With the advent of affordable next-gen sequencing, we have launched an ambitious effort to bring genomics to the research, conservation, and management of tropical trees. In order to explore the greatest range of possibilities, we chose to start with whole genome shot-gun sequencing on the Illumina platform. The sequencing has all been done at the Michael Smith Genome Sciences Center in British Columbia, Canada. One of the main challenges of this approach for tropical biology is the lack of closely related ‘model’ organisms to use as reference genomes for assembly and analysis. While this limitation makes a finished physical map of the entire genome impossible, initial results indicate that a substantial portion of the genome can be assembled and analyzed without an existing reference. The development of open source de novo assembly software has been a major advance in this regard. While most analytic approaches rely upon the re-assembly of the short DNA fragments into larger contigs, we have also developed two techniques for the direct analysis of the data, completely without assembly, treating the DNA sequence data as a virtual tube of highly fragmented DNA. Using these rapidly advancing technologies, we hope to ‘leapfrog’ genetic research of some of the most poorly understood organisms in the world into the forefront.
We are currently working on four different projects. Two of these projects are related to the development of DNA fingerprinting techniques for the enforcement of international trade regulations and the sustainable management of remaining populations. The other two projects are aimed at diverse and ecologically important genera in the Asian tropics. We hope to employ a ‘framework species’ approach, where several exemplar species are chosen because they define the phenotypic and geographic boundaries around basic ecological and evolutionary questions. The genomes of these species are sequenced and comparative analyses can be used to discover the informative genomic differences in the context of these questions.
DNA tools to determine the legality of international trade in tropical timbers
We are now studying two endangered species of tropical tree (Gonystylus bancanus and Intsia palembanica). We are developing these genetic resources in association with Certisource, the National University of Malaysia, Global Forestry Services, and Federal Research Institute for Rural Areas, Forestry and Fisheries (Germany). The discovery of geographic and individual genetic markers will allow accurate and objective tracking of wood through the supply chain, from the forest to the consumer. We hope to develop techniques which can be used for wood at any point along the supply chain, from the log pond to the showroom.
Applying a ‘framework species’ in tropical ecology and evolution
We are focusing on two genera, Lithocarpus (Fagaceae) and Ficus (Moraceae). These two genera present a wide range of interesting questions, which will be explained some other time…
