The Tasmanian devil (Sarcophilus harrisii), the last remaining large marsupial carnivore, now faces extinction because of a strange and deadly infection, a transmissible cancer known as Transmissible Devil Facial Tumor Disease (TDFTD). In a previous NCBI Insights post, we discussed gene expression data from the tumors that established their neural origin and showed the tumors were likely derived from Schwann cells. In this post, we’ll consider some of the genome sequencing projects in the NCBI databases and explore evidence that the tumor originated in a different individual than the affected animal supporting the idea that the tumor cells themselves are infectious agents.
As mentioned in the previous post, a good way for you to access Tasmanian devil data at NCBI is through the BioProject database. If you search BioProject with “Tasmanian devil”[Organism] as a search term, you will retrieve five BioProject records. Two of these represent transcriptome studies (PRJNA79479 and PRJNA118101) discussed in the earlier post. The other three are genome-sequencing projects (PRJNA65325, PRJNA51853, and PRJNA167725), including the NCBI Reference Genome project.
Tasmanian devil nuclear and mitochondrial genome projects
PRJNA65325 contains data submitted by the J. Craig Venter Institute and the Schuster group at Penn State University. The project has provided a combined 13x assembly from two Tasmanian devils: a male named Cedric and a female named Spirit. The master record for the shotgun assembly from next generation data is AFEY00000000, which contains 457,732 contigs assembled into 148,774 unplaced scaffolds. This assembly has a total length, including gaps, of 3,232,424,150 bases.
Miller et al. (2011, PMCID: 3145710) report this sequence and its analysis. The authors also examined nuclear and mitochondrial variation in Tasmanian devil populations, confirming that Tasmanian devils have a low genetic diversity, and provided a conservation breeding strategy to preserve the current genetic diversity.
In addition to the nuclear genome, the study provides a set of 14 mitochondrial genome sequences (JX475454-JX475467) from modern Tasmanian devils and museum specimens (JX475454, JX475462, JX475464, and JX475465). The modern mitochondrial sequences include those from Cedric (JX475455) and Spirit (JX475463), as well as a tumor sample from Spirit (JX475460).
Comparison of Tasmanian devil and tumor mitochondrial genome sequences
The tumor mitochondrial sequence (JX475460) is most similar to Tasmanian devil sequences from eastern Tasmania, but distinct from the host (Spirit) mitochondrial sequence (JX475463). That the tumor mitochondrial sequence was different from that of the host animal was compelling evidence that the tumor did not arise from the cells of the host animal. This also suggested that the tumor first arose in populations in the east of Tasmania.
You can use the NCBI “BLAST 2 or more sequences service” and the “Distance Tree of Results” display to confirm the affinities of the tumor sequence and identify the mitochondrial lineages reported in the study (Figure 1). The link immediately below sets up a search of the tumor genome against the 13 other complete mitochondrial genome sequences from the study as well as the mitochondrial genome sequence (JN216828) from the Tasmanian devil called Salem that was the source for the Sanger Tasmanian devil genome project (PRJNA51853).
From the results of this search, you can click the “Distance Tree of Results” to see the relationships among these mitochondrial genomes. As reported in the study, the tumor genome sequence is most closely related to the mitochondrial genomes of Spirit and other Tasmanian devils with haplogroup A from eastern Tasmania.
The above example illustrates how molecular evidence deposited in the NCBI databases and NCBI tools allows independent confirmation of results in the biomedical literature.