The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants

Abstract

The entire mitochondrial genome of rice (Oryza sativa L.), a monocot plant, has been sequenced. It was found to comprise 490,520 bp, with an average G+C content of 43.8%. Three rRNA genes, 17 tRNA genes and five pseudo tRNA sequences were identified. In addition, eleven ribosomal protein genes and two pseudo ribosomal protein genes were found, which are homologous to 13 of the 16 genes for ribosomal proteins in the mitochondrial genome of the liverwort (Marchantia polymorpha). A greater degree of variation in terms of presence/absence and integrity of genes was observed among the ribosomal protein genes and tRNA genes of rice, Arabidopsis and sugar beet. Transcription and post-transcriptional modification (RNA editing) in the rice mitochondrial sequence were also examined. In all, 491 Cs in the genomic DNA were converted to Ts in cDNA. The frequency of RNA editing differed markedly depending upon the ORF considered. Sequences derived from plastid and nuclear genomes make up 6.3% and 13.4% of the mitochondrial genome, respectively. The degree of conservation of plastid sequences in the mitochondrial genome ranged from 61% to 100%, suggesting that sequence migration has occurred very frequently. Three plastid DNA fragments that were incorporated into the mitochondrial genome were subsequently transferred to the nuclear genome. Nineteen fragments that were similar to transposon or retrotransposon sequences, but different from those found in the mitochondrial genomes of dicots, were identified. The results indicate frequent and independent DNA sequence flow to and from the mitochondrial genome during the evolution of flowering plants, and this may account for the range of genetic variation observed between the mitochondrial genomes of higher plants.

Multi-step formation, evolution, and functionalization of new cytoplasmic male sterility genes in the plant mitochondrial genomes

“…In plants, the large mitochondrial genomes contain more genes and putative ORFs; many of them are of unknown function. For example, in the mitochondrial genomes of O. rufipogon and O. sativa, besides the known functional genes, there are 32 and 21 putative genes (ORFs) of unknown function, respectively [21,27]. This study demonstrates that during the new gene origination process in the mitochondrial genomes, other non-CMS genes, together with the CMS genes, could also be generated.…”

“…However, orf314, which is present in many rice cultivars (Table 1), was not expressed in anthers and other tissues of Nip, except for its low-level expression in seedling roots ( Figure 3). This result could explain why orf314, which was previously annotated as orf288 [21] due to a sequencing error that resulted in a mis-identification of the start codon, does not cause CMS even though its ORF sequence is similar to that of WA314 (there are 13 aa differences between the encoded proteins) and can interact with COX11 (see below). Mitochondrial genes are often transcribed as multiple mRNA species with different transcription initiation sites driven by distinct promoters [22]; for example, WA352c has three transcripts, one co-transcribed with rpl5 (producing a dicistronic transcript with the rpl5 and WA352c ORFs) and two transcribed independently (producing monocistronic transcripts with the WA352c ORF only) [10].…”

Interactions of Mitochondrial and Nuclear Genes That Affect Male Gametophyte Development

“…The Boro CMS cytoplasm contains an ORF of 79 codons, termed orf79, which is similar to coxI at its N terminus (Figure 1). Of the first 28 predicted amino acids of ORF79, 19 are identical to those of rice cox1 as described in the complete rice mtDNA sequence (Notsu et al, 2002). Of particular interest is the 80% similarity of the remainder of ORF79 to the unidentified reading frame in sorghum A3 cytoplasm (Tang et al, 1999).…”

Genomics-based dissection of the cross-talk of chloroplasts with the nucleus and mitochondria in Arabidopsis

“…On the contrary, migration of chondrome-derived sequences to plastid DNA has not been described yet. Between 1% and 6% of the mitochondrial genomes of Arabidopsis thaliana, sugar beet and rice derive from plastid DNA, while retrotransposons seem to be the source of nucleus-derived mitochondrial DNA (Unseld et al, 1997;Kubo et al, 2000;Notsu et al, 2002). However, only very few of such promiscuous DNA sequences are functional, namely plastid-derived mitochondrial tRNA genes.…”