Plant Physiology 136:3486-3503 (2004)
© 2004 American Society of Plant Biologists
GENOME ANALYSIS
Sequence and Comparative Analysis of the Maize NB Mitochondrial Genome1,[w]
Sandra W. Clifton*,
Patrick Minx,
Christiane M.-R. Fauron,
Michael Gibson2,
James O. Allen,
Hui Sun,
Melissa Thompson3,
W. Brad Barbazuk,
Suman Kanuganti,
Catherine Tayloe,
Louis Meyer,
Richard K. Wilson and
Kathleen J. Newton
Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri 63108 (S.W.C., P.M., H.S., R.K.W.); University of Utah, Eccles Institute of Genetics, Salt Lake City, Utah 84112 (C.M.-R.F., M.G.); Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (J.O.A., M.T., S.K., C.T., L.M., K.J.N.); and Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (B.B.)
The NB mitochondrial genome found in most fertile varieties of commercial maize (Zea mays subsp. mays) was sequenced. The 569,630-bp genome maps as a circle containing 58 identified genes encoding 33 known proteins, 3 ribosomal RNAs, and 21 tRNAs that recognize 14 amino acids. Among the 22 group II introns identified, 7 are trans-spliced. There are 121 open reading frames (ORFs) of at least 300 bp, only 3 of which exist in the mitochondrial genome of rice (Oryza sativa). In total, the identified mitochondrial genes, pseudogenes, ORFs, and cis-spliced introns extend over 127,555 bp (22.39%) of the genome. Integrated plastid DNA accounts for an additional 25,281 bp (4.44%) of the mitochondrial DNA, and phylogenetic analyses raise the possibility that copy correction with DNA from the plastid is an ongoing process. Although the genome contains six pairs of large repeats that cover 17.35% of the genome, small repeats (20–500 bp) account for only 5.59%, and transposable element sequences are extremely rare. MultiPip alignments show that maize mitochondrial DNA has little sequence similarity with other plant mitochondrial genomes, including that of rice, outside of the known functional genes. After eliminating genes, introns, ORFs, and plastid-derived DNA, nearly three-fourths of the maize NB mitochondrial genome is still of unknown origin and function.
1 This work was supported by the National Science Foundation Plant Genome Research Program (grant no. DBI–0110168).
2 Present address: Magpie Systems, 4085 South 300 West, Salt Lake City, UT 84107.
3 Present address: Genome Science and Technology Program, University of Tennessee, Knoxville, TN 37996.
[w] The online version of this article contains Web-only data.
www.plantphysiol.org/cgi/doi/10.1104/pp.104.044602.
* Corresponding author; e-mail sclifton{at}watson.wustl.edu; fax 314–286–1810.
Received April 16, 2004;
returned for revision August 25, 2004;
accepted August 25, 2004.
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