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Originally published as Genetics Published Articles Ahead of Print on July 29, 2007.
Genetics, Vol. 177, 1173-1192, October 2007, Copyright © 2007
doi:10.1534/genetics.107.073312
Comparisons Among Two Fertile and Three Male-Sterile Mitochondrial Genomes of Maize
James O. Allen*,
Christiane M. Fauron
,
Patrick Minx
,
Leah Roark*,
Swetha Oddiraju*,
Guan Ning Lin*,
Louis Meyer*,
Hui Sun,
Kyung Kim,
Chunyan Wang,
Feiyu Du,
Dong Xu
,
Michael Gibson,
Jill Cifrese,
Sandra W. Clifton and
Kathleen J. Newton*,1
* Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, Eccles Institute of Genetics, University of Utah, Salt Lake City, Utah 84112, Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri 63108 and Department of Computer Science and Christopher S. Bond Life Science Center, University of Missouri, Columbia, Missouri 65211
1 Corresponding author: Division of Biological Sciences, 324 Tucker Hall, University of Missouri, Columbia, MO 65211.
E-mail: newtonk{at}missouri.edu
We have sequenced five distinct mitochondrial genomes in maize: two fertile cytotypes (NA and the previously reported NB) and three cytoplasmic-male-sterile cytotypes (CMS-C, CMS-S, and CMS-T). Their genome sizes range from 535,825 bp in CMS-T to 739,719 bp in CMS-C. Large duplications (0.5–120 kb) account for most of the size increases. Plastid DNA accounts for 2.3–4.6% of each mitochondrial genome. The genomes share a minimum set of 51 genes for 33 conserved proteins, three ribosomal RNAs, and 15 transfer RNAs. Numbers of duplicate genes and plastid-derived tRNAs vary among cytotypes. A high level of sequence conservation exists both within and outside of genes (1.65–7.04 substitutions/10 kb in pairwise comparisons). However, sequence losses and gains are common: integrated plastid and plasmid sequences, as well as noncoding "native" mitochondrial sequences, can be lost with no phenotypic consequence. The organization of the different maize mitochondrial genomes varies dramatically; even between the two fertile cytotypes, there are 16 rearrangements. Comparing the finished shotgun sequences of multiple mitochondrial genomes from the same species suggests which genes and open reading frames are potentially functional, including which chimeric ORFs are candidate genes for cytoplasmic male sterility. This method identified the known CMS-associated ORFs in CMS-S and CMS-T, but not in CMS-C.
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