Elephant shark genome sequence leads to discovery of color perception in deep-sea fish

The elephant shark, a primitive deep-sea fish that belongs to the oldest living family of jawed vertebrates, can see color much like humans can.

This discovery, published in the March 2009 issue of Genome Research, may enhance scientists' understanding of how color vision evolved in early vertebrates over the last 450 million years of evolution.

“It was unexpected that a 'primitive' vertebrate like the elephant shark had the potential for color vision like humans. The discovery shows that it has acquired the traits for color vision during evolution in parallel with humans,” said Byrappa Venkatesh, Ph.D., who with David Hunt, Ph.D., headed the research team responsible for this surprising discovery.

Dr. Venkatesh is a scientist at Singapore's Institute of Molecular and Cell Biology (IMCB), while Dr. Hunt is based at the Institute of Ophthalmology at University College London (UCL).

The research team found that the elephant shark had three cone pigments for color vision and, like humans, it accomplished this through gene duplication.

Dr. Venkatesh said that the finding underscores the research utility of the elephant shark, which IMCB scientists proposed in 2005 as a valuable reference genome to understand the human genome.

In a separate paper titled, “Large number of ultraconserved elements were already present in the jawed vertebrate ancestor,” published in the journal Molecular Biology and Evolution in March 2009, the research team reported that they had discovered that the protein sequences in elephant shark were evolving at a slower rate than in other vertebrates.

This finding indicates that the elephant shark had retained more features of the ancestral genome than other vertebrates belonging to the same evolutionary tree and hence was a useful model for gaining insight into the ancestral genome, in which the human genome also has its roots.

In several scientific publications, Dr. Venkatesh's team has described research showing that the human DNA sequence was more similar to elephant shark than to any other fish.

Dr. Venkatesh added, “We expect the sequencing of the whole genome of the elephant shark to be completed by early 2010, the availability of which will then enable scientists to explore the important functional elements in both the human and elephant shark genome that have remained unchanged during the last 450 million years of evolution.”

The findings reported in Genome Research and Molecular Biology and Evolution were generated less than two years after IMCB secured National Institutes of Health funding to sequence the whole genome of the elephant shark.

For more information, please contact:
Wang Yunshi
Corporate Communications
Agency for Science, Technology and Research (A*STAR)
Tel: (65) 6826 6443
Email: wang_yunshi@a-star.edu.sg
This news release refers to research findings published in the following journal articles:
1. “Into the blue: gene duplication and loss underlie colour vision adaptations in a deep-sea chimaera, the elephant shark Callorhinchus milii”, Genome Research (2009) 19: 415-426.

Authors: Davies, W.L., Carvalho, L.S., Tay, B., Brenner, S., Hunt, D.M. and Venkatesh, B*.

2. “Large number of ultraconserved elements were already present in the jawed vertebrate ancestor”, Molecular Biology and Evolution (2009) 26: 487-490.

Authors: Wang, J., Lee, A.P., Kodzius, R., Brenner, S. and Venkatesh, B.

3. “Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome”, PLoS Biology (2007) 5(4): e101.

Authors: Venkatesh, B., Kirkness, E.F., Loh, Y.H., Halpern, A.L., Lee, A.P., Johnson, J., Dandona, N., Viswanathan, L.D., Tay, A., Venter, J.C., Strausberg, R.L. and Brenner, S.

4. “Ancient noncoding elements conserved in the human genome”, Science (2006) 314, 1892.

Authors: Venkatesh, B., Kirkness, E.F., Loh, Y.H., Halpern, A.L., Lee, A.P., Johnson, J., Dandona, N., Viswanathan, L.D., Tay, A., Venter, J.C., Strausberg, R.L. and Brenner, S.

Institute of Molecular and Cell Biology (IMCB):

The Institute of Molecular and Cell Biology (IMCB) is a member of Singapore's Agency for Science, Technology and Research (A*STAR) and is funded through A*STAR's Biomedical Research Council (BMRC). It is a world-class research institute that focuses its activities on six major fields: Cell Biology, Developmental Biology, Structural Biology, Infectious Diseases, Cancer Biology and Translational Research, with core strengths in cell cycling, cell signaling, cell death, cell motility and protein trafficking. Its recent achievements include leading an international consortium that successfully sequenced the entire pufferfish (Fugu) genome. The IMCB was awarded the Nikkei Prize 2000 for Technological Innovation in recognition of its growth into a leading international research centre and its collaboration with industry and research institutes worldwide. Established in 1987, the Institute currently has 35 independent research groups with more than 400 staff members.

Agency for Science, Technology and Research (A*STAR):

A*STAR is Singapore's lead agency for fostering world-class scientific research and talent for a vibrant knowledge-based Singapore. A*STAR actively nurtures public sector research and development in Biomedical Sciences, Physical Sciences and Engineering, with a particular focus on fields essential to Singapore's manufacturing industry and new growth industries. It oversees 22 research institutes, consortia and centres, and supports extramural research with the universities, hospital research centres and other local and international partners. At the heart of this knowledge intensive work is human capital. Top local and international scientific talent drive knowledge creation at A*STAR research institutes. The agency also sends scholars for undergraduate, graduate and post-doctoral training in the best universities, a reflection of the high priority A*STAR places on nurturing the next generation of scientific talent.