Sequencing and comparing whole mitochondrial genomes of animals

Jeffrey L. Boore, J. Robert Macey, Mónica Medina

Research output: Contribution to journalArticlepeer-review

193 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)311-348
Number of pages38
JournalMethods in enzymology
StatePublished - 2005

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology


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