However, when Jr6 was used as a query, other chromosomes contained greater numbers of collinear cdBES located in duplicated SBs other than Jr15.
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.
Finally, non-TE single-exon genes located in segmentally duplicated regions that lacked a duplicate gene were targeted for investigation.
This could be due to differential gene loss of lineage-specific genes (ALSGs, CBS Gs in segmentally duplicated versus non-segmentally duplicated regions or alternatively that the ALSGs and CBSGs are located in segmentally duplicated blocks which have rapidly evolved and thus are not detected using similarity based segmental duplication methods.
Primer pair 2* was completely located in the duplicated gene rrnS (rrnS 1 or rrnS 2 ); thus they may directly concatenate the sequence between the duplicated gene and artificially lose the gene block of K1-C-Q1-rrnL5'- N- rrnS 2. The block, 2,147 bp, may be too large to be amplified under competition with a smaller fragment.
Numbers and percentages of walnut cdBES collinear with genes in the grape and poplar pseudomolecules located in SBs duplicated in the walnut genome.
Of 3,742 collinear cdBES in the Jr-Vv comparison, 77.3 % were located in SBs duplicated on different Jr chromosomes.
In that analysis, 72.2 % of the 3,543 collinear cdBES were located in SBs duplicated on different Jr chromosomes.
In these regions, the associated markers were located in strictly duplicated intervals of six blocks which are syntenic with A. thaliana.
