We have split the sea lion genome data into contigs greater than 10kb and contigs greater than 15kb. This is to make things simpler for downstream analysis. Let us know if you want other data.
Access to the raw data and assemblies requires an additional password. Please contact Liz Dinsdale if you would like to access that data.
Please note that access to this data is provided on a collaborative basis. Please don’t publish any genome scale comparisons on the data without discussing them with Liz first. Let us know if there you have any problems or questions.
, shows the results of the first semester of work on sequencing the sea lion and analyzing the data. Thanks to all who helped!
The data generated by the students is of publication quality and can be used to investigate sea lion genome and health issues.
For example, an international group of researchers is interested in using the DNA sequences to explore the sea lion’s high incidence of genitourinary (GU) carcinoma. About 17-20 % of known adult sea lion deaths are linked with these carcinomas.
Their research has found that aberrant genomic features are recurrent across several animals, for example dogs and humans, suggesting there is a conserved pathogenesis. To explore the conserved nature of the genomic aberrations a comparison has recently been conducted against the genomic data from the Tasmanian devil. Since California sea lions are a carnivores (as are dogs) with high levels of carcinomas they are a good model to explore the phylogenetic relationship of the cancers. Thus the group is teaming up with the SDSU students and is using the California Sea lion genome as another piece in the puzzle of understanding the development and evolution of these carcinomas.
The students are going to continue sequencing the Sea lion in Spring semester 2011 and further analyze the more complete genome set in Fall semester 2011. This is a unique set of data that is available for those interested in Sea Lion biology, ecology and evolution. We would be happy to share this data with you, but realize it was the efforts of 20 undergraduate Biology students who did the sequencing and 20 undergraduate computer science students who have started with the annotation. The use of this data requires the acknowledgement of students and professors. Please contact Dr Elizabeth Dinsdale for information on collaboration.
California sea lions are found along the west coast of Canada, USA and Mexico, with the largest populations occurring in the islands of California. A distinct population is found in the Galapagos Islands. Sea lions are known for their, playfulness, intelligence and near acrobatic abilities underwater. These animals are often seen in performances at zoos and sea worlds.
The males are dark brown and can reach 390 kg and 2.1 m in length. The females are a lighter brown and slightly smaller growing to 220 kg and 1.8 m in length. Males form a bump on the tops of their skull called a sagittal, when they reach 5 years of age. Sea lions are members of the Otariid family, having external ears and the ability to rotate their front and back flippers, which enables them to “walk” on land. They have a dog like face, but preliminary comparisons of the genome shows greater similarity with the Panda genome.
The assembled genome was turned over to the bioinformatic undergraduate class at San Diego State University and National Autonomous University of Mexico to start the annotation process. These students enjoyed the challenge of tackling this large dataset and describing the wealth of information that it contained. The bioinformatic students conducted a number of analyses including identifying the repeat regions, phylogenetic analysis, and gene identification using Artimis, Genescan, Genemark, Glimmer and gene annotation using Artemis and Blast2Go.
Both classes have been a huge success with students providing very positive feedback and learning a large sweep of new techniques. Many biology students were influenced to take the bioinformatics course, something they were unlikely to do prior to taking the sequencing course. Several of the students have been employed because of the experience that they gained in the course.