Comparisons among two fertile and three male-sterile mitochondrial genomes of maize

Abstract

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.

Figure 1.—

Linear representations of maize mitochondrial genomes. The relative positions of genes are indicated by horizontal lines, color coded by function, as indicated in the key at the bottom left. Cis-spliced exons are connected by a caret. tRNA genes are indicated by short lines. Transcription direction is down for genes on the right and up for those on the left of each genome bar. For very closely spaced genes, spacing has been increased for visibility. Arrowed boxes within each genome bar indicate large repeats (>0.5 kb), color coded according to the key at the bottom right, with arrowheads indicating orientation. Genes in repeats contain the suffix -1 or -2. Rectangular green boxes/lines indicate transferred plastid sequences. Genes in plastid sequences contain the suffix -cp. Scale is in kilobases.

Figure 2.—

Multiple rearrangements lead to small syntenic regions. The NA, C, S, and T mitochondrial genomes are arranged relative to the linearized NB map. NB gene positions are indicated by vertical lines colored as in Figure 1. Horizontal gray bars (A–F) indicate regions of synteny (15–66 kb) among all five maize mitochondrial genomes. Colored boxes indicate regions that are present in NB as repeats of >500 bp, using the color scheme of Figure 1. Some very closely spaced rearrangements may be even closer than indicated due to line separation requirements for visibility.

Figure 3.—

Conservation of maize mitochondrial genomic sequences. Multipip representation of the first 20 kb of the NB map. The region is typical in that sequences are either present and highly conserved or absent. This region is unusual in that large portions of the NB genome are not present in three of the genomes. Multipip (Schwartz et al. 2000, 2003) aligns the sequences of each taxon to the reference (NB), irrespective of the locations of those sequences in the other taxa, and plots them according to the percentage of identity to the reference genome (vertical scale). The solid block indicates a gene, open blocks indicate ORFs, and arrows indicate the direction of transcription.