title: Methods for obtaining and analyzing whole chloroplast genome sequences.
abstract: 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.
authors.affiliation: Section of Integrative Biology, The University of Texas at Austin, Institute of Cellular and Molecular Biology, Austin, Texas 78712-0253, USA.
authors.forename: Robert K
authors.initials: RK
authors.lastname: Jansen
authors.forename: Linda A
authors.initials: LA
authors.lastname: Raubeson
authors.forename: Jeffrey L
authors.initials: JL
authors.lastname: Boore
authors.forename: Claude W
authors.initials: CW
authors.lastname: dePamphilis
authors.forename: Timothy W
authors.initials: TW
authors.lastname: Chumley
authors.forename: Rosemarie C
authors.initials: RC
authors.lastname: Haberle
authors.forename: Stacia K
authors.initials: SK
authors.lastname: Wyman
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Alverson
authors.forename: Rhiannon
authors.initials: R
authors.lastname: Peery
authors.forename: Sallie J
authors.initials: SJ
authors.lastname: Herman
authors.forename: H Matthew
authors.initials: HM
authors.lastname: Fourcade
authors.forename: Jennifer V
authors.initials: JV
authors.lastname: Kuehl
authors.forename: Joel R
authors.initials: JR
authors.lastname: McNeal
authors.forename: James
authors.initials: J
authors.lastname: Leebens-Mack
authors.forename: Liying
authors.initials: L
authors.lastname: Cui
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D002736:Chloroplasts / Q000235:genetics*; D003001:Cloning, Molecular / Q000379:methods; D018742:DNA, Chloroplast / Q000235:genetics / Q000302:isolation & purification; D030541:Databases, Genetic; D056890:Eukaryota / Q000235:genetics; D019143:Evolution, Molecular; D023281:Genomics / Q000266:history / Q000379:methods* / Q000706:statistics & numerical data; D049673:History, 20th Century; D020407:Internet; D008969:Molecular Sequence Data; D021141:Nucleic Acid Amplification Techniques; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D010944:Plants / Q000235:genetics; D016133:Polymerase Chain Reaction / Q000379:methods; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software
chemical_list: D018742:DNA, Chloroplast; D010940:Plant Proteins