H. Matthew Fourcade

Methods for Obtaining and Analyzing Whole Chloroplast Genome Sequences

During the past decade, there has been a rapid increase in our understanding of plastid genome organization and evolution due to the availability of many new completely sequenced genomes. There are 45 complete genomes published and ongoing projects are likely to increase this sampling to nearly 200 genomes during the next 5 years. Several groups of researchers including ours have been developing new techniques for gathering and analyzing entire plastid genome sequences and details of these developments are summarized in this chapter. The most important developments that enhance our ability to generate whole chloroplast genome sequences involve the generation of pure fractions of chloroplast genomes by whole genome amplification using rolling circle amplification, cloning genomes into Fosmid or bacterial artificial chromosome (BAC) vectors, and the development of an organellar annotation program (Dual Organellar GenoMe Annotator [DOGMA]). In addition to providing details of these methods, we provide an overview of methods for analyzing complete plastid genome sequences for repeats and gene content, as well as approaches for using gene order and sequence data for phylogeny reconstruction. This explosive increase in the number of sequenced plastid genomes and improved computational tools will provide many insights into the evolution of these genomes and much new data for assessing relationships at deep nodes in plants and other photosynthetic organisms.

The First Complete Mitochondrial Genome Sequences for Stomatopod Crustaceans: Implications for Phylogeny

We report the first complete mitochondrial genome sequences of stomatopods and compare their features to each other and to those of other crustaceans. Phylogenetic analyses of the concatenated mitochondrial protein-coding sequences were used to explore relationships within the Stomatopoda, within the malacostracan crustaceans, and among crustaceans and insects. Although these analyses support the monophyly of both Malacostraca and, within it, Stomatopoda, it also confirms the view of a paraphyletic Crustacea, with Malacostraca being more closely related to insects than to the branchiopod crustaceans.