22nd May 2010
The preliminary 8X draft assembly of the E. grandis genome, which is being sequenced by the US Department of Energy (DOE) Joint Genome Institute (JGI), is available from today in our public Eucalyptus Genome Database (EucalyptusDB). Members of the Eucalyptus research community and the wider plant genomics community are invited to make use of this resource, which is already widely accessed.
Some notes on this release:
- The genome browser in EucalyptusDB has been updated to Generic Genome Browser (GBrowse) version 2.0.
- The browser for the preliminary 4.5X (checkpoint) assembly will remain accessible, but is currently also being updated to GBrowse 2.0.
- The 8X assembly released on EucalyptusDB is the first draft assembly that incorporates all of the Sanger sequences produced for the E. grandis genome. The assembly is still being updated and the current release is therefore likely to be incomplete in some regions and will change in the next release. A more complete draft assembly and draft annotation will be released on Phytozome later in 2010.
- The draft 8X assembly consists of 6043 genome scaffolds covering 693 Mbp. This total is somewhat inflated due to the fact that approximately 20% of the genome is currently assembling into two parallel haplotypes (both included in the 693 Mbp) due to very high heterozygosity in some regions of the E. grandis genome. This will be resolved in the next release of the genome assembly.
The initial analysis of a high quality draft E. grandis genome sequence will be published in 2011. The principal investigators and collaborators of the E. grandis Genome Project intend to publish genome-wide analyses of features such as genes, protein families, metabolic pathways, non-coding RNA and repetitive DNA in the main genome paper, associated papers and in subsequent publications. Interested persons are encouraged to contact the principle investigators (Zander Myburg, Dario Grattapaglia or Jerry Tuskan to coordinate collaborative efforts aimed at producing such publications.
We also invite members of the Eucalyptus research community and all other interested persons to register as members on the EUCAGEN website.
22nd Apr 2010
Sven Bergmann is an Associate Professor at the University of Lausanne in the Department of Medical Genetics, and is affiliated with the Swiss Institute for Bioinformatics. (more…)
22nd Mar 2010
The ACGT was recently represented at the Food and Agricultural Organisation of the United Nations (FAO) International technical conference on Agricultural Biotechnologies in Developing Countries (ABDC-10). (more…)
22nd Feb 2010
A world-class building promising to be an excellent example of a green building that is both effective and user-friendly will be erected at the University of Pretoria.
A sod-turning ceremony was held at the construction site of the new Plant Science building on Friday 29 January 2010. In her welcoming speech Prof Cheryl de la Rey, Vice-Chancellor and Principal of the University of Pretoria, described the occasion as symbolic of the successes of the Faculty of Natural and Agricultural Sciences and the University of Pretoria. Prof de la Rey said that this event marked the University’s commitment to 2010 as the International Year of Biodiversity and that it was a “celebration of past successes and new beginnings”.
Click here to read more
21st Feb 2010
February 2010 Related info National Health Laboratory Service
The ACGT was recently represented at the annual SAMI (South African Malaria Initiative) Conference 2010 in Cape St Francis. The meeting, which was held from 26 – 28 January, was followed by an open SAMI Steering Committee Meeting. (more…)
22nd Nov 2009
The ACGT recently hosted an international workshop at the University of Pretoria (UP) aimed at sharing knowledge on the use of molecular tools for cassava breeding – in particular, SNP (single nucleotide polymorphism) Marker Technology. The workshop, which was held from 9 – 12 November 2009, was attended by cassava breeders from a range of African countries – including Tanzania, Nigeria, Ghana, Malawi and Uganda – as well as from Brazil.
Organised as part of the CGIAR Generation Challenge Programme (GCP) Cassava Project, the workshop introduced participants to DNA variation and SNP Marker Technology and its applications. Also included as part of the programme was a demonstration of the recently installed Illumina BeadXpress platform at UP.
Cassava is an important root crop in unfavourable environments in poor areas of developing countries and is of both industrial and commercial significance. The crop is often cultivated in dry areas as well as being susceptible to certain devastating pests and diseases such as Cassava Mosaic Disease (CMD). As such, there is a great need for research towards improvement of drought tolerance and the combating of disease in cassava.
In keeping with the aims of the GCP Cassava Project, the SNP workshop sought to create a platform for cassava breeders learn about the progress and latest developments in molecular tools and the opportunities that exist for their application in the breeding process.
According to Emmanuel Okogbenin of the National Root Crops Research Institute (NRCRI) in Nigeria, the rapid evolution of the genomics of cassava makes it vital for breeders to constantly be aware of the opportunities that are available to them to improve their work. “The workshop has provided a good networking platform. Working together as a community, we will be able to improve access to facilities and the tools needed to enhance speed and efficiency in the breeding process”, he said.
Anthony Pariyo from Uganda – where cassava is the second most important crop after bananas – believes access to cutting-edge technologies like SNP has the potential to revolutionise cassava breeding in his country over the next 20 years. “Previous methods relied solely on the phenotype. Being unable to see what was happening on the inside of the plant made it difficult to keep up with the fast evolution of diseases. From this workshop we have learned about the genotyping and marker support services that are available through GCP. These will help us to move our materials faster and greatly improve efficiency”, said Pariyo.
Applied Biotechnologist, Jedidah Danson from the African Centre for Crop Improvement (ACCI), represented the University of KwaZulu-Natal – where ACCI is running a PhD programme on conventional breeding. According to her, SNP technology adds great value in terms of the volume and quality of data produced. “This technique generates the kind of data that will not only be applicable but invaluable to our students”, she added.
21st Nov 2009
The SABINA network has successfully secured European Union funding for a project which aims to support natural products research and policy development in the Southern African region.
The project, titled Policy and support actions for Southern African Natural Product partnership (POL-SABINA) will receive €950 000 over three years from the EU African, Carribean and Pacific Group of States (ACP) programme.
The activities of POL-SABINA will be directed towards co-ordination and networking in applied research and the development of a knowledge management system (Virtual Research Environment) for SABINA. A major focus will also be on the development of policies to support the scientific use of natural products. This aspect will involve the NEPAD SANBIO office and look at intellectual property issues as well as trans-boundary access and benefit-sharing.
Additional focus areas include the provision of training to the scientific community in research methodology, project management, research fund management and grant writing; linking the SABINA network to policy makers, farmers and entrepreneurs; establishing external peer review and evaluation procedures for SABINA; and extending the nodes to other institutions in SADC region.
20th Nov 2009
ACGT contributor, Prof Chrissie Rey of Wits University presented her Inaugural Lecture titled Plant Biotechnology: key to future food security in Africa on 19 October 2009. Representing the University’s School of Molecular and Cell Biology, Prof Rey’s talk focused on the background, promise and impact of biotechnology with a particular focus on cassava.
Plant Biotechnology offers innovative genetic solutions to improving food crops, in particular for resource-poor people on the sub-Saharan African continent. In 2003, the New Partnership for Africa’s Development (NEPAD) and the International Food Policy Research Institute championed the humble cassava as the key to future food security in Africa.
Professor Rey runs the Cassava Biotechnology Programme, which undertakes research to improve cassava germplasm with regards to resistance to Cassava Mosaic Disease (CMD). She is working in conjunction with Mozambique in developing cassava for the southern African region, and building capacity for cassava transformation.
19th Nov 2009
The ACGT was recently represented at the 2nd Stakeholders Meeting of the African Network for Drugs and Diagnostics Innovation (ANDI) to discuss plans for the first African-owned and managed innovation fund to finance drugs and diagnostics research. The meeting was held at the Medical Research Council (MRC) in Cape Town from 4 – 7 October 2009.
Administered through the World Health Organisation Special Programme for Research and Training in Tropical Diseases (WHO-TDR), the ANDI network concept was launched in Abuja, Nigeria, in 2008. Its main goal is promoting and sustaining African-led product research and development innovation though the discovery, development and delivery of affordable new tools, including those based on traditional medicines.
The meeting was attended by close to 300 researchers and other stakeholders – including African research institutions; ministries of health and science & technology; science academies; policy makers; donor agencies; health product manufacturers; NGOs; international organisations; Africans in the diaspora and others interested in supporting R&D in Africa. As part of this contingent, the ACGT was represented by its Director, Dr Jane Morris, through her role as chairperson of the steering committee of the South African Malaria Initiative (SAMI). Also present were ACGT contributors from the University of Pretoria and the Biosciences and Materials Science & Manufacturing units of the CSIR.
The three-day event featured over 100 scientific presentations on a wide range of topics to demonstrate the level of R&D innovation and capabilities in the African continent. In addition, the ANDI Task Force – comprising of members of WHO-TDR, the African Development Bank (ADB) and the European Commission – presented its report and the proposed ANDI strategy and business plan for 2010–2015, which was subsequently approved by meeting participants.
The plan calls for a R4.4 billion endowment fund in Africa that will generate a sustainable income of up to R230 million a year to support African drug and diagnostic innovation by funding direct research and networking between scientists, contributing to building a sustainable research environment and helping translate research into products.
The ANDI Task Force is now in discussion with various international and multilateral organisations to source funding, including the ADB – which has provisionally agreed to manage the funds. Initial funders will decide where on the continent ANDI will be based, and five research hubs are planned for Central, North, East, West, and Southern Africa.
For more information on the meeting, visit the ANDI 2009 website.
18th Nov 2009
The ACGT received a visit in early November from a representative of the USA-based Centre for Strategic and International Studies (CSIS) Africa Programme. The aim of the visit was to source expert views and information on the latest scientific developments in the field of GM crops.
The CSIS is currently conducting a major project on food security in Africa and looking at ways to better engage with African stakeholders. A key element of the project research involves relooking the debate over GMOs. To this end, Richard Downie – a CSIS Africa Programme research fellow, was in South Africa from 2 – 6 November to interview key individuals and organisations in the country to gauge the current status of the debate.
During his visit, Downie met with ACGT Director, Dr Jane Morris, to get an overview of the current status of and latest scientific developments in the South African GM field. The information contributed by the ACGT will be included in a draft report on which contributing organisations and individuals will be invited to comment.
According to Downie, the CSIS has undertaken this initiative in an attempt to afford African stakeholders an opportunity to have a voice in a discussion that has previously been dominated by those of Europeans and North Americans.
One of the world’s preeminent international policy institutions, the CSIS is a bipartisan, nonprofit organization headquartered in Washington, DC. CSIS conducts research and analysis and develops policy initiatives that look into the future and anticipate change. Its Africa Programme conducts centrist, activist, and forward looking research and analysis on major elements of U.S. policy toward Africa.