New Zealand forestry enters the genomics era - towards a genome sequence of radiata pine

Authors: Phillip L. Wilcox, Lucy J. Macdonald
Publication: New Zealand Journal of Forestry, Volume N.Z.J.For. 2015, Issue N.Z.J.For. 60(1) 2015, pp 17-22, May 2015
Publisher: New Zealand Institute of Forestry

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Abstract: The number of species for which an entire genetic code or genome has been sequenced is rising steeply. The first sequence of the human genome was announced in June 2000, 10 years after the project started. Since then genome sequencing has become both increasingly affordable, with the advent of cheap high-throughput DNA sequencing, and more technically feasible with advances in data analyses. Significant efforts have been made worldwide to sequence the genomes of an everincreasing number of organisms including the mouse, chimpanzee, rice, maize and many others (Ellegren, 2014). Once the genetic code of an organism has been deciphered, the way the knowledge is used can have profound effects. The human genome sequence has accelerated the development of a multitude of medical diagnostics and treatments, as well as providing new insights into human biology, disease, evolution and culture (Koboldt et al., 2013; Hood & Rowen, 2013). Black cottonwood (Populus trichocarpa Torr. and Gray) was the first forest tree species to be sequenced (Tuskan et al., 2006). More recently, the first genome sequences have been published of the following conifers: Norway spruce (Picea abies (L.) H. Karst), white spruce (Picea glauca Moench) (Birol et al., 2013; Nystedt et al., 2013) and loblolly pine (Pinus taeda L.) (Neale et al., 2014). The Eucalytus grandis W. Hill genome, another non-conifer species, has also been recently released (Myburg et al., 2014). Scion, with assistance from other organisations, has begun sequencing the huge megagenome of Pinus radiata D. Don, New Zealand’s most commercially important tree species. The first working draft assembly will be completed next year. As with all other large genome assemblies, this first working draft will only be a partially complete genome and is the start of a longer endeavour. Due to the nature and complexity of large genomes in general, and conifer genomes in particular, to complete and fully understand the genome will require input from a larger international community of researchers. Nonetheless, a partially completed genome, when combined with other resources, will be a powerful tool to inform other research. This paper discusses the basic concepts of genome sequencing, considers how the radiata pine genome sequence could be used, and the possible consequences for the New Zealand forest industry.

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