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...

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Bibliographic Details
Published in:	Methods in enzymology Vol. 395; p. 348
Main Authors:	Jansen, Robert K, Raubeson, Linda A, Boore, Jeffrey L, dePamphilis, Claude W, Chumley, Timothy W, Haberle, Rosemarie C, Wyman, Stacia K, Alverson, Andrew J, Peery, Rhiannon, Herman, Sallie J, Fourcade, H Matthew, Kuehl, Jennifer V, McNeal, Joel R, Leebens-Mack, James, Cui, Liying
Format:	Journal Article
Language:	English
Published:	United States 2005
Subjects:	Amino Acid Sequence Base Sequence Chloroplasts - genetics Cloning, Molecular - methods Databases, Genetic DNA, Chloroplast - genetics DNA, Chloroplast - isolation & purification Eukaryota - genetics Evolution, Molecular Genomics - history Genomics - methods Genomics - statistics & numerical data History, 20th Century Internet Molecular Sequence Data Nucleic Acid Amplification Techniques Phylogeny Plant Proteins - genetics Plants - genetics Polymerase Chain Reaction - methods Repetitive Sequences, Nucleic Acid Sequence Analysis, DNA - methods Software
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Summary:	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.
ISSN:	0076-6879
DOI:	10.1016/S0076-6879(05)95020-9