Whole-genome dataset for bread wheat now available in Ensembl Plants
Whole-genome dataset for bread wheat now available in Ensembl Plants
13 Jan 2014 - 15:13
Today, an improved genome sequence for bread wheat including more than 100,000 genes has been released in Ensembl Plants. The data will provide wheat researchers and plant breeders with valuable tools to improve this vital crop’s yield in different environments. Generated under the auspices of the International Wheat Genome Sequencing Consortium (IWGSC), the Chromosome Survey Sequence represents the most complete version of the wheat genome to date.
The bread wheat genome is large and complex: it is at least five times larger than the human genome, but contains a huge number of repeated sequences. Bread wheat is derived from three different grasses, which hybridised during domestication. Modern wheat crops retain the three separate ancestral genomes. Bread wheat therefore has three distinct ‘sub-genomes’, each of which contributes seven chromosomes.
Trying to sequence and assemble each of these sub-genomes individually is as difficult as sequencing the genomes of a human, chimp and gorilla all at once. The IWGSC project sequenced the three wheat sub-genomes one chromosome at a time, which made it possible for the first time to assign each assembled chromosome fragment to the correct sub-genome.
The improved bread wheat genome data will be a vital resource for improving crops. By studying its internal structure, scientists can also gain insights into how wheat was domesticated and and how traits relating to pest resistance and drought/stress tolerance have developed.
The project was truly international in scope. The Genome Analysis Centre (TGAC) in the UK carried out a major part of the sequencing and assembly work, sequencing 14 of the 21 chromosomes and generating all of the chromosome assemblies. The gene models were predicted by the Helmholtz Centre Munich (MIPS/HMGU), Germany using a new gene dataset produced by the INRA Centre for Génétique, Diversité et Ecophysiologie des Céréales (INRA GDEC) in France, as well as other public datasets. Other contributors to the sequence data were the University of Queensland (Australia), University of Saskatoon (Canada), Genoscope (France), Kansas State University (USA), Hedmark University College (Norway), National Institute of Agrobiological Sciences (Japan).
The improved bread wheat genome data are now available via Ensembl Plants at EMBL-EBI. They can also be accessed via the IWGSC’s data repository at Unité de Recherches en Génomique Info (URGI, France).
Director of TGAC, Mario Caccamo, says: “Here at TGAC, one of our main research priorities is to address the grand challenge of maintaining food security through the application of genomic technologies, so we are very proud to be part of IWGSC’s ground-breaking project and to provide genetic data that is imperative to the future sustainability of the bread wheat crop.”
Extensive comparative analyses between wheat and other cereal genomes is available in Ensembl Plants. Dr Paul Kersey, who leads non-vertebrate genomics resources at EMBL-EBI, says: “It is fantastic to be able to release these data in the public domain, and to provide tools that help researchers explore the ancestry of the wheat genome.”
Dr Klaus Mayer, leader of the MIPS/HMGU bioinformatics group, says: “Socioeconomic importance and the sheer complexity of the wheat genome impose a major challenge that can only be approached by a concerted, multidisciplinary approach. We are very pleased to be part of this undertaking, and through close collaboration with IWGSC and our UK-based colleagues, to contribute to this major breakthrough.”
IWGSC Executive Director, Kellye Eversole, says: “We are very pleased to see Ensembl Plants incorporate our data into their database and to provide tools and resources that complement those already available at URGI.”
Notes to Editors
The Genome Analysis Centre (TGAC) is a research institute focused on the development of genomics and computational biology. TGAC is based within the Norwich Research Park and receives strategic funding from the Biotechnology and Biological Science Research Council (BBSRC) - £9.2M in 2012-2013 - as well as support from other research funders. TGAC is one of eight institutes that receive strategic funding from BBSRC. TGAC 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. www.tgac.ac.uk
The European Bioinformatics Institute is part of EMBL, Europe’s flagship laboratory for the life sciences. EMBL-EBI provides freely available data from life science experiments covering the full spectrum of molecular biology, and about 20% of the institute is devoted to investigator-led research using computational approaches to unravel the secrets of life. Our extensive training programme helps researchers in academia and industry to make the most of the incredible amount of data being produced every day in life science experiments. We are a non-profit, intergovernmental organisation funded by EMBL member states. Our 500 staff hail from 43 countries, and we welcome a regular stream of visiting scientists throughout the year. We are located on the Wellcome Trust Genome Campus in Hinxton, Cambridge in the United Kingdom. www.ebi.ac.uk
The MIPS research group is located at the Helmholtz Zentrum München, the German Research Center for Environmental Health. The MIPS plant research group has a history in contributing to a range of plant genome sequencing and resequncing projects, in comparative analysis of plant genomes and in developing widely recognized plant genomic information systems and database resources. The research group is among the internationally most reputed groups in plant genome oriented bioinformatics and has been highly influential in shaping the field by important and widely recognized contributions and analysis on a wide range of currently studied plant genomes. Our goal is to contribute to the understanding of the fundamental principles of plant genome functioning and the molecular interfaces for the interaction with the environment. mips.helmholtz-muenchen.de/plant/
The International Wheat Genome Sequencing Consortium (IWGSC), with more than 1,000 members in 57 countries, is an international, collaborative consortium, established in 2005 by a group of wheat growers, plant scientists, and public and private breeders. The vision of the IWGSC is a publicly available, high quality genome sequence of bread wheat that will enable breeders to develop improved varieties of wheat and lay a foundation for basic research in wheat, cereals, and plants. IWGSC data are available at URGI through a Sequence Repository: http://wheat-urgi.versailles.inra.fr/Seq-Repository. To learn more about the IWGSC, please visit: www.wheatgenome.org. To follow our activities and news related to wheat genomics, follow us on Twitter® at https://twitter.com/wheatgenome. For additional information, contact Kellye Eversole, IWGSC Executive Director at email@example.com or by telephone at +1.202.352.4210 (cell) or +1.301.618.9541(voice mail).
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, and with an annual budget of around £467M (2012-2013), 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. For more information about BBSRC, our science and our impact see: www.bbsrc.ac.uk. For more information about BBSRC strategically funded institutes see: www.bbsrc.ac.uk/institutes.