Complete animal genomes become easier to map thanks to revolutionary new method
Researchers at the Royal Veterinary College (RVC) and the University of Kent have developed a new cost effective approach to mapping and assembling genomes, using a novel method that is particularly effective for bird species. Developed with funding from the Biotechnology and Biological Sciences Research Council (BBSRC), this new method enables geneticists to assemble complete (chromosome-level) genome assemblies.
Genetics studies have long faced the major problem that although sequencing an animal genome is easy and cheap, assembling sequences to complete chromosomes level is difficult and expensive. Chromosome level genome assembly is much more useful to genetic science and practical application, but without significant investment, has been difficult to achieve for many species. Traditional methods of chromosome level genome assembly were time intensive and cost-inefficient in comparison to simple genome sequencing. As a result, most animal genomes that have been sequenced are not assembled to chromosomes level.
The new method developed by the RVC and University of Kent Comparative Genomics teams, and released in a new paper entitled ‘Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set’, allows geneticists to reach chromosome level genome assembly both cost-effectively and fast. The team’s specific breakthrough is to use universal probes to anchor scaffolds to chromosomes physically.
The method of using probes to map genomes has existed for a long time, but this research with contribution from the Cambridge companies Cytocell Ltd and Digital Scientific UK is the first to make a complete panel of universal probes that work equally well on any avian (and often even on reptile) genomes. This means that once DNA has been extracted from ~250 probes, these can be used as universal probes, and it is possible to apply them to any avian genome equally successfully. It then becomes an extremely cost effective way of assembling a complete genome to chromosome level, relative to designing probe libraries, choosing probes, verifying and mapping them for each genome separately.
Until this study, the genomes of only three bird species had been published as assembled to complete chromosome level. Yet using this method, the research team were able to map and assemble the complete genome of pigeons and the peregrine falcon, with all other bird species also easily accessible. This new method will have significant practical implications, for example in the farming industry, as mapping the genomes of bird species such as poultry, will enable a deeper understanding of genetic characteristics. It will also enable diseases to be tackled at a genetic level.
Birds were used to develop and test this method because avian and reptilian genome sequences are more evolutionary conserved than mammals, making it easier to select universal probes. Avian genomes are also three times smaller than mammals’. However, based on the success of this method, the research team will now apply the same approach to mammals.
This research was made possible thanks to the Biotechnology and Biological Sciences Research Council (BBSRC) which invests in world class bioscience projects and research across the UK.
Notes to editors
The research paper entitled ‘Upgrading short read animal genome assemblies to chromosome level using comparative genomics and universal probe set’ is published in the peer reviewed academic journal Genome Research.
- The Department of Comparative Biomedical Sciences, RVC
- The School of Biosciences, University of Kent
- The School of Human and Life Sciences, Canterbury Christ Church University
- The Institute of Biological, Environmental and Rural Sciences, Aberystwyth University
- Denis M Larkin, RVC
- Darren K. Griffin, University of Kent
- Joana Damas
- Rebecca O’Connor
- Marta Farré
- Vasileios Panagiotis E. Lenis
- Henry J. Martell
- Anjali Mandawala
- Katie Fowler
- Sunitha Joseph
- Martin T. Swain
Research was funded by the Biotechnology and Biological Sciences Research Council (BBSRC)
About University of Kent
Established in 1965, the University of Kent – the UK’s European university – now has almost 20,000 students across campuses or study centres at Canterbury, Medway, Tonbridge, Brussels, Paris, Athens and Rome.
It has been ranked: 23rd in the Guardian University Guide 2017; 23rd in the Times and Sunday Times University Guide 2017; and 23rd in the Complete University Guide 2017.
In the Times Higher Education (THE) World University Rankings 2015-16, Kent is in the top 10% of the world’s leading universities for international outlook and 66th in its table of the most international universities in the world. The THE also ranked the University as 20th in its ‘Table of Tables’ 2016.
Kent is ranked 17th in the UK for research intensity (REF 2014). It has world-leading research in all subjects and 97% of its research is deemed by the REF to be of international quality.
In the National Student Survey 2016, Kent achieved the fourth highest score for overall student satisfaction, out of all publicly funded, multi-faculty universities.
Along with the universities of East Anglia and Essex, Kent is a member of the Eastern Arc Research Consortium, visit www.kent.ac.uk/about/partnerships/eastern-arc.html for more information.
The University is worth £0.7Bn to the economy of the south east and supports more than 7,800 jobs in the region. Student off-campus spend contributes £293.3M and 2,532 full-time-equivalent jobs to those totals.
In 2014, Kent received its second Queen’s Anniversary Prize for Higher and Further Education.
About the Royal Veterinary College
The Royal Veterinary College (RVC) is the UK's largest and longest established independent veterinary school and is a constituent College of the University of London. The RVC offers undergraduate, postgraduate and CPD programmes in veterinary medicine, veterinary nursing and biological sciences, being ranked in the top 10 universities nationally for biosciences degrees. It is currently the only veterinary school in the world to hold full accreditation from AVMA, EAEVE, RCVS and AVBC.
A research-led institution, in the most recent Research Excellence Framework (REF2014) the RVC maintained its position as the top HEFCE funded veterinary focused research institution.
The College also provides animal owners and the veterinary profession with access to expert veterinary care and advice through its teaching hospitals; the Beaumont Sainsbury Animal Hospital in central London, the Queen Mother Hospital for Animals (Europe's largest small animal referral centre), the Equine Referral Hospital, and the Farm Animal Clinical Centre located at the Hertfordshire campus. www.rvc.ac.uk
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 £473 million in world-class bioscience, people and research infrastructure in 2015-16. 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.
Tags: animal health bioscience genetics Royal Veterinary College University of Kent press release