AboutThis learning module is designed to be used either as basic material for a class or as a self-tutorial. It is geared towards scientists or upper-level students who have a good background in biology and genetics, an awareness of recombinant DNA technologies (which are implied but not thoroughly discussed here), and at least some knowledge of the structure of DNA and DNA sequencing. Section 2 does include an overview of basic concepts, but is meant to be more of a refresher than to be all inclusive. Specifically, the module is aimed at plant breeders, molecular biologists, and other plant scientists who are on the fringe of, but not fully engaged in, genomics research. The idea is to provide this audience with information which will help them to better understand current research in the field and what implications it may have for them.
To accommodate different backgrounds and needs, the module is organized into four sections:
1. About genomics and getting started. This section describes how genomics arose, both conceptually and in terms of technological advances. It defines genomics and explains its potential and why it is so important to today's scientific research.
2. Genomics: Basic concepts. This section includes what is necessary to understand before it is possible to comprehend comparative genomics. It includes the genetic code, and definitions of key genomics concepts such as homology, synteny, orthology etc.
3. Methodologies and computation: Tools of comparative genomics. The longest and most intensive of the sections, this describes the use of databases, concepts and key software programs for sequence retrieval and alignment, methods for finding genes, the use of ESTs and other selective sequencing methods, and the study of gene expression using microarrays.
4. Applications and discoveries. Here, a few of the applications of the tools of comparative genomics are discussed, as well as the limitations of them, and what we have learned so far from this field of research. This includes lessons from the Arabidopsis sequencing project, comparative work in the grasses, and current understanding of the genome in terms of gene structure, the number of genes in a genome, and both gene function and the functionality of non-genic regions. Finally, ongoing research and possibilities of the future are discussed, as well as ethical considerations.
The topics are designed to include not simply the scientific concepts but also an understanding of the historical context and implications. Text boxes on some slides give supplemental facts and quotes that may help in understanding the context or simply be of interest.
At the end of each section is a list of resources for additional information specific to the topics in that section. A separate set of slides includes lists of resources for additional information on or beyond the overall topic of genomics and comparative genomics. A glossary is included, as well as a list of other helpful glossaries.