TY - JOUR
T1 - Sequencing and comparing whole mitochondrial genomes of animals
AU - Boore, Jeffrey L.
AU - Macey, J. Robert
AU - Medina, Mónica
N1 - Funding Information:
We are grateful to lab members and guests who have worked to refine many of these bench techniques, including Ronald Bonett, David Engle, Jonathan Fong, H. Matthew Fourcade, Matthew Fujita, Kevin Helfenbein, Jennifer Kuehl, Kirsten Lindstrom, Susan Masta, Jenna Morgan, Rachel Mueller, Dan Mulcahy, James Parham, Gabriela Parra, Marco Passamonti, Marcos Perez-Losada, Ernesto Recuero, Inaki Ruiz-Trillo, Wes Savage, Renfu Shao, Brian Simison, Matthias Stoeck, Tori Takaoka, and Yvonne Vallès. Thanks to Douda Bensasson, Jeff Froula, Allen Haim, and Stacia Wyman for work on databases and software for determining, cataloging, and comparing gene arrangements. Thanks to the National Science Foundation for support (DEB-0089624, EAR-0120646, DEB-9807100, DEB-9726064). This is LBNL-55278; part of this work was performed under the auspices of the U.S. Department of Energy, Office of Biological and Environmental Research, by the University of California, Lawrence Berkeley National Laboratory, under contract no. DE-AC03-76SF00098.
PY - 2005
Y1 - 2005
N2 - 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.
AB - 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.
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U2 - 10.1016/S0076-6879(05)95019-2
DO - 10.1016/S0076-6879(05)95019-2
M3 - Article
C2 - 15865975
AN - SCOPUS:19944400426
SN - 0076-6879
VL - 395
SP - 311
EP - 348
JO - Methods in enzymology
JF - Methods in enzymology
ER -