University of Utah
Washington University
Universisty of Missouri
New genetic map of Zea mays mitochondrial genome (nb) derived from sequence data --Fauron, C, Gibson, M, Clifton, S, Minx, P, Spieth, J, Newton, K, Rugen, M A National Science Foundation-funded Plant Genome Project focused on the organization, evolution and expression of the mitochondrial genomes of maize and its relatives, has resulted in the preliminary data analysis presented here. Currently, six mitochondrial genomes within the genus Zea are being sequenced, including fertile (NB and NA genotypes) and male sterile (CMS-T and CMS-C genotypes) maize, Zea parviglumis (the probable progenitor of maize) and Zea perennis. In addition, the mtDNA sequences of related grasses, Tripsacum dactyloides and Sorghum bicolor, are being determined.

The sequencing of the Zea mays mays NB mitochondrial genome is now complete. The final assembly generated a circular map of 569,630 basepairs with an average G+C content of 43.9%. The size compares well with the previous restriction enzyme analyses (Fauron and Havlik, NAR 16:10395, 1988), which generated a map of 570kb.

The previous arbitrary start point of the NB map (shown in the last update published in MNL70:133, 1996) was defined at a SmaI site internal to the 5.2 kb repeat in NB. For sequence annotation purposes, it was decided that the start point should be located in a region devoid of any features (including repeats); therefore, a new starting point (labeled start on the figure) is the first base of the XhoI site located 5 to the previous SmaI start point (shown as an asterisk* on the figure). This region seems to be conserved among other maize cytotypes.

Sequence data can be found at the Washington University Genome Sequencing Center web site (, and additional information about this genome project can be found at our project web site (

Table 1. List of known genes for the mitochondrial genome of normal NB maize.
Genes Synonym Product
atp1   ATPase subunit 1
atp1   ATPase subunit 1
atp6   ATPase subunit 6
atp8 orfB ATPase subunit 8
atp9   ATPase subunit 9
ccmB ccb206 cytochrome c biogenesis B
ccmC ccb256 cytochrome c biogenesis C
ccmFC ccl1 cytochrome c biogenesis FC (2 exons)
ccmFN ccl1 cytochrome c biogenesis FN
cob   apocytochrome b
cox2    cytochrome c oxidase subunit 2 (2 exons)
cox3   cytochrome c oxidase subunit 3
coxI   cytochrome c oxidase subunit 1
mat-r   maturase
nad1 exon 1   exon1 of NADH dehydrogenase subunit 1
nad1 exon 1   exon1 of NADH dehydrogenase subunit 1
nad1 exons 2, 3   exons 2 & 3 nad1
nad2 exons 1, 2   exon 1 and 2of NADH dehydrogenase subunit 2
nad2 exons 3, 4, 5   exons 3, 4 and 5 of NADH dehydrogenase subunit 2
nad2 exons 4, 5   exons 4 and 5 of NADH dehydrogenase subunit 2
nad3   NADH dehydrogenase subunit 3
nad4    NADH dehydrogenase subunit 4 (4 exons)
nad4L   NADH dehydrogenase subunit 4L
nad5 exon 1, 2   exons 1 and 2 of NADH dehydrogenase subunit 5
nad5 exon 3   exon3 of NADH dehydrogenase subunit 5
nad5 exon 4, 5   exons 4 and 5 of NADH dehydrogenase subunit 5
nad6   NADH dehydrogenase subunit 6
nad7   NADH dehydrogenase subunit 7 (5 exons)
nad9   NADH dehydrogenase subunit 9
orf25   protein orf25 
orfX   protein orfX
pseudo trnL    pseudo tRNA-Leu (2 exons)
rpl16   ribosomal protein L16
rps1   ribosomal protein S1
rps12   ribosomal protein S12
rps13   ribosomal protein S13
rps2A   ribosomal protein S2
rps2B   ribosomal protein S2
rps3    ribosomal protein S3
rps4   ribosomal protein S4
rps7   ribosomal protein S7
rrn18   18S ribosomal RNA
rrn26   26S ribosomal RNA
rrn5   5S ribosomal RNA
trnC   tRNA-Cys 
trnD   tRNA -Asp
trnD   tRNA-Asp
trnD   tRNA-Asp
trnE   tRNA-Glu
trnE   tRNA-Glu
trnF   tRNA-Phe
trnH   tRNA-His
trnI   tRNA-Ile
trnL   tRNA-Lys
trnL   tRNA Leu
trnL   tRNA Leu (2 exons)
trnM   tRNA-Met
trnM   tRNA-Met
trnM   tRNA-Met
trnN   tRNA -Asn
trnN   tRNA-Asn
trnP   tRNA-Pro
trnP   tRNA-Pro
trnQ   tRNA-Gln
trnR   tRNA-Arg
trnR   tRNA-Arg
trnS   tRNA-Ser
trnS   tRNA-Ser
trnY   tRNA-Tyr


Table 2. List of repeats larger than 0.5 kb.
Repeats Size (bp) copy1 start copy1 end copy2 start copy2 end
17 kb - inverted 16870 113649 130518 59371 42502
15 kb -direct 14946 453701 468636 522638 537573
11 kb - direct 11092 164398 175489 63778 74869
5.3 kb - direct 5277 245065 250334 1555 6824
0.7 kb - direct 689 21428 22152 541232 541950
0.5 kb - direct 549 13415 13963 499862 500410

Figure 1. The mitochondrial genome of normal NB maize. The outside circular ring shows the known genes. Genes that are encoded on the plus strand are located on the outside and genes encoded in the minus strand on the inside. The middle circle shows SmaI and XhoI restriction fragments sites derived from the sequence. Start (XhoI site-see text) is located at the 12 o'clock position. The inside ring shows the homologous regions between maize NB mtDNA and the maize chloroplast genome.

Please Note: Notes submitted to the Maize Genetics Cooperation Newsletter may be cited only with consent of the authors.

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