Yokobori, S., Watanabe, Y., and Oshima, T. (2003). Mitochondrial genome of Ciona savignyi (Urochordata, Ascidiacea, Enterogona): Comparison of gene arrangement and tRNA genes with Halocynthia roretzi mitochondrial genome. J. Mol. Evol. 57, 574–587. Yost, H. J., Phillips, C. R., Boore, J. L., Bertman, J., Whalen, B., and Danilchik, M. V. (1995). Relocation of mitochondrial RNA to the prospective dorsal midline during Xenopus embryogenesis. Dev. Biol. 170, 83–90. Zardoya, R., and Meyer, A. (2001). On the origin of and phylogenetic relationships among living amphibians. Proc. Natl. Acad. Sci. USA 98(13), 7380–7383. [20] Methods for Obtaining and Analyzing Whole Chloroplast Genome Sequences By Robert K. Jansen,Linda A. Raubeson,Jeffrey L. Boore, Claude W. dePamphilis,Timothy W. Chumley,Rosemarie C. Haberle, Stacia K. Wyman,Andrew J. Alverson,Rhiannon Peery, Sallie J. Herman, H. Matthew Fourcade,Jennifer V. Kuehl, Joel R. McNeal,James Leebens-Mack, and Liying Cui Abstract During the past decade, there has been a rapid increase in our under- standing of plastid genome organization and evolution due to the availabil- ity of many new completely sequenced genomes. There are 45 complete genomes published and ongoing projects are likely to increase this sam- pling 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 ge- nome 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 de- tails 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 recon- struction. 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. 348 comparing macromolecules [20] Copyright 2005, Elsevier Inc. All rights reserved. METHODS IN ENZYMOLOGY, VOL. 395 0076-6879/05 $35.00