Ancient fish genome decoded

An international research team with Victoria University has decoded the genome of an ancient fish to learn more about evolution.

College of Health & Biomedicine Dean Professor Gregory Blatch worked with a team led by Dr Chris Amemiya from Benaroya Research Institute and Dr Jessica Alföldi of the Broad Institute of MIT and Harvard University, both in the USA.

The groundbreaking project to sequence the African coelacanth's genome has resulted in an academic paper featured on the front cover of the latest issue of Nature journal.

The sea-cave dwelling coelacanth fish was once thought to be extinct until a living specimen was discovered off the Eastern Cape coast of South Africa in 1938.

Coelacanths today closely resemble the fossilized skeletons of their more than 300-million-year-old ancestors and genome sequence confirms what many researchers had long suspected: genes in coelacanths are evolving more slowly than in other organisms.

Researchers hypothesize that this slow rate of change may be because coelacanths simply did not need to change while living at ocean depths where relatively little has changed over the millennia.

Because of their resemblance to fossils dating back millions of years, coelacanths are often referred to as "living fossils" – a term coined by Charles Darwin.

Professor Blatch worked with a colleague from Rhodes University, Dr Adrienne Edkins, to analyse the coelacanth genes involved in protection from stress.

"We have felt very privileged to make a small contribution to a truly international effort to reveal the coelacanth genome", says Professor Blatch.

In addition to sequencing the full genome – nearly 3 billion "letters" or bases of DNA – from the coelacanth, the researchers also looked at RNA content from coelacanth (both the African and Indonesian species).

This information allowed them to compare genes in use in the brain, kidneys, liver, spleen and gut of coelacanth and 20 other vertebrate species, including Lungfish.

"The coelacanth is a critical organism to study in order to understand what is often called the water-to-land transition," Professor Blatch said.

"While Lungfish may be more closely related to land animals, its genome - at 100 billion bases in length - is simply too unwieldy for scientists to sequence, assemble, and analyze."

The coelacanth's more modest-sized genome ­- comparable in length to our own - is yielding valuable clues about the genetic changes that may have allowed tetrapods to flourish on land.

Researchers are also looking at what genes were lost when vertebrates came on land as well as what regulatory elements – parts of the genome that govern where, when, and to what degree genes are active – can be identified.

Professor Blatch and Professor Rosemary Dorrington of Rhodes University, South Africa, initiated the South African coelacanth genome initiative after the discovery of coelacanths off Sodwana Bay by recreational divers in 2000.

"We had no idea how ambitious the project would be - the coelacanth genome is equivalent in size to the human genome, the sequencing of which took 10 years to complete and involved more than 20 research institutes and hundreds of researchers," Professor Dorrington said.

Professor Blatch is also a Rhodes University Visiting Professor.

See all news