December 2019 RefSeq annotations: human, Tasmanian devil and more

tasmanian devil sits, looking to the right

In December, the NCBI Eukaryotic Genome Annotation Pipeline released new annotations in RefSeq for the following organisms:

  • Anarrhichthys ocellatus (wolf-eel)
  • Apis florea (little honeybee)
  • Contarinia nasturtii (swede midge)
  • Cucumis sativus (cucumber)
  • Galleria mellonella (greater wax moth)
  • Homo sapiens (human)
  • Nasonia vitripennis (jewel wasp)
  • Oncorhynchus kisutch (coho salmon)
  • Oreochromis aureus (blue tilapia)
  • Piliocolobus tephrosceles (Ugandan red Colobus)
  • Sarcophilus harrisii (Tasmanian devil)
  • Xenopus tropicalis (tropical clawed frog)

See more details on the Eukaryotic RefSeq Genome Annotation Status page.

The Tasmanian Devil 2: The tumor and Tasmanian devil mitochondrial genomes

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. Continue reading

The Tasmanian Devil and Cancer as an Infectious Disease: Analysis of transcriptome data

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 Devil Facial Tumor Disease.  These tumor infections are apparently passed to other devils through bites during mating or during squabbles over carrion when devils gather to feed. In this unusual situation, the cancer cells themselves are the infectious agent.

The failure of devil immune systems to recognize and destroy the foreign tumor cells may be related to a decline in genetic diversity and may serve as a warning about the vulnerability of species with reduced gene pools.  The advent of next-generation sequencing has provided an unprecedented opportunity to track the spread and identify the origin of this unusual zoonosis, as well as to examine the population structure of an endangered mammal and generate a complete genome sequence for this unique marsupial.

Continue reading