Posted by eucagen on May 5, 2006
Brasília, May 25, 2006
The Brazilian Network of Eucalyptus Genome Research, better known as the GENOLYPTUS project, will make important contributions to advance the prospects of having a draft sequence of the Eucalyptus genome. Convened at the annual meeting held in Porto Alegre between April 26 and 28, the steering committee of the Genolyptus project decided that it will give full support to the international initiative of submitting a proposal to the Joint Genome Institute (JGI), the sequencing powerhouse of the US Department of Energy, to generate a draft sequence of the Eucalyptus grandis genome.
On behalf of over 80 research scientists, breeders and graduate students from 14 private forest based companies, six universities and EMBRAPA, all part of the Brazilian project, Dr. Dario Grattapaglia, coordinator of GENOLYPTUS pointed out that “ This initiative will certainly represent a major advancement toward an increased understanding of tree biology and will accelerate the development of molecular breeding technology for increased sustainability of forest based operations worldwide that produce pulp, paper, energy and wood. We are ready to help make this project a success, and we call on all other eucalypt research organizations internationally to join us in supporting this initiative”.
The formation of an international collaborative network around the Eucalyptus genome started some three years ago at an IUFRO Tree Biotechnology conference in Umea, Sweden in 2003. After a series of meetings in Australia and Japan in the last two years, DOE scientist, Dr. Jerry Tuskan, announced at the Tree Biotechnology conference held in Nov 2005 in Pretoria, South Africa, that JGI would consider a proposal for a Eucalyptus genome sequencing project in the context of the “Genomes to Energy” focus area of the recently launched Laboratory Science Program at JGI.
Contingent upon the approval of a Eucalyptus grandis draft sequencing project by JGI, the GENOLYPTUS network, through its participating institutions, will contribute the following genomic resources to assist the assembly and annotation phases of the genome project:
1) A reference linkage map for Eucalyptus with over 400 microsatellite markers derived from genomic sequences and ESTs mapped on existing full-sib pedigrees;
2) The construction of a publicly available, high coverage, BAC genomic library and the assembly of a fluorescent fingerprinting-based physical map in collaboration with the Arizona Genomics Institute;
3) The annotated GENOLYPTUS sequence database comprising around 20,000 unigenes derived from the sequencing of over 20 cDNA libraries.
Besides the genomic resources, GENOLYPTUS, through one of its participating companies Suzano, will be privileged to provide a top performance selfed tree of Eucalyptus grandis to be used as the target genome to be sequenced and physically mapped. “A more homozygous genome should greatly facilitate the genome assembly. Additionally, this tree has been cloned and will be made fully available to the public in the form of in vitro micropropagules” indicated Dr. Grattapaglia.
The availability of a draft sequence of the Eucalyptus grandis genome will generate extraordinary opportunities for reaching a much higher level of understanding of the unique biology of forest trees and will have obvious implications in eucalypt based production forestry as well as environmentally relevant issues such as carbon sequestration and water use efficiency in the tropics
The detailed genome sequencing proposal to be submitted by June 2006 is now being finalized by a group of scientists from several countries world-wide, led by Dr. Zander Myburg from South Africa, the coordinator of the international Eucalyptus Genome Network.
Posted by eucagen on January 15, 2006
Background
Towards the end of 2004, it was announced to the general Eucalyptus research community that Kazusa DNA Research Institute in Japan had commenced with the sequencing of the Eucalyptus genome, using DNA from an E. camaldulensis clone (CPT1) donated by Oji Paper. This generated much excitement in the Eucalyptus research community and stimulated many questions related to the public release of the genome sequence and the availability of biological materials used in the genome sequencing effort. It was clear that the sequencing of the Eucalyptus genome would create several opportunities for postgenomic research, especially where genomic resources could be generated that would make the genome sequence more accessible to the general community. In addition to seeking answers regarding the release of the genome sequence and availability of biological materials, there existed a need for the community to get to know the team that is sequencing the eucalypt genome and to communicate the specific needs of the community to this team. It was therefore decided to invite a small number of researchers to Japan for what was essentially a fact-finding mission to explore the possibilities for postgenomic research in Eucalyptus. One of the objectives of this Eucalyptus Genome Research Planning meeting was to prepare a draft genome research plan that would be presented and discussed at the next business meeting of the International Eucalyptus Genome Consortium that will take place during the IUFRO Tree Biotechnology 2005 Meeting in Pretoria, South Africa (6-11 November 2005, www.iufro.up.ac.za).
Aim of the meeting
The ongoing Eucalyptus genome sequencing project in Japan and future opportunities for the IEuGC were discussed at a Eucalyptus Genome Breakfast Meeting on Wednesday 9 November 2005 (06:30 – 08:30 am). The aim of the meeting was to critically assess the future role of the IEuGC and to nominate a team of international coordinators that will be responsible for various proposed future activities of the Consortium.
Agenda
Date: Wednesday, 9 November 2005
Venue: IUFRO Tree Biotechnology 2005, Sanlam Auditorium, University of Pretoria, Pretoria, South Africa
06:30 Eucalyptus Genome Breakfast (sponsored by the Forest Molecular Genetics Programme, University of Pretoria)
07:00 Business Meeting of the IEuGC Consortium
- Welcoming (Zander Myburg)
- The E. camaldulensis genome sequencing project in Japan (Takashi Hibino, Zander Myburg)
- Invitation to submit a proposal to DOE-JGI for a public Eucalyptus genome sequencing project (Jerry Tuskan)
- Future role of the IEuGC (Open discussion, Zander Myburg)
- Nomination/Election of international coordinators for the IEuGC
08:25 Meeting ends
Outcomes of the Meeting (Meeting Report)
The Eucalyptus Genome Breakfast Meeting was attended by 44 Eucalyptus researchers and other interested scientists at the IUFRO Tree Biotechnology 2005 meeting. The meeting was hosted and chaired by Dr. Zander Myburg.
EUCAGEN Business Meeting at IUFRO 2005 Tree Biotech Meeting
E. camaldulensis genome sequencing project:
The meeting started with a presentation by Dr. Takashi Hibino of Oji Paper who presented an overview of the E. camaldulensis genome sequencing project ongoing at KAZUSA DNA Research Institute. This project was initiated in July 2004 and is funded by the Chiba state prefecture. The project leader at KAZUSA is Dr. Satoshi Tabata. The aim of the project is to generate a genome representative sequence of an E. camaldulensis clone (CPT1) donated by Oji Paper. This is a clone that has been selected for high transformation efficiency and will in future become available as a possible Eucalyptus transformation model (’lab rat’). The basic genome sequencing approach has been a 1X whole genome shotgun sample sequencing (Phase 1 - completed - aimed at obtaining basic genome information such as repetitive sequence content) followed by shotgun sequencing of BAC clones that are selected to be low in repetitive DNA (Phase 2 - ongoing at 1X per year). The sample sequencing phase revealed relatively low repetitive DNA content (approx 4%). Dr. Hibino highlighted the following opportunities for collaboration with the international community:
- Access to the draft genome sequence
Access to the draft genome sequence will be based on specific collaborative proposals (i.e. researchers who wish to have access to the draft E. camaldulensis genome sequence may propose specific collaborative projects with KAZUSA DNA Research Institute).
- High-resolution genetic mapping of CPT1
No genetic linkage maps are available yet for this seedling clone. Oji Paper is inducing flowering in order to obtain pollen for making crosses. A high-resolution genetic linkage map will allow anchoring of the genome sequence onto the genetic linkage map.
- Microarray resources
Oji Paper has already produced a 22K Agilent oligo array, which is available for collaboration projects. In addition, Oji Paper, KAZUSA and Agilent will produce a 44K oligoarray that will be available late in 2006 (based on CPT1 genome sequence and the EST database of Oji Paper).
- Genetic transformation model (’lab rat’)
Oji Paper is willing to supply the transformation protocols and CPT1 tissue culture plantlets to Consortium members in order to establish this genotype as a possible transformation model system.
- A central bioinformatics resource for Eucalyptus
This will probably be the most important resource for the wider Eucalyptus research community. It is not yet clear where such a resource will reside. KAZUSA will release the completed E. camaldulensis genome sequence through a public database, but the release date has not been scheduled yet.
Invitation to submit a proposal to DOE-JGI for a public Eucalyptus genome sequencing project
Dr. Jerry Tuskan announced that DOE-JGI will be sequencing a number of plant genomes as part of its Laboratory Science Program (LSP). He encouraged the Consortium to submit a proposal for the sequencing of the genome of a Eucalyptus tree species. If successful, the sequencing project could be completed as early as 2007. The proposal (more details here) should detail (A) the taxonomic importance of Eucalyptus tree species, (B) the scientific interest in the Eucalyptus genome and (C) the economic importance of Eucalyptus. The Eucalyptus research community should nominate the most appropriate species and genotype for genome sequencing.
Preparation for a possible DOE-JGI Eucalyptus genome sequencing project:
The rest of the meeting was focused on preparations for a possible public genome sequencing project by DOE. The target species was a matter of debate, as well as the most appropriate genotype. The following tentative decisions were taken:
- Species and genotype to be sequenced
Two obvious candidates for a public genome sequencing project are E. grandis and E. globulus. Despite strong support for E. globulus from Australian researchers at the meeting (and its smaller genome size) it was decided that E. grandis would be supported as target for genome sequencing by DOE-JGI. Reasons for this include the wider use of this species for plantation forestry and greater scope for making interspecific hybrid pedigrees for genome mapping. It was also proposed that a selfed (S1) genotype of E. grandis should be targeted for sequencing, because this would reduce problems related to high heterozygosity during genome assembly. One of the member companies of the Genolyptus consortium offered to donate tissues from an S1 individual for this purpose.
- Physical genome mapping
It was decided that Consortium members will pursue the physical mapping of the E. grandis genome, as well as the E. globulus genome. (Note: Dario Grattapaglia has subsequently obtained a quote from Arizona Genomics Institute for the construction of BAC libraries for E. grandis and E. globulus (approx 50 000 clones each) and for the fluorescent fingerprinting of the BAC clones). The E. grandis BAC clones will also be made available to JGI for BAC end sequencing. So far, preliminary support has been obtained for the E. grandis BAC library and fingerprinting (see Project page)
- Genetic linkage mapping
The strong emphasis on tree improvement in Eucalyptus and scope for molecular breeding of eucalypts warrant investment in high-density, high-resolution genetic linkage maps that can be used to anchor the genome sequence assembly and to generate an integrated genetic and physical mapping framework. This will facilitate rapid chromosome walking and isolation of genes underlying QTLs or major gene effects. It was decided that Consortium members should pursue the construction of such genetic linkage maps in specific collaborative efforts. This may be a way to link E. globulus genome information (especially the growing amount of QTL data for this species) to the E. grandis genome sequence and potentially to an E. globulus physical map (when support for such a map can be found). A proposal to generate high-density genetic linkage maps of an E. globulus and E. grandis individual has been submitted in Australia (see Project page).
- Preparation of a proposal to DOE-JGI for the sequencing of the E. grandis genome
The deadline for this proposal has been extended to June 2006, which is the earliest that the peer-review mechanism for large-scale sequencing proposals under the DOE-JGI Laboratory Science Program will be in place. More information on the DOE proposal preparation process is available here.
