Projects
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To facilitate our ability to document structural variation caused by Transposons we have to generate accurate reference genomes in the plants that we use as parents in our transposon activation pipelines. To this end we are engaged in producing a number of de novo reference genomes for grapevine and Hops. We are adopting the use of both short-read Illumina based sequencing and ultra-long read sequencing using Oxford Nanopore Minion sequencing.
We are developing a reference genome for Hops to assist with identification of newly mobile transposons
De Novo Reference genome for Hops
We are currently in the process of generating a new reference assembly of the hop genome in a variety of particular interest to the New Zealand Hop industry. Unlike existing references for this species we are attempting this work in a triploid variety. This is a vital step to provide reference genomic information in the 'parents' of the populations we plan to produce which carry the new transposon polymorphisms we will launch in the same manner as we have for grapevine
We are developing a reference genome for Sauvignon blanc as part of a SSIF funded project to assist with identification of newly mobile transposons. This work will feed into a recently submitted MBIE Endeavour project that if funded will lead to the project being extended into the varietal.
De Novo reference genome for Sauvignon blanc
One of the biggest limitations of our work with transposons in grape is the lack of a reference genome in the varieties we are producing transposon activated populations in. To this end, in conjunction with Plant & Food Research Ltd., we are resequencing and generating heterozygous reference genome resources for both Sauvignon blanc clone UCD-1
We are developing a reference genome for Pinot noir as part of a SSIF funded project to assist with identification of newly mobile transposons
De novo reference genome for Pinot noir
As per the Sauvignon blanc project we are also producing a reeference genome for Pinot noir UCD-5