A series of press releases, including one by Science Publishing, recently announced the first findings of the Avian Phylogenomics Consortium, who analyzed genome sequences and annotation data for 48 bird genomes representing all of the bird taxonomic orders. All of the sequenced genomes, along with any annotation provided by the submitter, are available in NCBI resources including Assembly, Nucleotide, Protein, the Sequence Read Archive (SRA), and BLAST, or from species-specific GenBank genomes FTP directories. RNA-Seq data for some of the bird species can be found in SRA.
With the exception of three very fragmented assemblies, NCBI annotated the genome assemblies submitted by the Avian Phylogenomics Consortium using NCBI’s Eukaryotic Genome Annotation Pipeline, and these annotations are now part of the RefSeq project. The RefSeq project also generated annotations for an additional 6 bird assemblies, for a total of 51 RefSeq genomes. A summary of all the bird genomes that have RefSeq annotation is here.
Figure 1. A selection of the bird genomes with RefSeq annotation. At the top right is a legend describing resource links for each bird genome. Detailed annotation reports, accessible through the “AR” link in the far right column, are available for those genomes annotated in 2014. RefSeq annotation is on organism-specific BLAST pages (the “B” link) and on FTP (the “F” link). Click on the picture to go to the summary table.
RNA-Seq data was used to generate annotations for 12 of the 51 bird assemblies. The number of protein-coding genes per genome ranges from >13,300 to >21,100 (chicken) with an average of 14,932 protein-coding genes. Orthology to human proteins was also calculated using simple metrics of local synteny and sequence similarity, and on average, roughly 11,000 orthologous proteins were identified per avian genome. These results are shown in the Homology section of NCBI Gene records (see Figure 2 below). Continue reading
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
On a typical day, researchers download about 30 terabytes of data from NCBI in an effort to make discoveries. NCBI began providing online access to data in the early 1990s, starting with the GenBank database of DNA sequences. Over the years we’ve greatly expanded the types and quantity of data available. You can now find on our site descriptions and data from experimental studies such as next-generation sequencing projects, bioactivity assays for small molecules, microarray datasets and genome-wide association studies.
The White House recently recognized these efforts by awarding NCBI Director David J. Lipman with the “Open Science” Champion of Change Award . The scientific community has recognized the benefits of open data. Access to this information serves as a source of both original and supplemental data for exploration and validation [2-4], which improves the power of experimental data  while increasing the speed and decreasing the cost of discovery .
In this post, we summarize three recent cases where researchers used data from an NCBI resource/database to make significant discoveries.
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.