Archives

• Funding for joint science projects announced (Thursday, 23 July 2009)
  Prof Neil Gemmell of Otago and Dr Kristy Demmers of AgResearch will use genomic comparisons between three sequenced non-placental mammals (platypus, opossum and wallaby) and 17 sequenced placental mammals (including humans, cows and mice) to identify the key genes which help form the placenta during pregnancy. The research seeks to shed light on the genetic basis of placenta formation, which may lead to reductions in early pregnancy failure and increased offspring growth and survival, with implications for both human and animal reproductive health.
• Australian First: Kangaroo Genome Mapped (18 Nov. 2008)
  Australian researchers are launching the world first detailed map of the kangaroo genome, completing the first phase of the kangaroo genomics project.
• Alien Possums Gobbling New Zealand Forests, Birds
  With its bushy tail, tall ears, and pink nose, Australia's brush-tailed possum could be the poster child for cute critters.
  But here in New Zealand - where millions of the animals eat native plants, trees, and birds by the bushel - the marsupials are possums non grata.
• Platypus genome mapping boon for human and livestock researchers (Thursday, 8 May 2008)
  In decoding the genome of the platypus, a team of researchers from the United States, Australia, England, Germany, Israel, Japan, Spain and New Zealand has revealed important information that will enhance our understanding of other mammals and may lead to the development of new approaches to combat disease in livestock and humans and enhance livestock productivity
• Opossum makes the cover on Nature (Thursday, 10 May 2007)
  "Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences" by Mikkelsen TS et al.
  We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes....
• First marsupial genome decoded (Wednesday, 9 May 2007)
  Scientists sequence genome of opossum Monodelphis domestica; comparison with human highlights junk DNA as creative force in genome evolution
• Researching prostate problems (Wednesday, 20 December 2006)
  The brush tailed possum may well carry a key that will help scientists develop new treatments for, and perhaps eventually prevent, some prostate problems in men.
• Possum field trials a success (Wednesday, 20 December 2006)
  A new threat to possums is on the horizon, with the successful release of genetically marked parasites in a field trial at Kahurangi National Park at the top of the South Island.
• Potential tool for possum population control (Thursday, 9 November 2006)
  AgResearch scientists have found two enteroviruses in wild possums that could be used to carry vaccines for possum biocontrols such as contraception.
• Possum in a pickle (Monday, 30 October 2006)
  A recent trip to the UK to present breakthrough research in possum biocontrol led to an unlikely meeting for AgResearch scientist Dr Gail Shuttleworth.
• Public Possumbase Opossum Gbrowse Update (August 2006)
• Opossum genome browser is now available! (July 2006)
• New contig build and BLAST database available (June 2006)
• Contigs available for download (June 2006)
• AgResearch collects samples
• New Approach To Funding Possum Research Hailed As Triumph (Media Release, 9 December 2004)

Public Possumbase Opossum Gbrowse Update (August 2006)

The public Possumbase Opossum Gbrowse has just been updated with several new tracks with the alignments for non-opossum mRNA and refseq genes provided by UCSC and a new build of the possum ESTs:

• Non-Opossum RefSeq Genes
  This track shows known protein-coding genes from organisms other than opossum, taken from the NCBI mRNA reference sequences collection (RefSeq). The mRNAs were aligned against the opossum genome using blat; those with an alignment of less than 15% were discarded. When a single mRNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.5% of the best and at least 25% base identity with the genomic sequence were kept.
• Non-Opossum mRNAs from Genbank
  This track displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank from organisms other than opossum. The mRNAs were aligned against the opossum genome using translated blat. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only those alignments having a base identity level within 1% of the best and at least 25% base identity with the genomic sequence were kept.
• CS40 contig build of the AgResearch Possum ESTs

Example here: http://www.possumbase.org.nz/cgi-bin/gbrowse/mondom4/?reset=1

Opossum genome browser is now available! (July 2006)

AgResearch created a database of expressed sequence tags (ESTs) for the Brushtail possum (Trichosurus vulpecula). The ESTs were compared (mapped) against the genomic sequence of the closest available relative, the gray short-tailed opossum Monodelphis domestica.
 

The opossum contigs have been sequenced and assembled by the Broad Institute. The current build is called mondom4 (January 2006) and is shown in the topmost line (track) of the genome browser (GBrowse). Other available tracks are:

• Human RefSeq Proteins (Release 18, July 2006)
  This track shows known protein-coding genes from human, taken from the NCBI reference sequences collection (RefSeq). Human RefSeq proteins were compared against the opossum contigs using TBLASTN
• Ensembl Genes (Genebuild, June 2006)
  This track shows the opossum genome as annotated by Ensembl. Ensembl Genes were compared against the opossum contigs using BLAT. The Ensembl team has the following to say about their genebuild: "The gene set for Opossum was built using a modified version of the standard Ensembl genebuild pipeline. The species-specific sequence resources (opossum cDNA and protein) are very limited, so the vast majority of gene models are based on genewise alignments of proteins from other species. Most of the proteins being aligned were from species genetically distant to opossum. To improve the accuracy of models generated from these proteins, the genewise alignments were made to stretches of genomic sequence rather than to 'miniseqs'. Opossum and human cDNAs were aligned and used to add UTRs to the genewise predictions where possible. The gene models were assessed by generating sets of potential orthologs to genes from other mammalian species. Potentially missing predictions and partial gene predictions were identified by examining the orthologs, and exonerate used to build new gene models for these based on the human ortholog peptide sequence."
• Chicken Reference mRNAs (Release 18, July 2006)
  This track shows known chicken mRNAs, taken from the NCBI reference sequences collection (RefSeq). Chicken mRNAs were compared against the opossum contigs using GMAP.  Chicken-human alignments can be used to detect exons (Thomas et al., 2003 Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424: 788-93. )
• Marsupial mRNAs
  This track shows all known marsupial mRNAs, taken from the NCBI reference sequences collection (RefSeq). Marsupial mRNAs were compared against the opossum contigs using GMAP
• AgResearch Possum ESTs
  This track shows all of AgResearch"s possum ESTs mapped against the opossum contigs using GMAP

See the below figure for a taxonomic overview:

Try GBrowse.

New contig build and BLAST database available (June 2006)

A new build, CS40, containing all Trichosurus vulpecula mRNA at June 2006 has been assembled into contigs and is available as a BLAST database from our BLAST page

Contigs available for download (June 2006)

A file containing all Trichosurus vulpecula mRNA at June 2006 assembled into contigs and annotated via blast against nr protein is available for download from the "Data Downloads" link.
The file is in FASTA format with each description line containing:

• DNA composition.
• Library expression of contig.
• Top hit against nr protein.
• Expectation value.

AgResearch collects samples

After a video conference with the Possum project committee on the subject of libraries and tissues, it was decided to have Clontech generate 8 normalised libraries of the following type:

• Ovarian pooled various ovarian tissue and cycle-stages (W)
• Immune (W)
• Gut small/large intestine, Peyers patch (I)
• Kidney (I)
• Liver (I)
• Reproductive tract (female) (W)
• Brain/Pituitary (I)
• Embryonic/developmental (W) 

AgResearch Wallaceville (W) to collect 4 samples and AgResearch Invermay (I) to collect 4 samples (with help of Grant Butt of Otago University).

Invermay samples are likely to be sent to Clontech early May 2005. Collection of Wallaceville samples is likely to be completed by November 2005 (delay due to breeding/developmental cycles). Approximately 6 weeks should be allowed for library construction.

Overall, 150,000 sequences are to be generated. The distribution of these across the libraries will be dependent on feedback from our initial gene-discovery-rate assessments made on the early sequencing.

New Approach To Funding Possum Research Hailed As Triumph (Media Release, 9 December 2004)

AgResearch says the announcement today of multi-million dollar funding for a new research initiative to find better ways to control possums is a triumph because it provides long-term financial support for expert scientists to collaborate with each other and end-users to find an effective solution.

The Foundation for Research, Science and Technology today announced it will provide $2.5 million per annum for up to eight years for a possum control research programme led by AgResearch in collaboration with Landcare Research.

AgResearch Chief Executive, Dr Andy West, says the funding initiative is unprecedented.

The novel aspect of the new funding approach is the length of the funding contract. It allows much greater stability and job security for the scientists involved.

Long-term funding for this collaborative approach by research experts, who will be working with end-users, should lead to an enormous pay-off for New Zealand, with the real winner being New Zealand's environment. It will help ensure possum control methods can be much more effectively implemented, said Dr West.

The new funding approach also ensures regular evaluation of the quality of outcomes being achieved. This means even better accountability for the tax-payers" dollars invested.

The Foundation's support for the new collaborative approach means we will work hand-in-glove with the organisations who most need a solution for possum control including the Department of Conservation, the Animal Health Board, Ministry of Agriculture and Forestry and regional councils. They will have significant input into the research programme.

The Foundation is trialling this new process for investing in research programmes known as "outcome based investments" (OBIs) which places emphasis on the final outcomes of research. The new investment contracts are longer than previously negotiated and a key feature is the level of collaboration between researchers and end users.

Further information:
Allanah James
AgResearch Manager Corporate Affairs
029 983 3989;
03 989 33989