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The Complete Sequence Of The Rice (Oryza Sativa L.) Mitochondrial Genome: Frequent DNA Sequence Acquisition And Loss During The Evolution Of Flowering Plants
Y. Notsu, S. Masood, T. Nishikawa, N. Kubo, G. Akiduki, M. Nakazono, A. Hirai, K. Kadowaki
Published 2002 · Medicine, Biology
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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.
This paper references
REPuter: fast computation of maximal repeats in complete genomes
S. Kurtz (1999)
Genetic and physical maps and a clone bank of mitochondrial DNA from rice
M. Iwahashi (2004)
Genome structure and gene content in protist mitochondrial DNAs.
M. Gray (1998)
A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica)
J. Yu (2002)
Wheat mitochondria ccmB encodes the membrane domain of a putative ABC transporter involved in cytochrome c biogenesis.
S. E. Faivre-Nitschke (2001)
A draft sequence of the rice genome (Oryza sativa L. ssp. japonica).
S. Goff (2002)
Differential organization of mitochondrial genes in rice with normal and male-sterile cytoplasms.
門脇 光一 (1989)
The complete nucleotide sequence of the mitochondrial genome of sugar beet (Beta vulgaris L.) reveals a novel gene for tRNA (GCA)
T Kubo (2000)
Basic local alignment search tool.
S. Altschul (1990)
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
T. Lowe (1997)
The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides
M. Unseld (1997)
Complex mtDNA constitutes an approximate 620-kb insertion on Arabidopsis thaliana chromosome 2: Implication of potential sequencing errors caused by large-unit repeats
R. Stupar (2001)
A chimeric gene containing the 5′ portion of atp6 is associated with cytoplasmic male-sterility of rice
K. Kadowaki (2004)
A promiscuous chloroplast DNA fragment is transcribed in plant mitochondria but the encoded RNA is not edited
P. Zeltz (2004)
A single nuclear transcript encoding mitochondrial RPS14 and SDHB of rice is processed by alternative splicing: common use of the same mitochondrial targeting signal for different proteins.
N. Kubo (1999)
A ribosomal protein L2 gene is transcribed, spliced, and edited at one site in rice mitochondria
N. Kubo (2004)
Identification of the entire set of transferred chloroplast DNA sequences in the mitochondrial genome of rice
M. Nakazono (2004)
Genes for the ribosomal S4 protein encoded in higher plant mitochondria are transcribed, edited, and translated
H. Handa (1998)
A Comprehensive Rice Transcript Map Containing 6591 Expressed Sequence Tag Sites
J. Wu (2002)
copia-, gypsy- and LINE-like retrotransposon fragments in the mitochondrial genome of Arabidopsis thaliana.
V. Knoop (1996)
Involvement of 5′ flanking sequence for specifying RNA editing sites in plant mitochondria
N. Kubo (1997)
Targeting presequence acquisition after mitochondrial gene transfer to the nucleus occurs by duplication of existing targeting signals.
K. Kadowaki (1996)
Maize mitochondrial DNA contains a sequence homologous to the ribulose-1,5-bisphosphate carboxylase large subunit gene of chloroplast DNA
D. Lonsdale (1983)
Transcription and editing status of ribosomal protein S2 gene in rice mitochondria
N Kubo (2001)
Transfer of the mitochondrial rps10 gene to the nucleus in rice: acquisition of the 5′ untranslated region followed by gene duplication
N. Kubo (2000)
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
The Arabidopsis Genome Initiative (2000)
Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA. A primitive form of plant mitochondrial genome.
K. Oda (1992)
Complete structure of the chloroplast genome of Arabidopsis thaliana.
S. Sato (1999)
The Plant Mitochondrial Genome: Physical Structure, Information Content, RNA Editing, and Gene Migration to the Nucleus
W. Schuster (1994)
Excess RNA Editing in Rice Mitochondrial atp9 Transcripts
M. Ishikawa (1993)
Transcription of plastid-derived tRNA genes in rice mitochondria
S. Miyata (1998)
RNA editing of transcripts of the gene for apocytochrome b (cob) in rice mitochondria.
Y. Ito (1996)
Truncated and dispersed rpl2 and rps19 pseudogenes are co-transcribed with neighbouring downstream genes in wheat mitochondria
S. Subramanian (2001)
The complete nucleotide sequence of the mitochondrial genome of sugar beet (Beta vulgaris L.) reveals a novel gene for tRNACys(GCA)
T. Kubo (2000)
The complete sequence of the rice (Oryza stiva) chloroplast genome: intermolecular recombination between distinct tRNA
J Hiratsuka (1989)
Mitochondrial DNA polymorphism in male-sterile cytoplasm of rice
K. Kadowaki (2004)
This paper is referenced by
Interchangeable parts: The evolutionarily dynamic tRNA population in plant mitochondria.
J. Warren (2020)
Gene duplication, transfer, and evolution in the chloroplast genome.
A. Xiong (2009)
Mitochondrial RNA import: from diversity of natural mechanisms to potential applications.
François Sieber (2011)
Identification of mitochondrial genome rearrangements unique to novel cytoplasmic male sterility in radish (Raphanus sativus L.)
Young-Pyo Lee (2008)
Re-sequencing of mitochondrial genes in a standard rice cultivar Nipponbare
Takushi Toda (2012)
Discordant patterns of morphological and genetic divergence in the closely related species Schizanthus hookeri and S. grahamii (Solanaceae)
Fernanda Pérez (2011)
Mitochondrial Genetics of Alloplasmic Male-Sterile Brassica napus Lines
M. Leino (2005)
A fragment of chloroplast DNA was transferred horizontally, probably from non-eudicots, to mitochondrial genome of Phaseolus
M. Woloszynska (2004)
Interactions of Mitochondrial and Nuclear Genes That Affect Male Gametophyte Development
M. Hanson (2004)
Coevolution of Organelle RNA Editing and Nuclear Specificity Factors in Early Land Plants
Mareike Schallenberg-Rüdinger (2016)
Plant-type mitochondrial RNA editing in the protist Naegleria gruberi.
Mareike Rüdinger (2011)
Who was the mother of cultivated rice? Differentiation of chloroplast genome structure among cultivated rice and ancestral wild species.
K. Kadowaki (2005)
Organellar genome analysis reveals endosymbiotic gene transfers in tomato
H. Kim (2018)
Distribution of introns in the mitochondrial gene nad1 in land plants: phylogenetic and molecular evolutionary implications.
O. Dombrovska (2004)
A Reevaluation of Rice Mitochondrial Evolution Based on the Complete Sequence of Male-Fertile and Male-Sterile Mitochondrial Genomes1[C][W][OA]
S. Bentolila (2011)
Expression Analysis of Genes for Callose Synthases and Rho-Type Small GTP-Binding Proteins That Are Related to Callose Synthesis in Rice Anther
T. Yamaguchi (2006)
Annotation of the rice genome
Shu Ouyang (2007)
Chloroplast DNA insertions into the nuclear genome of rice: the genes, sites and ages of insertion involved
X. Guo (2007)
Sequencing of a Segment of a Monilophyte Species Mitochondrial Genome Reveals Features Highly Similar to those of Seed Plant mtDNAs
S. Panarese (2008)
Development of New Molecular Markers for the Identification of Male Sterile Cytoplasm in Peppers (Capsicum annuum L.)
W. Min (2011)
Ribosomal protein L10 is encoded in the mitochondrial genome of many land plants and green algae
Jeffrey P. Mower (2009)
PREPACT 2.0: Predicting C-to-U and U-to-C RNA Editing in Organelle Genome Sequences with Multiple References and Curated RNA Editing Annotation
H. Lenz (2013)
Plant Mitochondrial Omics: State-of-the-Art Knowledge
M. Ghulam (2015)
Import of RNAs into Plant Mitochondria
A. Duchêne (2011)
Nuclear DYW-Type PPR Gene Families Diversify with Increasing RNA Editing Frequencies in Liverwort and Moss Mitochondria
Mareike Rüdinger (2012)
Mitochondrial Data in Monocot Phylologenetics
G. Peterson (2006)
A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome
T. R. E. S. Figueira (2012)
The Role of Horizontal Transfer in Shaping the Plant Mitochondrial Genome
Jeffrey P. Mower (2012)
Diversity and Evolution of Plastids and Their Genomes
E. Kim (2008)
Horizontal acquisition of multiple mitochondrial genes from a parasitic plant followed by gene conversion with host mitochondrial genes
Jeffrey P. Mower (2010)
Rice OGR1 encodes a pentatricopeptide repeat-DYW protein and is essential for RNA editing in mitochondria.
Sung-Ryul Kim (2009)
In organello editing of mitochondrial atp9, cox2, and nad9 transcripts
M. Staudinger (2004)See more