Download Sea Lion Genome Data

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.

Students in the Class

Sequencing class collaborators Spring 2010

  • John Davidson,
  • Robert Morey,
  • John Wokuluk,
  • Victor Seguritan,
  • Kristen Aguinaldo,
  • Heather Hochrein,
  • Christine Sager,
  • Elena Kozma,
  • Jose Arciniega,
  • Chelsea Kidwell,
  • John Haggerty,
  • Haaris Masoud,
  • Richard Giesen,
  • Nick Celms,
  • Svetlana Mukhoed,
  • Michele Mckeand,
  • Joelle Andrews,
  • Matthew Doherty,
  • Noriko Cassman,
  • Julia Busch,
  • Thiago Bruce

 

Bioinformatics class collaborators, Fall 2010

 

  • Aladdin Shadyab
  • Ana Georgina Cobián Güemes
  • Archana Srinivas
  • Aurora Labastida
  • Bharath Bharadwaj
  • Brad Hull
  • Brenda Janice Sánchez
  • Carlos Vazquez
  • Cuauhtemoc (Temo) Gomez-Barroso
  • Daniel Cuevas
  • Funso Adegbemle
  • Jeong Ho Choi
  • Matt Haggerty
  • Jorge Quintana
  • Jose Banos
  • Maria de los Dolores Soto del Rio
  • Martha G. López-Guerrero
  • Martha Rendon
  • Matt Doherty
  • Matt Maybeno
  • Matthew Shaw
  • Melissa Moghaddam
  • Michael Arnoult
  • Min Soo Kim
  • Minerva Trejo
  • Nicholas Celms
  • Noriko Cassman
  • Ofelia Edith Carreón Rodríguez
  • Robert Morey
  • Rogelio Hernandez
  • Shamayim Ramirez
  • Stephanie Feudjio Feupe
  • Tania Rosas
  • Viridiana Avila
  • Patricia Oliver
  • Rosa Gutierrez

 

 

 

Sequencing class collaborators Spring 2011

  • Nisha Agarwal,
  • Leylla Badeanlou,
  • Bharath Bharadwaj,
  • Miranda Brett,
  • Sowmya Chinta,
  • Beverly Ann Dimaano,
  • Keri Elkins,
  • Kelley Fracchia,
  • Amanda Hrezo,
  • Roxanne Kotzebue,
  • Afonso Mello,
  • Megan Morris,
  • Jimmy Rabbers,
  • Arnika Sharma,
  • James Shaw,
  • Rohini Singh,
  • Daniel Sitzmann,
  • Archana Srinivas,
  • Katherine Utterback
  • David Velasco Sanchez,
  • Kevin Walsh,
  • Stephanie Ward

Bioinformatics class collaborators, Fall 2011

  • Adriel Carolino
  • Ashu Chawla
  • Dennis Didulo
  • Donabel Roberts
  • Jose Barona-Gracia
  • Matthew Hagen
  • Matthew Munoz
  • Nathan Baer
  • Nisha Agarwal
  • Robert Moulton
  • Rohini Singh
  • Shashank Sathe
  • Yujing Liang (Tiff)
  • Victoria Zadorozhny

Here are some photos of the students taking the sequencing class

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Collaborators

We can’t do this alone! Lots of people have helped with this project, most notably our local collaborators – both in the United States and Mexico at Hubbs Sea World Research Institute, San Diego, California, USA, Universidad Autónoma de Baja California, Ensenada, Baja California, Mexico and Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico. Sequencing is being supported by Roche 454 Life Sciences

 

Sea Lion Cancer Consortium

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.
Members of the group
Matthew Breen, NCSU CVM and UNC Lineberger Comprehensive Cancer Center
Frances Gulland, Marine Mammal Center, USA
Denise Greig, Marine Mammal Center
Elizabeth Murchinson, Sanger Center, UK


Sequencing and collaborations

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.

Sea Lions

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.

Photo credit: Elizabeth Dinsdale. Copyright Elizabeth Dinsdale, 2010

Californian Students Sequencing the California Sea Lion

To immerse undergraduate students in the genomic era, San Diego State University undertook a project to sequence the California Sea lion. The project has two major components and associated courses; a “hands on” sequencing courses and a bioinformatic course. The sequencing course teaches students to prepare DNA and sequence it on a Roche 454 Lifesciences flx machine. The students conduct the entire process from DNA extraction to loading the plate and running the machine. At the end of 13 weeks the students had sequenced 24 billion base pairs of sea lion genome. The students chose several contigs to investigate as part of their assessment. The Sea lion genome was assembled on Newbler, and 1.3 million contigs with an average length of 1,434 Bp were generated. The assembled DNA totals 1,951,532,210 bp with 13,352,265 bp in contigs > 10kb, and 972,007 bp in contigs > 15 kb. The N50 sizes are 2,127 bp for all contigs, 11,249 for the 10 kb contigs, and 16,472 for the 15 kb contigs

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.

A beautiful sea lion

Photo credit: Elizabeth Dinsdale. Copyright Elizabeth Dinsdale, 2010

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