Scientists led by Dr Yann Guiguen from the French National Institute for Agricultural Research have successfully sequenced the genome of the rainbow trout, Oncorhynchus mykiss.
The rainbow trout, an elongated fish with sides that fade from green below the dorsal fin to yellow and white, belongs to Salmonidae, a family of fishes that also includes salmon, char, and grayling.
This fish has straddled the worlds of nature and nurture, naturally thriving in a range of temperatures and water quality while responding to domestication so well that it has been spread by human hand from the Pacific Rim to thrive in waters on six continents.
In their research, Dr Guiguen and his colleagues focused on the rate at which genes have evolved since a rare genome doubling event occurred in the rainbow trout about 100 million years ago.
Unlike most evolutionary processes involving mutations and the selection of advantageous traits, a doubling event acts like the copied draft of a piece of writing that can be edited and recast without the risk of destroying the earlier version.
Ordinarily, the consequences of such doubling events are lost to science as they get cast out by selective forces in subsequent generations. But because 100 million years is a relatively short time, evolutionarily speaking, the trout researchers could in effect glimpse the fish’s evolutionary editing process.
“In humans and most vertebrates the duplication events were older so there are fewer duplicated genes still present. Most of the duplicated genes get lost or modified so much that they are no longer recognizable as duplicates over time. In the trout and salmon we can see an earlier stage in the process and many duplicated genes are still present,” said Dr Gary Thorgaard of Washington State University, a co-author of the paper published in the journal Nature Communications.
The team used both the genome sequence and gene expression data from the rainbow trout to show that roughly half of all protein coding genes have been deleted since its genetic doubling event.
It has retained almost all its microRNA genes, which help regulate gene expression.
The scientists also found the fish retained original or nearly original genes involved in embryonic development and development of connections between nerve cells.
The timing associated with these changes suggests gene evolution after an event such as this is a much slower process than previously thought.
“It seems that the rate of evolution can vary in different situations,” Dr Thorgaard said.
“Some animals, like the lungfish and coelacanth, are ‘living fossils’ that have been around for hundreds of millions of years without changing very much. Others, like the polar bear, seem to have evolved quite recently. After the trout gene duplication, the process happened more slowly than it has in most other vertebrate animals, and we can still watch it going on.”
Camille Berthelot et al. 2014. The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nature Communications 5, article number: 3657; doi: 10.1038/ncomms4657