Rice Mitochondrial Genome

Rice Mitochondrial Genome Page

Here is the rice mitochondrial genome information page. We have read the entire rice mitochondrial genome in 2002, and shown detailed information here since 2003.

Publication: Mol. Genet. Genomics 2002 268: 434-445.

Entire Sequence	Physical Map	Genes (including RNA editing information)	Plastid-like Seq in mt Genome
Nuclear-like Seq in mt Genome	tRNA	Genomic Dynamism	Link

Entire Sequence

You can refer entire sequence of rice mitochondrial genome in DDBJ, EMBL and Genbank. We registered the sequence into two accessions, AB076665 and AB076666, in accordance with the guide of DDBJ. You also can get the genome sequence from here.

Entiere Sequence Data (490,520 bp)

Physical Map

Fig. 1 Physical map of rice mitochondrial genome

The total length of the rice mitochondrial genome was 490,520 bp, with an average G+C content of 43.8%. High G+C values were observed in three rDNA regions (rrn5, rrn18 and rrn26) and in the nad7 region, whereas low values were found in the plastidderived regions. There were six major pairs of directly repeated sequences in the rice mitochondrial genome, having lengths of 3.1, 4.1, 4.7, 23.0, 46.1 and 46.6 kb, respectively. Altogether, repeated sequences account for 127.6 kb, or 26.0%, of the entire genome.

Genes (including RNA editing information)

A total of 35 genes for known proteins, three ribosomal RNAs (rrn5, rrn18, rrn26), two pseudo ribosomal protein genes, 17 kinds of tRNAs, and five pseudo tRNAs were identified. No apparent strand bias was observed for the presence of genes. ORFs capable of encoding more than 150 amino acids were sought based on universal codon usage. In addition to the 35 protein-coding genes mentioned, 19 other ORFs were deduced; however, only 10 of these were found to be transcribed. No indication of RNA editing was observed in any of these 10 ORFs.

Gene information

Plastid-like Seq in mt Genome

The mitochondrial DNA of higher plants contains many sequences of plastid origin (Lonsdale et al. 1983). In the rice mitochondrial genome, seventeen stretches of plastid-like sequences, ranging in size from 32 bp to 6653 bp, were identified. These sequences comprised 22,593 bp, accounting for 6.3% of the mitochondrial genome. The plastid-like sequences were first identified by Nakazono and Hirai (1993). Unseld et al. (1997) also reported that the Arabidopsis mitochondrial genome contains fragments of plastid genes, such as psbD, ORF350, rbcL, trnM, and ndhB genes, ranging in size from 30 to 930 bp. The sequences that have migrated from the plastid to the mitochondrial genome are not the same in rice and Arabidopsis. By comparing the plastid fragments in the mitochondrial genome of rice with the plastid genome sequence, substitutions were identi.ed at 1140 positions out of 22,593 bp. Deletions and insertions were found at 45 and 23 sites, respectively. Thus deletions have occurred more frequently than insertions in the plastid sequences present in the mitochondrial genome. The degree of similarity of each sequence to the plastid genome varied from 61% to 100%, suggesting that migration of plastid sequences into the mitochondrial genome has occurred very frequently. All of the protein-coding genes of plastid origin in rice mitochondria seems to be non functional, as a result of many sequence alterations and the absence of RNA editing. In contrast, seven tRNAs of plastid origin are likely to be functional.

Plastid-like sequence in mitochondrial genome

Nuclear-like Seq in mt Genome

Fig. 2 Schematic representation of the distribution of 25mitochondrial fragments on chromosomes 1 and 4 of the rice nuclear genome.

In order to identify sequences of the mitochondrial genome that have been transferred to or from the nuclear genome, the BLASTN program was employed, using a threshold value of 300 bp. Sequences longer than 300 bp that showed signi.cant homology to the nuclear genome of rice were identified (Fig. 1). Forty-three sequences were found which covered 13.4% (48,060 bp) of the rice mitochondrial genome. Similarity to the nuclear genome ranged from 65% to 100%. Six fragments (rps2, cob, rrn26, rrn5, part of rrn18, and native trnS) contained mitochondrial sequences that had already been identified in the mitochondrial genome. These might have migrated from the mitochondrial to the nuclear genome. Of the 43 fragments, 11 and 14 fragments were identified in a single BAC clone (Accession No. AL117265) derived from rice chromosome 4 and a single PAC clone (Accession No. AP003418) from rice chromosome 1, respectively. The order of the 14 and the 11 fragments of nuclear genome di.ered strikingly from the order of the corresponding sequences in the mitochondrial genome (Fig. 2). For example, fragment No. 4 of chromosome 1 is closely located between Nos. 10 and 32, whereas these three fragments are located far apart in the mitochondrial genome. Nuclear sequences might have been transferred to the mitochondrial genome or vice versa. Extensive reshu.ing of the fragmented DNA is indicated in either case, although the mechanism of such events and the orientation of sequence .ow is not clearly understood. Stupar et al. (2001) have reported the presence of a 630 kb mitochondrial sequence on Arabidopsis chromosome 2. Such a long DNA insertion has so far not been found in the rice nuclear genome.
Mitochondrial sequences that showed similarity to nuclear retrotransposon and transposon sequences have been identi.ed in Arabidopsis and sugar beet (Knoop et al. 1996; Kubo et al. 2000b), but not in liverwort (Oda et al. 1992). In the rice mitochondrial genome, BLASTX analysis detected fragments (of various sizes) of 16 retrotransposons and three transposons (Table 5). The sequences varied in length (from 96 to 1555 bp) and the elements were dispersed in the rice mitochondrial genome. The degree of amino acid sequence similarity to the protein products of their nuclear counterparts was also very variable. No similarity was found among the elements from rice, Arabidopsis, and sugar beet. These results suggest independent transfer of the 19 rice sequences from the nucleus to the mitochondrial genome during the evolution of flowering plants.
Part of a DNA-directed DNA polymerase-related sequence was also identified in the rice mitochondrial genome (positions 372,642-373,210). Our analysis found that a similar sequence was present in the sugar beet mitochondrial genome but not in Arabidopsis or liverwort mitochondrial genome. This implies either loss of the DNA polymerase-related sequence from the Arabidopsis mitochondrial genome or independent acquisition of the sequence by rice and sugar beet mitochondrial genomes in the course of flowering plant evolution.

Sequence fragments from retrotransposon and transposon in the rice mitochondrial genome

tRNA

Twenty-three tRNA sequences for 17 species of amino acid were identified in the rice mitochondrial genome (Table 3). Of these, 12 tRNAs (C, E, I, P, Q, D, K, S, S, Y, M and fM) were of mitochondrial origin and the other 11 (H, W, F, N, M, C, V, I, P, R and S) were considered to be plastid-like tRNAs because they display high homology (97.3-100%) to sequences in the plastid genome (Hiratsuka et al. 1989). Of the 23 sequences identified, tRNAs for V, I, R, C and P were considered to be non-functional pseudogenes. Thus, functional tRNAs for six amino acids (G, A, V, L, T and R) are absent from the rice mitochondrial genome (Table 3), although tRNAs for 20 amino acids are necessary for protein synthesis in mitochondria. These results suggest that the missing tRNAs are supplied by the nuclear genome. Thus, 11 tRNAs involved in mitochondrial biogenesis in rice are of mitochondrial origin, seven are of plastid origin and probably six are of nuclear origin. With respect to trnS and trnM, both mitochondrial and plastid-like tRNAs were identified in the rice mitochondrial genome. Miyata et al. (1998) have reported that the plastid-like trnS and trnM are transcribed and processed in rice mitochondria. Further investigation is needed to elucidate the relative levels of expression of the two types of trnS and trnM.

In Table 3, the tRNA gene content of the rice mitochondrial genome is compared with those in Arabidopsis and sugar beet. Differences were observed with respect to presence/absence or origin of tRNAs for G, V, I, C, M, F, D, Y and R among these three plant species. It has been reported that the liverwort mitochonmdrial genome encodes 27 tRNAs, none of which are of plastid origin (Oda et al. 1992). These results strongly imply frequent tRNA gene transfer from the mitochondrial genome to the nuclear genome, as well as the incorporation of plastid DNA sequences into the mitochondrial genome during the evolution of flowering plants.

Differences in the status of tRNAs encoded by the mitochondrial genomes

Genomic Dynamism

Fig. 3 Schematic representation of sequence transfer events during the evolution of the rice mitochondrial genome.

Six sequences (1.5 kb, 1.2 kb, 0.9 kb, 0.1 kb and two of 0.2 kb) were identified in all three rice genomes (Table 6). They appear to have originated from the plastid genome, because all fragments have known plastid sequences. In fragments I, II and III, none of the nucleotide alterations show co-linearity between the nuclear and the mitochondrial sequences, suggesting that these sequences were transferred independently from the plastid to the other genomes. In fragments IV, V and VI, we found the same nucleotide alterations at several positions in both the mitochondrial and the nuclear sequences. The plastid sequences in the nuclear genome were shorter than the corresponding fragments in the mitochondrial genome. Interestingly, each of these plastid sequences in the nuclear genome is associated with a mitochondrial sequence which is adjacent to the respective plastid sequence in the mitochondrial genome. Hence, it is likely that the sequences were first transferred from plastid to mitochondrion, and subsequently moved from the mitochondrial genome to the nuclear genome (Fig. 3).

DNA sequence flow among the three plant genomes has thus occurred quite frequently. Sequence transfer from the mitochondrial to the nuclear genome is indicated for five ribosomal protein genes, six tRNAs and six fragments longer than 300 bp (Fig. 3, 1). Transfer from the nuclear to the mitochondrial genome is exemplified by 19 sequence fragments having homology with known retrotransposon and transposon sequences (Fig. 3, 2). Thirty-seven fragments longer than 300 bp have been identified in both the mitochondrial and nuclear genomes, although the origin of these sequences is not known (Fig. 3, 3). The same region of plastid sequence (in the case of fragments I, II and III) was independently transferred from the plastid to both the nuclear and mitochondrial genomes (Fig. 3, 4). Plastid fragments IV, V and VI first migrated from the plastid to the mitochondrial genome, and subsequently part of each fragment was transferred from the mitochondrial to the nuclear genome (Fig. 3, 5). Seventeen plastid fragments have been transferred from the plastid to the mitochondrial genome and remain there (Fig. 3, 6).

Common sequences found in all the three genomes of rice