Structural dynamics of cereal mitochondrial genomes as revealed by complete nucleotide sequencing of the wheat mitochondrial genome

The application of a new gene-based strategy for sequencing the wheat mitochondrial genome shows its structure to be a 452 528 bp circular molecule, and provides nucleotide-level evidence of intra-molecular recombination. Single, reciprocal and double recombinant products, and the nucleotide sequences of the repeats that mediate their formation have been identified. The genome has 55 genes with exons, including 35 protein-coding, 3 rRNA and 17 tRNA genes. Nucleotide sequences of seven wheat genes have been determined here for the first time. Nine genes have an exon–intron structure. Gene amplification responsible for the production of multicopy mitochondrial genes, in general, is species-specific, suggesting the recent origin of these genes. About 16, 17, 15, 3.0 and 0.2% of wheat mitochondrial DNA (mtDNA) may be of genic (including introns), open reading frame, repetitive sequence, chloroplast and retro-element origin, respectively. The gene order of the wheat mitochondrial gene map shows little synteny to the rice and maize maps, indicative that thorough gene shuffling occurred during speciation. Almost all unique mtDNA sequences of wheat, as compared with rice and maize mtDNAs, are redundant DNA. Features of the gene-based strategy are discussed, and a mechanistic model of mitochondrial gene amplification is proposed

Center for Plant Sciences : Research activity annual report 2022

地球上には、多様な種の植物が存在し、光合成を中心とする物質生産を行っている。植物科学研究センターでは、植物のもつ多様性とその物質生産能力に着目し、その能力をゲノム解析、分子生物学的解析、生化学的解析などの手法を駆使して明らかにしている。また、多様な植物の能力を最大限に利用して利用価値の高い農作物を育種するための技術開発を行うとともに、それらを利用して持続可能な社会の実現にむけた取り組みを行っている。本報告では、令和4 年度における植物科学研究センターの研究成果について概説する。departmental bulletin pape

Polymorphic minisatellites in the mitochondrial DNAs of Oryza and Brassica

Polymorphic analyses of angiosperm mitochondrial DNA are rare in comparison with chloroplast DNA, because few target sequences in angiosperm mitochondrial DNA are known. Minisatellites, a tandem array of repeated sequences with a repeat unit of 10 to similar to 100 bp, are popular target sequences of animal mitochondria, but Beta vulgaris is the only known angiosperm species for which such an analysis has been conducted. From this lack of information, it was uncertain as to whether polymorphic minisatellites existed in other angiosperm species. Ten plant mitochondrial DNAs were found to contain minisatellite-like repeated sequences, most of which were located in intergenic regions but a few occurred in gene coding and intronic regions. Oryza and Brassica accessions were selected as models for the investigation of minisatellite polymorphism because substantial systematic information existed. PCR analysis of 42 Oryza accessions revealed length polymorphisms in four of the five minisatellites. The mitochondrial haplotypes of the 16 Oryza accessions with chromosomal complement (genome) types of CC, BBCC and CCDD were identical but were clearly distinguished from BB-genome accessions, a result consistent with the notion that the cytoplasmic donor parent of the amphidiploid species might be the CC-genome species. Twenty-nine accessions of six major cultivated species of Brassica were classified into five mitochondrial haplotypes based on two polymorphic minisatellites out of six loci. The haplotypes of Brassica juncea and Brassica carinata accessions were identical to Brassica rapa and Brassica nigra accessions, respectively. The haplotypes of Brassica napus accessions were heterogeneous and unique, results that were consistent with previous studies

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

<p>Abstract</p> <p>Background</p> <p>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 <it>Brassicaceae</it>. Although the gene <it>orf138</it> has been isolated as a determinant of Ogura-type CMS, no homologous sequence to <it>orf138</it> has been found in public databases. Therefore, how <it>orf138</it> 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 <it>orf138</it>.</p> <p>Results</p> <p>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 <it>atp9</it>. As for tRNA, normal-type contained 17 tRNAs, while Ogura-type contained 17 tRNAs and one additional <it>trnfM</it>. The gene <it>orf138</it> 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 <it>orf138</it> 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 <it>Brassicaceae</it> species, although no homology was found for the remaining 20% of sequences.</p> <p>Conclusions</p> <p>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 <it>Brassicaceae</it> 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 <it>Brassicaceae</it>, and novel genes such as <it>orf138</it> could have been created by the shuffling process of mitochondrial genome.</p

Intraspecific variations of the cytoplasmic male sterility genes orf108 and orf117 in Brassica maurorum and Moricandia arvensis, and the specificity of the mRNA processing

The mitochondrial gene orf108 co-transcribed with atp1 and causes cytoplasmic male sterility in Brassica crops, is widely distributed across wild species and genera of Brassicaceae. However, intraspecific variations in the presence of orf108 have not yet been studied, and the mechanisms for the wide distribution of the gene remain unclear. We analyzed the presence and sequence variations of orf108 in two wild species, Brassica maurorum and Moricandia arvensis. After polymerase chain reaction amplification of the 5′ region of atp1 and the coding sequence of orf108, we determined the DNA sequences. B. maurorum and M. arvensis showed variations for the presence of orf108 or orf117 (orf108The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author