World first radiata pine genome draft completed
At 25 billion base pairs, the radiata pine genome is an enormous puzzle that had never been put together until now. A research team led by Scion scientists completed a world first draft assembly of the radiata pine genome, marking the beginning of a new era of precision forestry for a species critically important to New Zealand.
This is important work that will underpin the future of the New Zealand forest industry.
The process was not without its challenges. The research team led by Dr Emily Telfer since 2015, and including Dr Richard Winkworth from Massey University and Dr Jill Wegrzyn from the University of Connecticut, were initially going to use the genome of the already sequenced loblolly pine from the USA as a reference to help put the radiata pine genome together. But because the radiata genome is so large, it had to be broken down into 100 smaller data sets, which would have extended the computer assembly run time to eight years.
Not to be discouraged, Emily and the Forest Informatics Computer Science team, led by Melissa Evans, set about acquiring one of the most powerful computers in New Zealand. With six terabytes of RAM, 72 2.4Ghz Xeon cores and 250 terabytes of direct attached storage, a de novo draft assembly was completed in September 2017.
“The potential benefits of unlocking the radiata pine genome are game changers for forestry. With better understanding of the genome, scientists can begin to develop markers for breeding and gene selection, carry out functional genomics for understanding complex gene interaction and begin comparative evolutionary studies,” says Emily. “This technology will also give scientists the ability to respond faster to biosecurity incursions and the environmental challenges of climate change.
“And it’s great news for the forestry industry as this means accelerated breeding with genomic selection, and, after further study and annotation of the genome, we can begin to understand how specific genes impact a tree’s performance and resilience. This is important work that will underpin the future of the New Zealand forest industry.”
The genome assembly began in 2013 led by Dr Phil Wilcox and Lucy Macdonald, with input and guidance from the international conifer genomics community. The assembly also benefits the international scientific and forest growing community. Radiata pine is the backbone of New Zealand’s forestry industry. It is also the most widely planted pine in the world and is grown commercially in Australia, Chile, Spain and South Africa.
The research team is now working to reduce the number of pieces of the puzzle by joining long sequences together. A type of sequencing technology called PacBio is being used to run the process. The next steps are to identify genes and regulatory regions that influence the growth and resilience of radiata pine.