The comparison of the gene orders in a set of genomes can be used to infer their phylogenetic relationships and to reconstruct ancestral gene orders. For three genomes this is done by solving the "median problem for breakpoints"; this solution can then be incorporated into a routine for estimating optimal gene orders for all the ancestral genomes in a fixed phylogeny. For the difficult (and most prevalent) case where the genomes contain partially different sets of genes, we present a general heuristic for the median problem for induced breakpoints. A fixed-phylogeny optimization based on this is applied in a phylogenetic study of a set of completely sequenced protist mitochondrial genomes, confirming some of the recent sequence-based groupings which have been proposed and, conversely, confirming the usefulness of the breakpoint method as a phylogenetic tool even for small genomes.
%0 Journal Article
%1 Sankoff00
%A Sankoff, D
%A Bryant, D
%A Deneault, M
%A Lang, B F
%A Burger, G
%C Centre de recherches mathematiques, Universite de Montreal, Quebec. sankoff@crm.umontreal.ca
%D 2000
%J J Comput Biol
%K *Evolution; Biology; Cells; Computational DNA, Eukaryotic Genetic; Mitochondrial/*genetics; Models, Phylogeny from:davidjamesbryant
%N 3-4
%P 521--535
%R 10.1089/106652700750050925
%T Early eukaryote evolution based on mitochondrial gene order breakpoints.
%V 7
%X The comparison of the gene orders in a set of genomes can be used to infer their phylogenetic relationships and to reconstruct ancestral gene orders. For three genomes this is done by solving the "median problem for breakpoints"; this solution can then be incorporated into a routine for estimating optimal gene orders for all the ancestral genomes in a fixed phylogeny. For the difficult (and most prevalent) case where the genomes contain partially different sets of genes, we present a general heuristic for the median problem for induced breakpoints. A fixed-phylogeny optimization based on this is applied in a phylogenetic study of a set of completely sequenced protist mitochondrial genomes, confirming some of the recent sequence-based groupings which have been proposed and, conversely, confirming the usefulness of the breakpoint method as a phylogenetic tool even for small genomes.
@article{Sankoff00,
abstract = {The comparison of the gene orders in a set of genomes can be used to infer their phylogenetic relationships and to reconstruct ancestral gene orders. For three genomes this is done by solving the "median problem for breakpoints"; this solution can then be incorporated into a routine for estimating optimal gene orders for all the ancestral genomes in a fixed phylogeny. For the difficult (and most prevalent) case where the genomes contain partially different sets of genes, we present a general heuristic for the median problem for induced breakpoints. A fixed-phylogeny optimization based on this is applied in a phylogenetic study of a set of completely sequenced protist mitochondrial genomes, confirming some of the recent sequence-based groupings which have been proposed and, conversely, confirming the usefulness of the breakpoint method as a phylogenetic tool even for small genomes.},
added-at = {2009-01-28T01:17:14.000+0100},
address = {Centre de recherches mathematiques, Universite de Montreal, Quebec. sankoff@crm.umontreal.ca},
au = {Sankoff, D and Bryant, D and Deneault, M and Lang, BF and Burger, G},
author = {Sankoff, D and Bryant, D and Deneault, M and Lang, B F and Burger, G},
biburl = {https://www.bibsonomy.org/bibtex/21a767a748c4f12d386c8c08410af77c4/compevol},
crdt = {2000/12/07 11:00},
da = {20010301},
date-added = {2009-01-28 12:07:05 +1300},
date-modified = {2009-01-28 13:04:38 +1300},
dcom = {20010412},
doi = {10.1089/106652700750050925},
edat = {2000/12/07 11:00},
interhash = {e98b1313e401d642bccaa479bfeaf4cd},
intrahash = {1a767a748c4f12d386c8c08410af77c4},
issn = {1066-5277 (Print)},
jid = {9433358},
journal = {J Comput Biol},
jt = {Journal of computational biology : a journal of computational molecular cell biology},
keywords = {*Evolution; Biology; Cells; Computational DNA, Eukaryotic Genetic; Mitochondrial/*genetics; Models, Phylogeny from:davidjamesbryant},
language = {eng},
lr = {20061115},
mhda = {2001/04/17 10:01},
number = {3-4},
own = {NLM},
pages = {521--535},
pl = {UNITED STATES},
pmid = {11108477},
pst = {ppublish},
pt = {Journal Article; Research Support, Non-U.S. Gov't},
rn = {0 (DNA, Mitochondrial)},
sb = {IM},
so = {J Comput Biol. 2000;7(3-4):521-35.},
stat = {MEDLINE},
timestamp = {2009-01-28T01:50:10.000+0100},
title = {Early eukaryote evolution based on mitochondrial gene order breakpoints.},
volume = 7,
year = 2000
}