Legend for Supplemental Figure 1
Pairwise sequence matches between duplication blocks reveal that the HBA-T3 genes of
Rattus and Peromyscus originated via independent, lineage-specific duplication events. In
Rattus, the T3 duplication block spans more than 15 kb and includes a linked HBA-HBQ
gene pair. In Peromyscus, by contrast, the T3 duplication block spans less than 5 kb and
includes a single HBA gene along with an HBA pseudogene fragment immediately
upstream. A: Dot plot of the Rattus α-globin gene cluster (50 kb) shows extensive
matches between the region spanning the T2 and T3 duplication blocks and the region
spanning the T1 and T2 duplication blocks (the circled off-diagonal element). This
pattern suggests the occurrence of an unequal crossing-over event that resulted in the
creation of a ‘new’ HBA-T2 - HBQ-T2 gene pair (derived from the original HBA-T1 HBQ-T1 gene pair), and the creation of a ‘new’ HBA-T3 - HBQ-T3 gene pair (derived
from the original HBA-T2 - HBQ-T2 gene pair). This scenario is diagrammed below the
dot-plot (HBZ is shown in grey, the HBA genes are shown in black, and the HBQ genes
are shown in cross-hatching). B: In comparison with the pattern observed in Rattus, the
dot plot of the Peromyscus α-globin gene cluster (40 kb) shows less extensive matches
between the HBA-T1 – HBA-T2 intergenic region and the HBQ-T2 – HBA-T3 intergenic
region (the circled off-diagonal element). The pattern of sequence matches suggests that
the HBA-T3 gene originated by an unequal crossing-over event upstream of the HBA-T2
coding sequence. A second unequal crossing-over event may explain the absence of a
HBQ-T3 gene immediately downstream of the newly created HBA-T3 gene. This
scenario is diagrammed below the dot-plot (HBZ is shown in grey, the HBA genes are
shown in black, the HBQ genes are shown in cross-hatching, and an exon 3 HBA
pseudogene fragment upstream of the original HBA-T2 gene is shown as a black
triangle).