Fig. 4: Genomic structure of M^III, M^Y and in comparison to M^II, M^V loci.

a Visualization of Mdmd sequences distribution in M^III-contigs. Only one complete Mdmd copy is found (blue line indicated by the red arrow). b Self-alignments of M^III-contigs show many tandem duplications clustering together (short blue lines, indicated by solid-lined boxes). Most of the duplications are Mdmd copies and their flanking sequences (red solid-lined boxes). Duplications of non-Mdmd sequences also exist (indicated by gray solid-lined boxes). c The end part of M^III-contig-1 shares homology to the beginning part of M^III-contig-2 (indicated by the red dashed-lined box). d Visualization of Mdmd sequences distribution in M^Y-contigs. Only one complete Mdmd copy is found in M^Y-contig-4 (blue line indicated by the red arrow). e M^Y-contig-4 show homology to regions of M^III- and M^V-contigs that contain intact Mdmd gene which is indicated by red shading. f Schematic drawing of homologous regions that contain intact Mdmd in M^III, M^V and M^Y. M^V and M^Y both have a block of tandem repeats is located downstream (~4 kb apart) of the intact Mdmd. g M^Y-contigs show homology to various parts of M^III-contigs. h Tandem repeats that are adjacent to intact Mdmd in M^V and M^Y are also found in M^III, but exist near one end of M^III-contig-2. i The coverage for M^III-specific regions in various male genomic datasets that contain sequences of M^II, M^III, M^V, and M^Y loci respectively. Schematic drawing shows Mdmd distribution (complete copy blue, truncated copies orange) in M^III-contigs. Other M-loci show various similarities to the M^III. I: Specific to M^III; II: Shared between M^III and LPR M^Y; III: Shared among M^III and all three M^Y; IV: Shared among M^II, M^III and all M^Y; V: Shared among all tested M-loci.