ArticlePlant physiology2006
The rice mitochondrial genomes and their variations.
Article in Plant physiology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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54 citing papers in PubMed.
- A Rapid and Reliable qPCR Method for Genetic Purity Testing of BT-Type CMS Rice Seed Lots.Current issues in molecular biology · 2026Article
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- Mitochondrial genome study ofFrontiers in plant science · 2024Article
- Mitochondrial genome variation and intergenomic sequence transfers inFrontiers in plant science · 2024Article
- Complete Mitochondrial Genome Assembly of an Upland Wild Rice Species,Life (Basel, Switzerland) · 2023Article
- Mitochondrial markers differentiate two distinct phylogenetic groups in indigenous rice landraces of northeast India: an evolutionary insight.Journal of genetics · 2023Article
- Novel regulators of mitochondrial genome integrity.Journal of biosciences · 2023Article
- Comparison of Mitochondrial Genomes between a Cytoplasmic Male-Sterile Line and Its Restorer Line for Identifying Candidate CMS Genes inInternational journal of molecular sciences · 2022Article
- The Complete Mitochondrial Genome ofGenes · 2022Article
- Assembly and comparative analysis of the complete mitochondrial genome ofFrontiers in plant science · 2022Article
- Current status of genomic resources on wild relatives of rice.Breeding science · 2020Article
- Article
- Intergenomic gene transfer in diploid and allopolyploid Gossypium.BMC plant biology · 2019Article
- Evidence for selection events during domestication by extensive mitochondrial genome analysis between japonica and indica in cultivated rice.Scientific reports · 2019Article
- Whole-genome sequencing of Brassica oleracea var. capitata reveals new diversity of the mitogenome.PloS one · 2018Article
- Genetic variation architecture of mitochondrial genome reveals the differentiation in Korean landrace and weedy rice.Scientific reports · 2017Article
- Multi-step formation, evolution, and functionalization of new cytoplasmic male sterility genes in the plant mitochondrial genomes.Cell research · 2017Article
- Rice Chloroplast Genome Variation Architecture and Phylogenetic Dissection in Diverse Oryza Species Assessed by Whole-Genome Resequencing.Rice (New York, N.Y.) · 2016Article
- Complete Chloroplast Genome Sequence and Annotation of the Tropical japonica Group of Asian Cultivated Rice (Oryza sativa L.).Genome announcements · 2016Article
- Mitochondrial Genome Analysis of Wild Rice (Oryza minuta) and Its Comparison with Other Related Species.PloS one · 2016Article
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4 authors.
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Abstract
Based on highly redundant and high-quality sequences, we assembled rice (Oryza sativa) mitochondrial genomes for two cultivars, 93-11 (an indica variety) and PA64S (an indica-like variety with maternal origin of japonica), which are paternal and maternal strains of an elite superhybrid rice Liang-You-Pei-Jiu (LYP-9), respectively. Following up with a previous analysis on rice chloroplast genomes, we divided mitochondrial sequence variations into two basic categories, intravarietal and intersubspecific. Intravarietal polymorphisms are variations within mitochondrial genomes of an individual variety. Intersubspecific polymorphisms are variations between subspecies among their major genotypes. In this study, we identified 96 single nucleotide polymorphisms (SNPs), 25 indels, and three segmental sequence variations as intersubspecific polymorphisms. A signature sequence fragment unique to indica varieties was confirmed experimentally and found in two wild rice samples, but absent in japonica varieties. The intersubspecific polymorphism rate for mitochondrial genomes is 0.02% for SNPs and 0.006% for indels, nearly 2.5 and 3 times lower than that of their chloroplast counterparts and 21 and 38 times lower than corresponding rates of the rice nuclear genome, respectively. The intravarietal polymorphism rates among analyzed mitochondrial genomes, such as 93-11 and PA64S, are 1.26% and 1.38% for SNPs and 1.13% and 1.09% for indels, respectively. Based on the total number of SNPs between the two mitochondrial genomes, we estimate that the divergence of indica and japonica mitochondrial genomes occurred approximately 45,000 to 250,000 years ago.
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