Preface
Genomics can be defined as the study of the structure, function and diversity of
genomes, genome being the collective term for all the genetic information contained
in a particular organism. The difference between genomic approaches and classical biological approaches is essentially one of scale, the aim of genomics being to
extend analyses that were originally limited to one or a small number of genes to
large numbers of genes or even to the complete set that make up a genome. One
consequence of this is that it is not always easy to define where classical approaches
end and genomics begins, and this has even led to suggestions that there is no essential difference between the two types of approach. This is an extreme view however
and, as the examples given in this book will illustrate, the need to develop highthroughput methodologies adapted to the analysis of multiple gene sets has led to
considerable technical advances and to the development of new ways of thinking
about biology.
Genomics as a discipline began with the first attempts to obtain large-scale
sequence data for individual organisms, either by sequencing the genomic DNA
or, where this was not practical, by sequencing large numbers of cDNAs. 1 This
was initially a very costly process and consequently early efforts were focused
on laboratory model organisms such as the bacteria Escherichia coli and the yeast
Saccharomyces cerevisiae followed by the animal species Caenorhabditis elegans
and Drosophila melanogaster and the plant Arabidopsis thaliana. The availability of extensive sequence data for these organisms then facilitated the development
of additional genomic tools such as microarray systems for the analysis of gene
expression and collections of sequence-tagged mutants.
Marine organisms were very poorly represented amongst these early genomic
models and were to some extent left behind as the application of genomic
approaches to several terrestrial models allowed an acceleration of our understanding of the biology, ecology and evolutionary history of these species. The situation
has been rectified to a certain extent in recent years, essentially due to the reduced
cost of DNA sequencing and associated enhanced capacity for analysis of very large
datasets. The reduction in costs has not only allowed the application of genomic
1 See the glossary for definitions of technical terms.
v
Genomics can be defined as the study of the structure, function and diversity of
genomes, genome being the collective term for all the genetic information contained
in a particular organism. The difference between genomic approaches and classical biological approaches is essentially one of scale, the aim of genomics being to
extend analyses that were originally limited to one or a small number of genes to
large numbers of genes or even to the complete set that make up a genome. One
consequence of this is that it is not always easy to define where classical approaches
end and genomics begins, and this has even led to suggestions that there is no essential difference between the two types of approach. This is an extreme view however
and, as the examples given in this book will illustrate, the need to develop highthroughput methodologies adapted to the analysis of multiple gene sets has led to
considerable technical advances and to the development of new ways of thinking
about biology.
Genomics as a discipline began with the first attempts to obtain large-scale
sequence data for individual organisms, either by sequencing the genomic DNA
or, where this was not practical, by sequencing large numbers of cDNAs. 1 This
was initially a very costly process and consequently early efforts were focused
on laboratory model organisms such as the bacteria Escherichia coli and the yeast
Saccharomyces cerevisiae followed by the animal species Caenorhabditis elegans
and Drosophila melanogaster and the plant Arabidopsis thaliana. The availability of extensive sequence data for these organisms then facilitated the development
of additional genomic tools such as microarray systems for the analysis of gene
expression and collections of sequence-tagged mutants.
Marine organisms were very poorly represented amongst these early genomic
models and were to some extent left behind as the application of genomic
approaches to several terrestrial models allowed an acceleration of our understanding of the biology, ecology and evolutionary history of these species. The situation
has been rectified to a certain extent in recent years, essentially due to the reduced
cost of DNA sequencing and associated enhanced capacity for analysis of very large
datasets. The reduction in costs has not only allowed the application of genomic
1 See the glossary for definitions of technical terms.
v