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An introduction to ultra-high-throughput DNA sequencing technologies and their application in genetics and functional genomics
Eucalypt forest trees supply high quality raw material for the pulp, paper and wood industries, and have been identified as important role-players in the search for renewable energy resources. Eucalypts are hardy, fast growing and have a high dry matter production and resprouting potential, which makes them one of the most widely used tree species in industrial hardwood plantations (Forrest and Moore, 2008; Rengel et al., 2009). In recent years, the global forestry industry has experienced a steady shift in location from the northern hemisphere to the tropics and subtropics, where it is actively competing with food crops for land space needed for expansion (Grattapaglia and Kirst, 2008). In South Africa, a recent report from the South African Department of Water Affairs and Forestry (DWAF) indicated that 1.25 million hectares (1.1%) of South Africa’s total land area are covered by forestry plantations, of which 36% (450 000 hectares) are planted with Eucalyptus species (http://www2.dwaf.gov.za/webapp/Documents/FSA-Abstracts2009.pdf). The economic importance of plantation trees as renewable energy and biomass producing crops makes them excellent candidates for genetic improvement studies.
Eucalypts have a high fiber count of uniform nature, a sought after property that has created high demands in the pulp, paper and raw wood industries (Moore et al., 2008). Large numbers of genes are affecting wood formation in forest trees, and have been actively investigated by various research groups focusing on key properties, such as wood density, pulp yield, cellulose content, fiber length and lignin content (for a review of the state of Eucalyptus breeding see Myburg et al., 2005). Improvements to biomass yield and fiber quality with improved breeding programs and the direct application of biotechnology advances to crop development will play increasingly important roles in the future of the eucalypt forestry industry.
Woody biomass has been identified as important in the search for renewable energy resources. The United States Department of Energy (US-DOE) announced in 2007 their goal to reduce the usage of gasoline in the United States by 20% by the year 2017 (http://genomicscience.energy.gov/biofuels/). To achieve this, an expansion of the annual renewable fuel supply from a variety of plant materials, including grasses, woodchips and agricultural wastes needs to occur. The bioenergy initiative activelysupported the research community in successfully determining the genomic sequence of the Populus trichocarpa genome (Tuskan et al., 2006) and the Eucalyptus grandis genome (version 1.0 released in January 2011, http://www.phytozome.net) by the Joint Genome Institute (JGI). It is expected that fast growing, short-rotation woody crops such as Eucalyptus and Populus and their respective hybrids will contribute up to 30% of the biomass of the so-called ”energy crops” (Hinchee et al., 2009).
Chapter 1. An introduction to ultra-high-throughput DNA sequencing technologies and
their application in genetics and functional genomics
1.1. Introduction .
1.2. Ultra-high-throughput DNA sequencing platforms .
1.3. High-throughput DNA sequencing applications in genetics and functional genomics
1.4. Core analyses associated with ultra-high-throughput Illumina sequence mRNA-Seq data
1.5. High-throughput DNA sequencing data management
1.6. Problem Statement .
1.7. Specific research questions and aims .
Chapter 2. A core bioinformatics workflow environment for ultra-high-throughput
transcriptome data analysis .
Chapter preface .
2.1. Introduction .
2.2. Materials and methods
2.3. Results and discussion .
2.4. Conclusion
Chapter 3. The assembly and annotation of a draft transcriptome sequence of a Eucalyptus hybrid tree
Chapter Preface .
3.1. Introduction .
3.2. Materials and methods .
3.3. Results .
3.4. Discussion
3.5. Conclusion
Chapter 4. Eucspresso: Towards the development of a Eucalyptus genome and transcriptome information resource
Preface
4.1. Introduction .
4.2. Materials and methods .
4.3. Results and discussion
4.4. Conclusion
Chapter 5. Concluding Discussion
Appendix A. Bioinformatics workflow
Appendix B. Extendinator
Appendix C. Transcriptome assembly
Appendix D. De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree
produced by Illumina mRNA-Seq
Bibliography
