Figure 1.
Physical map and ideogram of the devil genome.
The DAPI banding pattern for each chromosome is shown in grey. Genes contained within the same BAC clone are indicated in brackets. Chromosomes have been arranged in order according to two previously published karyotypes [19], [20], which differs from the karyotype presented by Pearse and Swift [8] in the order of chromosomes 1 and 2.
Table 1.
Number of genes mapped to each normal devil chromosome.
Figure 2.
Comparison of gene arrangement among devil, wallaby, and opossum chromosomes.
(A) Gene order for the region shaded in grey on devil chromosome 3 is well conserved between wallaby chromosome 5 and opossum chromosome 4. The white regions on devil chromosome 3 are homologous to wallaby chromosome 6 and opossum chromosome 7 (Figure S2). (B) A comparison of gene order on the devil X chromosome with wallaby and opossum X chromosomes, where extensive reshuffling of gene order is evident.
Figure 3.
Summary of chromosome painting results for DFTD Strain 1.
DFTD chromosomes have been colour-coded to reflect their homology to normal devil chromosomes. Two-colour FISH painting results are shown for the X chromosome (red) and autosomes 1, 2, 5 and 6 (green).
Figure 4.
Chromosome painting results unique to DFTD strain 2.
Differences detected between Strains 1 and 2 are limited to the detection of chromosome 4 on M4 and X chromosome on an additional marker chromosome, M5.
Figure 5.
Physical map of DFTD Strain 1.
Chromosomes have been coloured coded to reflect their homology to normal devil chromosomes. For chromosomes 2, 3, 4, and 6, gene names are indicated for each homologue to highlight differences in gene order or position between homologues. Despite a size difference between the two homologues of chromosome 3, gene order is the identical.
Figure 6.
Representative FISH results on DFTD chromosomes.
In each case an ideogram of the location of genes on the normal devil chromosome are indicated, with the colour of the line on the normal chromosome corresponding to the colour of the FISH signals on DFTD chromosomes (A) SOST and PGBD2 located on normal devil chromosome 4 localise to M2 and M4 in DFTD. (B) GNL1 and RUNX2 located on the short arm of normal devil chromosome 4, map to the long arm of DFTD chromosome 4, with GNL1 proximal and RUNX2 mapping to different locations on each homologue. (C) Chromosome 6 genes BET1L and RAPGEF2. BET1L has an additional copy in DFTD, mapping to different locations on the two copies of chromosome 6 as well as distal M3. (D) The X-borne gene MECP2 is detected in DFTD, mapping to the short arm of M4.
Figure 7.
Differences detected by gene mapping among Strains 1, 2, and the three different Strain 3s.
Genes SPERT, PCDH8 and SLAIN1 are found on both homologues of chromosome 3 in Strains 1 and 2 (gene names are only indicated next to one homologue) but a deletion of these genes has occurred on both homologues of Strain 3A, and one homologue of Strain 3B and 3C. Chromosome 4, which appears identical between Strains 1 and 2, is different among the Strain 3s. In Strain 3A, genes mapped only to the short arm of one copy of chromosome 4. Strain 3B has retained TPST1 on 4p, a gene mapping to M2 and M4 in all other strains, and the 4p SENP2 gene, has translocated to 4q. X chromosome genes THOC2 and HEPH map to different location on M2 in Strain 1 but colocalise in other strains. Strains 2 and 3 have an additional marker chromosome (M5), which contains SHARPIN and MECP2 in Strain 2 and 3, as well as CERK in Strain 3. Colour coding of chromosomes is the same as that used in Figure 3.
Table 2.
Genes deleted or increased in copy number in DFTD.
Figure 8.
Chromosome 1 rearrangements in DFTD and during marsupial evolution.
(A) A comparison of gene arrangement on the normal devil chromosome 1 to arrangement observed on DFTD chromosomes shows extensive rearrangement, with only one block of genes (KDSR to KCTD1) conserved in gene order between normal chromosome 1 and DFTD. Yellow regions on DFTD chromosomes indicate homology to normal devil chromosome 1. Genes shown in red mapped to only one location in DFTD, whereas the gene in blue mapped to three different locations. (B) Comparison of gene order of devil chromosome 1 with arrangement in wallaby (left) and opossum (right).
Table 3.
Predicted location of common tumour suppressor genes and oncogenes in the devil genome.