Sequence and comparative analysis of the maize NB mitochondrial genome

Abstract

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.

Figure 1.

Circular map of the maize NB mitochondrial genome generated from sequence data. Known protein-coding, tRNA and rRNA genes, and gene fragments are shown on the outside circle. Colors indicate genes by function: Complex I (nad; yellow), Complex III (cob; orange), Complex IV (cox; purple), Complex V (atp; red), cytochrome assembly (ccm; light blue), ribosomal proteins (dark blue), maturase (white), other ORFs (gray), rRNA and tRNAs (black), and genes transferred from the chloroplast (green). Single-letter designations indicate tRNAs. Large repeats are color coded within the outer ring. Regions homologous to R1 and S2/R2 are indicated by gray blocks. The middle circle indicates positions of ORFs (≥99 amino acid predicted sizes). The inner ring shows regions of chloroplast homology with matches of at least 80% identity and lengths of at least 100 bp (green).

Figure 2.

Three regions of plastid DNA found in the mitochondrial genome. A, Locations of plastid sequences in the plastid and mitochondrial genomes. Lower axis is plastid genome coordinates; the plastid IR extends from 82 kb to 105 kb. Boxes indicate regions of ctDNA present in the NB mtDNA; numbers above them are their coordinates (kb) in the mitochondrial genome. Lighter boxes are the components of the 4.1-kb region. Below the boxes are the MultiPip representations of sequence similarity between the maize plastid genome and the maize mitochondrial genome. Vertical scale is 50% to 100%. B, Alignment of sequences relevant to the 4.1-kb segment of ctDNA present in the maize and rice mitochondrial genomes. Purple and green colored boxes indicate regions A and C in section A that recombined to form the 4.1-kb segment. Lower alignment is an enlargement of the region of overlap between the A and C regions, showing their relationship to rpl23. Purple-to-green gradients indicate areas where recombination occurred, but where definitive assignment to A or C is not possible. C, Parsimony phylogenetic tree for the 4.1-kb plastid sequence in the mitochondrion. Depicted branch lengths for Arabidopsis and tobacco are substantially shorter than their actual lengths because highly divergent and thus unalignable sequences were deleted from the data set. Parsimony/maximum likelihood bootstrap values for 100 replicates are indicated on branches.

Figure 3.

Superfamilies of SDR elements. A, Elements in Superfamily 13 common to all 4 members of the superfamily are bold and underlined. Each line in Superfamily 13 is a family containing from 2 to 4 members (column 3) of length 25 to 36 bp (column 2). In the entire superfamily there are a total of 12 repeats covering 349 bp. B, The SDR families of Superfamily 2 are composed of members that themselves contain tandemly arranged pentanucleotide simple sequence repeat sequences, here alternately highlighted by bold underlining. C, Superfamily 1 possesses a sliding consensus, ultimately joining 30 families, and is the largest superfamily in the maize NB genome. Σ bp is the number of bp included in all copies of the repeats in each SDR family. All members of a given family are at least 90% identical in sequence.

Figure 4.

MultiPipMaker analysis of several sequenced mitochondrial genomes. Maize NB is the reference genome to which the mitochondrial genomes of rice, sugar beet, Arabidopsis, M. polymorpha, and R. americana, and the plastid genome of maize (Maier et al., 1995) are compared. At the top of the figure, positions of NB genes are marked by black boxes, and their orientations are shown by arrows. A number directly below the gene designation indicates the exon number. ORFs are shown as numbers (for their predicted sizes), and tRNAs are indicated by their single-letter designations. The full MultiPipMaker analysis is included in supplemental materials (Supplemental Fig. 1). A, A relatively gene-rich region of the NB genome, showing conservation of mitochondrial genes and a 10-kb region of sequence similarity between maize NB and rice that includes noncoding DNA. B, A gene-poor region of NB mtDNA, showing very little similarity with other mitochondrial genomes. C, The intron and 3′ region of cox2 is conserved with rice but becomes less so with increasing phylogenetic distance. A region at 547 kb with no obvious feature is highly conserved between maize NB and rice. D, 4.1 kb of plastid-derived DNA present in both maize NB and rice mtDNAs; plastid-derived genes are italicized.

Figure 5.

Composition of maize NB and rice mitochondrial genomes. A, Comparison of types of sequences. For each type (e.g. exons), the number of nucleotides accounted for is based upon genome complexity (520 kb for maize and 363 kb for rice). Percentage of each genome is also indicated. B, Amount of DNA present in repeats (90% identity criterion). The amount present in the total genome is shown for each species (570 kb for maize and 491 kb for rice).

Figure 6.

MultiPip comparison of the first 40 kb of the maize NA mitochondrial genome with the complete mitochondrial genomes of maize NB and rice, as well as the maize plastid genome. Representations are as for Figure 4. I to IV identify large regions of homology between NA and NB.