Sequencing and comparing whole mitochondrial genomes of animals.
Comparing complete animal mitochondrial genome sequences is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. Not only are they much more informative than shorter sequences of individual genes for inferring evolutionary relatedness, but these data also provide sets of genome-level characters, such as the relative arrangements of genes, which can be especially powerful. We describe here the protocols commonly used for physically isolating mitochondrial DNA (mtDNA), for amplifying these by polymerase chain reaction (PCR) or rolling circle amplification (RCA), for cloning, sequencing, assembly, validation, and gene annotation, and for comparing both sequences and gene arrangements. On several topics, we offer general observations based on our experiences with determining and comparing complete mitochondrial DNA sequences.
Boore
Jeffrey L
JL
Evolutionary Genomics Department, Department of Energy Joint Genome Institute & Lawrence, Berkeley National Lab, Walnut Creek, California 94598, USA.
Macey
J Robert
JR
Medina
Mónica
M
D000818:Animals; D001483:Base Sequence; D003001:Cloning, Molecular / Q000379:methods; D017931:DNA Primers / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics* / Q000302:isolation & purification; D015321:Gene Rearrangement; D023281:Genomics / Q000379:methods* / Q000706:statistics & numerical data; D006801:Humans; D008969:Molecular Sequence Data; D021141:Nucleic Acid Amplification Techniques; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D012346:RNA, Transfer, Amino Acyl / Q000737:chemistry / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software
D017931:DNA Primers; D004272:DNA, Mitochondrial; D012346:RNA, Transfer, Amino Acyl