on Campus Issue 4 • May 2013 • For daily updates visit www.uwc.ac.za
Inside UWC Green Week page3
IOC Africa Conference page 8
UWC and the Chinese delegation discuss traditional Chinese medicine page 10
Banyana Star Joins UWC page 18
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SANBI tackles coelacanth genome
M
embers of UWC’s South African National Bioinformatics Institute (SANBI-UWC) form part of an international team of researchers from 40 institutions – including Rhodes University, Oxford University, and the Broad Institute at Harvard University and MIT – who recently decoded the genome of a world-famous“living fossil”, the fish known as the African coelacanth (Latimeria chalumnae). South African lead researcher Professor Alan Christoffels was invited to participate in the study, together with his SANBI-UWC team, which included three postdocs – Drs Uljana Hesse, Sumir Panji and Barbara Picone – as well as software programmer Peter van Heusden and SANBI-UWC staff members Dr Junaid Gamieldien and Mario Jonas. The decoded three-billion-letter genome has confirmed that protein-coding genes in the coelacanth are indeed evolving more slowly than in other vertebrate organisms. The researchers hypothesise that this slow rate of change may be because coelacanths simply have not needed to change: they live primarily off the East African coast at ocean depths where little has changed over thousands of years, and have few natural predators. The coelacanth is one of the closest fish relatives of tetrapods (land-dwelling vertebrates). The genome was compared to the genomes of other vertebrate species, as well as to several genes from lungfish, to find out more about the evolutionary history of the water-to-land transition. One discovery emerging from the study was that the lungfish appears to be somewhat more closely related to tetrapods than the coelacanth. But by looking at what genes were lost in the move from water to land, several other unusual discoveries were made. “A number of gene families key to vertebrate
A museum specimen of a coelacanth. Picture credit: S. Merikal/Flickr finding many regulatory changes that influenced genes involved in smell perception and decoding airborne odours (it is hypothesised that land creatures needed new ways to detect chemicals around them). The international team of researchers also found: a number of immune-related regulatory differences between the coelacanth and tetrapod genomes (possibly a response to new pathogens on land); a modification to the most important gene involved in the ammonia excretion cycle (fish excrete ammonia directly, while land vertebrates convert ammonia into less toxic urea); and several key genetic regions that may have been “evolutionarily recruited” to form tetrapod innovations such as fingers and the mammalian placenta. Funding agencies that provided support for this project include the African Coelacanth Ecosystem Programme of the South African National Department of Science and Technology, which supported the collection of samples; and the National Human Genome Research Left to right: Prof Alan Christoffels (front row); Dr Uljana Institute, which supported the Broad Hesse; Peter van Heusden; Dr Barbara Picone; Mario Institute’s contributions, including Jonas (front row). Not pictured: Dr Junaid Gamieldien; Dr genome sequencing. Sumir Panji.
adaptation were found in the coelacanth genome,” explains Christoffels. “So, for example, we identified what is called ‘gene expansions’ – which are multiple copies of the same gene – and found that some of these are peculiar to coelacanth. This phenomenon usually indicates new adaptations in the context of an organism’s functions.” More specifically, SANBI-UWC researchers identified a class of olfactory genes whose function fits a model for vertebrate adaptation,