by concerted evolution as we observed "duplication before speciation" topologies and isolated single copies for ancient species.
In this respect, is striking that the chromosome 1 breakpoint in the t(1 17) translocation described here is also localized in a region of segmental duplication.
A region of gene duplication occurs immediately upstream of the Mthe_1511 ORF (locus tags Mthe_1512-1532).
