Spotted Gar genome links humans to vertebrate ancestry
09 March 2016
The Spotted Gar is an unusual fish whose genome sequence has been released in a recent study highlighted in Nature Genetics. This fish has surprising genetic similarities and ancestral qualities which are informative about the evolution of many vertebrate animals - including humans.
Led by Drs John Postlethwait and Ingo Braasch from the Institute of Neuroscience, University of Oregon, US, in collaboration with The Earlham Institute (EI), the study of the Spotted Gar (Lepisosteusoculatus) genome reveals that it is small and manageable. Furthermore, it lacks much shuffling and duplication that occurred in the ‘main’ fish ancestral line; it conserved its genome.
The Gar is particularly useful for biological studies because it bridges the gap between most fish and other vertebrates, allowing much more meaningful comparison than before. Its genome resembles the common ancestor of fish and four-limbed animals, such as birds. Indeed, the Gar’s chromosomes show only 17 major rearrangements from the chicken’s, despite the evolutionary gap between them.
Prof Di Palma, co-author of the study and Director of Science at EI, said: “The Spotted Gar is a superb reference species, an out-group that provides additional statistical power to help define much of the functional material in vertebrate genomes that otherwise remains obscure.”
Around 96 per cent of all known fish species are categorised as Teleosts (ray fins). The Gar belongs within the other four per cent and provides a highly informative comparative basis for evolutionary studies. For example, researchers have already used the Gar genome to find the genetic equivalent of wrist/ankle/digits in this living fish, confirming fossil evidence of an aquatic origin of fin-to-limb transition (1).
The Gar branched off from the Teleosts more than three hundred million years ago and conserved its genome more than might be expected since then. So far, we only know of one fish species that may have evolved more slowly – the coelacanth, often referred to as a ‘living fossil’.
To a casual observer, the Gar largely resembles a typical fish – but it does have rather unusual ‘ganoid’ scales, with a primitive sort of enamel for strength. Its genome sequence has two genes involved in mineralisation of enamels for those scales – evidence that ‘enamel genes’ evolved in early vertebrates before they were recruited to teeth. Teleost fish, by contrast, lack those enamel genes; only the Gar provides the clues for sorting out the evolutionary tree for that gene family (2).
Prof Di Palma, added: “The Gar genome clarifies the evolutionary history of many important gene families, including numerous ancestral noncoding elements.”
Prof John Postlethwait, commented: “Especially important for understanding human health and disease, the gar genome helps identify genetic sequences that are shared by human disease genes and teleost fish medical models like zebrafish; by studying those otherwise invisible shared elements, we will be able to better understand human complex diseases like diabetes, heart disease, addiction, and the bone loss that comes with ageing. ”
The scientific paper, titled: “The spotted gar genome illuminates vertebrate evolution and facilitates human-to-teleost comparisons” is published in Nature Genetics.
Notes to editors.
For more information, please contact:
Marketing & Communications Officer, Earlham Institute (EI)
- +44 (0)1603 450 107
1) Deep conservation of wrist and digit enhancers in fish PNAS 2015 112 (3) 803-808
2) Gene family of Secretory Calcium-Binding Phosphoproteins (SCBP)
“…the competition between fresh-water productions will have been less severe than elsewhere; new forms will have been more slowly formed, and old forms more slowly exterminated. And it is in fresh water that we find seven genera of Ganoid fishes, remnants…[that] have endured to the present day, from having inhabited a confined area, and from having thus been exposed to less severe competition.” – Charles Darwin, Origin of Species, 1859.
The Earlham Institute (EI) is a world-class research institute focusing on the development of genomics and computational biology. EI is based within the Norwich Research Park and receives strategic funding from the Biotechnology and Biological Science Research Council (BBSRC) - £7.4M in 2013/14 - as well as support from other research funders. EI is one of eight institutes that receive strategic funding from BBSRC. EI operates a National Capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation.
EI offers state of the art DNA sequencing facility, unique by its operation of multiple complementary technologies for data generation. The Institute is a UK hub for innovative Bioinformatics through research, analysis and interpretation of multiple, complex data sets. It hosts one of the largest computing hardware facilities dedicated to life science research in Europe. It is also actively involved in developing novel platforms to provide access to computational tools and processing capacity for multiple academic and industrial users and promoting applications of computational Bioscience. Additionally, the Institute offers a Training programme through courses and workshops, and an Outreach programme targeting schools, teachers and the general public through dialogue and science communication activities.
The Biotechnology and Biological Sciences Research Council (BBSRC) invests in world-class bioscience research and training on behalf of the UK public. Our aim is to further scientific knowledge, to promote economic growth, wealth and job creation and to improve quality of life in the UK and beyond.
Funded by Government, BBSRC invested over £509M in world-class bioscience in 2014-15 and is the leading funder of wheat research in the UK (over £100M investment on UK wheat research in the last 10 years). We support research and training in universities and strategically funded institutes. BBSRC research and the people we fund are helping society to meet major challenges, including food security, green energy and healthier, longer lives. Our investments underpin important UK economic sectors, such as farming, food, industrial biotechnology and pharmaceuticals.