The comparison of four mitochondrial genomes reveals cytoplasmic male sterility candidate genes in cotton

Abstract

Background: The mitochondrial genomes of higher plants vary remarkably in size, structure and sequence content, as demonstrated by the accumulation and activity of repetitive DNA sequences. Incompatibility between mitochondrial genome and nuclear genome leads to non-functional male reproductive organs and results in cytoplasmic male sterility (CMS). CMS has been used to produce F₁ hybrid seeds in a variety of plant species.

Results: Here we compared the mitochondrial genomes (mitogenomes) of Gossypium hirsutum sterile male lines CMS-2074A and CMS-2074S, as well as their restorer and maintainer lines. First, we noticed the mitogenome organization and sequences were conserved in these lines. Second, we discovered the mitogenomes of 2074A and 2074S underwent large-scale substitutions and rearrangements. Actually, there were five and six unique chimeric open reading frames (ORFs) in 2074A and 2074S, respectively, which were derived from the recombination between unique repetitive sequences and nearby functional genes. Third, we found out four chimeric ORFs that were differentially transcribed in sterile line (2074A) and fertile-restored line.

Conclusions: These four novel and recombinant ORFs are potential candidates that confer CMS character in 2074A. In addition, our observations suggest that CMS in cotton is associated with the accelerated rates of rearrangement, and that novel expression products are derived from recombinant ORFs.

Keywords: Chimeric ORFs; Comparative genomics; Cytoplasmic male sterility; Gossypium; Mitochondrial genomes; Transcriptomes.

Fig. 1

Linear maps of the four cotton mitogenomes. Known protein-coding genes, tRNA and rRNA genes, and gene fragments are shown on the line. Genes on the right side and left side of the line are transcribed direct and inverted, respectively. Colors indicate genes by function: Complex I (nad; yellow), Complex II (sdh; green), Complex III (cob; yellowish green), Complex IV (cox; light pink), Complex V (atp; olive-green), ribosomal proteins (brown), maturase (matR; orange), other genes (ccm and tRNA; purple), intron (white)

Fig. 2

The size distribution of repetitive content by the number of repeat pairs and total repeat length. The X position is repeat size category, which contains more than 10 kb, 1–10 kb, 0.5–1 kb, 101–500 bp, 41–100 bp, 31–40 bp, 21–30 bp. The Y positions are number of repeats pairs (primary axis) and proportion of total repeat length (secondary axis). The (a), (b), (c), (d) present 2074A, 2074S, 2074B, E5903 mitogenome, respectively

Fig. 3

Differential expression of mt genes in 2074A, 2074B and F₁-A. Log2 transformations of the expression fold changes (2074B/2074A and F₁-A/2074A) are represented by bars. Y axis denotes the levels of transformed expression fold changes

Fig. 4

The probability of transmembrane domains of Aorf4, Aorf9, Aorf2 and Aorf28 gene products