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A complete mitochondrial genome sequence of Ogura-type male-sterile cytoplasm and its comparative analysis with that of normal cytoplasm in radish (Raphanus sativus L.).

Tanaka Y, Tsuda M, Yasumoto K, Yamagishi H, Terachi T - BMC Genomics (2012)

Bottom Line: Ogura-type mitochondrial genome has four unique regions (2,803 bp, 1,601 bp, 451 bp and 15,255 bp in size) that are non-syntenic to normal-type genome, and the gene orf138 was found to be located at the edge of the largest unique region.Blast analysis performed to assign the unique regions showed that about 80% of the region was covered by short homologous sequences to the mitochondrial sequences of normal-type radish or other reported Brassicaceae species, although no homology was found for the remaining 20% of sequences.Ogura-type mitochondrial genome was highly rearranged compared with the normal-type genome by recombination through one large repeat and multiple short repeats.

View Article: PubMed Central - HTML - PubMed

Affiliation: 31 Laboratory, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto 603-8555, Japan. terachi@cc.kyoto-su.ac.jp

ABSTRACT

Background: Plant mitochondrial genome has unique features such as large size, frequent recombination and incorporation of foreign DNA. Cytoplasmic male sterility (CMS) is caused by rearrangement of the mitochondrial genome, and a novel chimeric open reading frame (ORF) created by shuffling of endogenous sequences is often responsible for CMS. The Ogura-type male-sterile cytoplasm is one of the most extensively studied cytoplasms in Brassicaceae. Although the gene orf138 has been isolated as a determinant of Ogura-type CMS, no homologous sequence to orf138 has been found in public databases. Therefore, how orf138 sequence was created is a mystery. In this study, we determined the complete nucleotide sequence of two radish mitochondrial genomes, namely, Ogura- and normal-type genomes, and analyzed them to reveal the origin of the gene orf138.

Results: Ogura- and normal-type mitochondrial genomes were assembled to 258,426-bp and 244,036-bp circular sequences, respectively. Normal-type mitochondrial genome contained 33 protein-coding and three rRNA genes, which are well conserved with the reported mitochondrial genome of rapeseed. Ogura-type genomes contained same genes and additional atp9. As for tRNA, normal-type contained 17 tRNAs, while Ogura-type contained 17 tRNAs and one additional trnfM. The gene orf138 was specific to Ogura-type mitochondrial genome, and no sequence homologous to it was found in normal-type genome. Comparative analysis of the two genomes revealed that radish mitochondrial genome consists of 11 syntenic regions (length >3 kb, similarity >99.9%). It was shown that short repeats and overlapped repeats present in the edge of syntenic regions were involved in recombination events during evolution to interconvert two types of mitochondrial genome. Ogura-type mitochondrial genome has four unique regions (2,803 bp, 1,601 bp, 451 bp and 15,255 bp in size) that are non-syntenic to normal-type genome, and the gene orf138 was found to be located at the edge of the largest unique region. Blast analysis performed to assign the unique regions showed that about 80% of the region was covered by short homologous sequences to the mitochondrial sequences of normal-type radish or other reported Brassicaceae species, although no homology was found for the remaining 20% of sequences.

Conclusions: Ogura-type mitochondrial genome was highly rearranged compared with the normal-type genome by recombination through one large repeat and multiple short repeats. The rearrangement has produced four unique regions in Ogura-type mitochondrial genome, and most of the unique regions are composed of known Brassicaceae mitochondrial sequences. This suggests that the regions unique to the Ogura-type genome were generated by integration and shuffling of pre-existing mitochondrial sequences during the evolution of Brassicaceae, and novel genes such as orf138 could have been created by the shuffling process of mitochondrial genome.

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The possible rearrangements that had occurred between two Ogura- and normal-type genomes via short repeated sequences. Large blank arrows indicate each syntenic region. Small arrows in the same color show the position and orientation of repeats. The length and location of the repeats are summarized in Additional file 1 and Additional file 2.
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Figure 3: The possible rearrangements that had occurred between two Ogura- and normal-type genomes via short repeated sequences. Large blank arrows indicate each syntenic region. Small arrows in the same color show the position and orientation of repeats. The length and location of the repeats are summarized in Additional file 1 and Additional file 2.

Mentions: Repeats in two mitochondrial genomes have been investigated. If a pair of sequences has over 90% similarity, the pair is defined as a repeat. A pair of large repeats of 9,732 bp was found in Ogura-type mitochondrial genome, while a pair of large repeats of 5,530 bp was identified in normal-type. Even though the length of large repeats is different, sequence of the large repeats are highly conserved within 5,530 bp. In Ogura-type mitochondrial genome, the large repeats are located in syntenic regions 5 and 11/6 (Figure 3, Ogura R1). A 9,732-bp sequence, corresponding to Ogura-type repeat, is conserved in syntenic region 5/6 of the normal-type genome, but it is truncated in syntenic region 11 because normal-type genome has a specific sequence between syntenic regions 1 and 11. In rapeseed mitochondrial genome, a 2,427-bp sequence that includes the gene cox2 was reported as a large direct repeat. Large repeated sequences found in Raphanus are completely different from those reported in rapeseed [18]. These large repeats are considered to be involved in the formation of a tripartite structure; each radish mitochondrial genome could recombine into two sub-genomic circles. Two expected sub-genomic circles are 130,760 bp and 127,666 bp in Ogura-type, while they are 139,398 bp and 104,638 bp in normal-type. In addition, these repeats are also related to reorganization among syntenic regions 5, 6 and 11 (Figure 3a).


A complete mitochondrial genome sequence of Ogura-type male-sterile cytoplasm and its comparative analysis with that of normal cytoplasm in radish (Raphanus sativus L.).

Tanaka Y, Tsuda M, Yasumoto K, Yamagishi H, Terachi T - BMC Genomics (2012)

The possible rearrangements that had occurred between two Ogura- and normal-type genomes via short repeated sequences. Large blank arrows indicate each syntenic region. Small arrows in the same color show the position and orientation of repeats. The length and location of the repeats are summarized in Additional file 1 and Additional file 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3473294&req=5

Figure 3: The possible rearrangements that had occurred between two Ogura- and normal-type genomes via short repeated sequences. Large blank arrows indicate each syntenic region. Small arrows in the same color show the position and orientation of repeats. The length and location of the repeats are summarized in Additional file 1 and Additional file 2.
Mentions: Repeats in two mitochondrial genomes have been investigated. If a pair of sequences has over 90% similarity, the pair is defined as a repeat. A pair of large repeats of 9,732 bp was found in Ogura-type mitochondrial genome, while a pair of large repeats of 5,530 bp was identified in normal-type. Even though the length of large repeats is different, sequence of the large repeats are highly conserved within 5,530 bp. In Ogura-type mitochondrial genome, the large repeats are located in syntenic regions 5 and 11/6 (Figure 3, Ogura R1). A 9,732-bp sequence, corresponding to Ogura-type repeat, is conserved in syntenic region 5/6 of the normal-type genome, but it is truncated in syntenic region 11 because normal-type genome has a specific sequence between syntenic regions 1 and 11. In rapeseed mitochondrial genome, a 2,427-bp sequence that includes the gene cox2 was reported as a large direct repeat. Large repeated sequences found in Raphanus are completely different from those reported in rapeseed [18]. These large repeats are considered to be involved in the formation of a tripartite structure; each radish mitochondrial genome could recombine into two sub-genomic circles. Two expected sub-genomic circles are 130,760 bp and 127,666 bp in Ogura-type, while they are 139,398 bp and 104,638 bp in normal-type. In addition, these repeats are also related to reorganization among syntenic regions 5, 6 and 11 (Figure 3a).

Bottom Line: Ogura-type mitochondrial genome has four unique regions (2,803 bp, 1,601 bp, 451 bp and 15,255 bp in size) that are non-syntenic to normal-type genome, and the gene orf138 was found to be located at the edge of the largest unique region.Blast analysis performed to assign the unique regions showed that about 80% of the region was covered by short homologous sequences to the mitochondrial sequences of normal-type radish or other reported Brassicaceae species, although no homology was found for the remaining 20% of sequences.Ogura-type mitochondrial genome was highly rearranged compared with the normal-type genome by recombination through one large repeat and multiple short repeats.

View Article: PubMed Central - HTML - PubMed

Affiliation: 31 Laboratory, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto 603-8555, Japan. terachi@cc.kyoto-su.ac.jp

ABSTRACT

Background: Plant mitochondrial genome has unique features such as large size, frequent recombination and incorporation of foreign DNA. Cytoplasmic male sterility (CMS) is caused by rearrangement of the mitochondrial genome, and a novel chimeric open reading frame (ORF) created by shuffling of endogenous sequences is often responsible for CMS. The Ogura-type male-sterile cytoplasm is one of the most extensively studied cytoplasms in Brassicaceae. Although the gene orf138 has been isolated as a determinant of Ogura-type CMS, no homologous sequence to orf138 has been found in public databases. Therefore, how orf138 sequence was created is a mystery. In this study, we determined the complete nucleotide sequence of two radish mitochondrial genomes, namely, Ogura- and normal-type genomes, and analyzed them to reveal the origin of the gene orf138.

Results: Ogura- and normal-type mitochondrial genomes were assembled to 258,426-bp and 244,036-bp circular sequences, respectively. Normal-type mitochondrial genome contained 33 protein-coding and three rRNA genes, which are well conserved with the reported mitochondrial genome of rapeseed. Ogura-type genomes contained same genes and additional atp9. As for tRNA, normal-type contained 17 tRNAs, while Ogura-type contained 17 tRNAs and one additional trnfM. The gene orf138 was specific to Ogura-type mitochondrial genome, and no sequence homologous to it was found in normal-type genome. Comparative analysis of the two genomes revealed that radish mitochondrial genome consists of 11 syntenic regions (length >3 kb, similarity >99.9%). It was shown that short repeats and overlapped repeats present in the edge of syntenic regions were involved in recombination events during evolution to interconvert two types of mitochondrial genome. Ogura-type mitochondrial genome has four unique regions (2,803 bp, 1,601 bp, 451 bp and 15,255 bp in size) that are non-syntenic to normal-type genome, and the gene orf138 was found to be located at the edge of the largest unique region. Blast analysis performed to assign the unique regions showed that about 80% of the region was covered by short homologous sequences to the mitochondrial sequences of normal-type radish or other reported Brassicaceae species, although no homology was found for the remaining 20% of sequences.

Conclusions: Ogura-type mitochondrial genome was highly rearranged compared with the normal-type genome by recombination through one large repeat and multiple short repeats. The rearrangement has produced four unique regions in Ogura-type mitochondrial genome, and most of the unique regions are composed of known Brassicaceae mitochondrial sequences. This suggests that the regions unique to the Ogura-type genome were generated by integration and shuffling of pre-existing mitochondrial sequences during the evolution of Brassicaceae, and novel genes such as orf138 could have been created by the shuffling process of mitochondrial genome.

Show MeSH
Related in: MedlinePlus