The recent revolution in molecular biology has spread through every field of biology including systematics and evolution. Researchers can now analyze the genomes of different species relatively quickly, and this is generating a great deal of data and theories about relationships between taxa as well as how they originated and diversified. Org

Mitochondria and chloroplasts are eukaryotic organelles that evolved from bacterial ancestors and harbor their own genomes. The gene products of these genomes work in concert with those of the nuclear genome to ensure proper organelle metabolism and biogenesis. This book explores the forces that have shaped the evolution of organelle genomes and the expression of the genes encoded by them. Some striking examples of trends in organelle evolution explored here are the reduction in genome size and gene coding content observed in most lineages, the complete loss of organelle DNA in certain lineages, and the unusual modes of gene expression that have emerged, such as the extensive and essential mRNA editing that occurs in plant mitochondria and chloroplasts. This book places particular emphasis on the current techniques used to study the evolution of organelle genomes and gene expression.

Mitochondria and chloroplasts are eukaryotic organelles that evolved from bacterial ancestors and harbor their own genomes. The gene products of these genomes work in concert with those of the nuclear genome to ensure proper organelle metabolism and biogenesis. This book explores the forces that have shaped the evolution of organelle genomes and the expression of the genes encoded by them. Some striking examples of trends in organelle evolution explored here are the reduction in genome size and gene coding content observed in most lineages, the complete loss of organelle DNA in certain lineages, and the unusual modes of gene expression that have emerged, such as the extensive and essential mRNA editing that occurs in plant mitochondria and chloroplasts. This book places particular emphasis on the current techniques used to study the evolution of organelle genomes and gene expression.

New techniques in molecular biology have brought spectacular new insights into the study of evolution at the molecular level. This book presents the resulting relatively new concept of "molecular phylogeny", with an overview of current accomplishments and the future direction of research on organelle origin and evolution and the biology of the "higher cell".

'The mind unlearns with difficulty what has long been impressed upon it. ' Seneca Reductionism, is, without question, the most successful analytical approach available to the experimental scientist. With the advent of techniques for cloning and sequencing DNA, and the development of a variety of molecular probes for localizing macromolecules in cells and tissues, the biologist now has available the most powerful reductionist tools ever invented. The application of these new technologies has led to a veritable explosion of facts regarding the types and organization of nucleotide sequences present in the genomes of eukaryotes. These data offer a level of precision and predictability which is unparalleled in biology. Recombinant DNA techniques were initially developed to gather information about the structure and organization of the DNA sequences within a genome. The power and potential of these techniques, however, extend far beyond simple data collection of this kind. In an attempt to use the new technology as a basis for analyzing development and evolution, attention was first focused on the topic of gene regulation, an approach that had proven so successful in prokaryotes. It is now clear that this has not been an adequate approach. Lewin (1984) has quoted Brenner as stating 'at the beginning it was said that the answer to the understanding of development was going to come from a knowledge of the molecular mechanisms of gene control. I doubt whether anyone believes this any more.

Genomics and Evolution of Eukaryotic Microbes synthesizes the rapidly emerging fields of eukaryotic diversity and genome evolution. Eukaryotes (cells with nuclei) evolved as microbes and have existed on Earth for approximately two billion years. The tremendous diversity of eukaryotic microbes (protists) is often overlooked by those who study the macroscopic eukaryotic lineages: plants, animals, and fungi. Yet, eukaryotic microbes are of critical importance to ecosystems, human health, and our desire to understand biodiversity on Earth. By bringing together groundbreaking data from genome studies of diverse eukaryotic microbes, this book elucidates the many novelties among eukaryotic genomes and provides a single resource for otherwise widely dispersed information. Eukaryotic microorganisms impact both our health and our environment. These organisms include some of the deadliest known pathogens such as Plasmodium falciparum, a causative agent of malaria, and Entamoeba histolytica an agent of dysentery. Eukaryotic microbes also play a significant role in environments through their involvement in global biogeochemical cycles. Such roles are perhaps best exemplified by the coccolithophores, including the species Emiliania huxleyi, which can create 'blooms' in the oceans that are visible from outer space (i.e. as large as the state of Alaska). Despite the great importance and breadth of eukaryotic microbes (the vast majority of major ukaryotic lineages are microbial, with plants, animals and fungi representing just three of an estimated 60-200 major lineages), our understanding of their diversity and phylogeny is only now rapidly expanding, in part bolstered by genomic studies. This book presents analyses and interpretations from experts in the field. Recent advances, particularly in DNA sequencing technologies, have made eukaryotic microbes more accessible to genome analyses. Unravelling the wealth of information on eukaryotic genomes will invariably revolutionize our understanding of eukaryotes, including their physiology, systematics, and ecology.

This book represents a unique combination of recently-emerged information on eukaryotic microbes, evolution and genomics. Eukaryotes, cells with nuclei, evolved as microbes and have existed on Earth for approximately 2 billion years. Although currently relatively understudied, eukaryotic microorganisms are of critical importance to ecosystems (through their involvement in global biogeochemical cycles), human health (they include some of the deadliest pathogens), and our desire tounderstand global biodiversity. Recent advances, particularly in DNA sequencing technologies, are making eukaryotic microbes more accessible through genome analyses. Insights from these studies are challenging previously held theories of genome evolution, based on studies of a limited number of plants,animals and fungi.