Genetic and physical maps and a clone bank of mitochondrial DNA from rice

Iwahashi, Motoko; Nakazono, Mikio; Kanno, Akira; Sugino, Kanae; Ishibashi, Takashi; Hirai, Atsushi

doi:10.1007/bf00229482

Cited by 37 publications

(15 citation statements)

References 11 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Our two genome assemblies were displayed as a master contig (Fig. 1) by referencing previously published sequences (Iwahashi et al, 1992;Notsu et al, 2002). The smaller contigs with either low coverage (i.e.…”

Section: Sequence Assembliesmentioning

confidence: 99%

The Rice Mitochondrial Genomes and Their Variations

Tian

Zheng²,

Hu³

et al. 2005

Plant Physiology

108

View full text Add to dashboard Cite

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.

show abstract

Section: Sequence Assembliesmentioning

confidence: 99%

The Rice Mitochondrial Genomes and Their Variations

Tian

Zheng²,

Hu³

et al. 2005

Plant Physiology

108

View full text Add to dashboard Cite

show abstract

“…The present experiment aims to clarify the phylogenetic relationships on the basis of mtDNA RFLP patterns. The genome size of rice mitochondria was estimated at 492 kbp (Iwahashi et al, 1992) which is 3.6 times larger than that of the rice chloroplast genome (134 kbp, Hirai et al, 1985).…”

mentioning

confidence: 99%

“…japonica cv. Nipponbare using λ-DASH phage vector (Iwahashi et al, 1992). Mitochondrial DNA fragments which include these genes were subcloned into the Sal I or Xba I sites of a plasmid vector, pUC19.…”

mentioning

confidence: 99%

“…In this experiment, we used eight rice mtDNA probes having a total size of 71.0 kbp, scattering over the entire mtDNA molecule. The probes probably hybridize to more than 100 kbp of the mtDNA molecule in the estimated 492 kbp rice mt DNA (Iwahashi et al 1992). The possibility that the mtDNA probes cross-hybridize with cpDNA molecule has been suggested (Nakazono and Hirai, 1993).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Phylogenetic relationships in the genus Oryza based on mitochodrial RFLPs.

et al. 1999

View full text Add to dashboard Cite

Restriction fragment length polymorphism (RFLP) of mitochondrial DNA in the genus Oryza was surveyed using 20 accessions including 11 species and a single endonuclease, EcoRI. RFLPs were visualized by Southern hybridization with eight rice mitochondrial DNA probes labeled non-radioactively with digoxigenin-dUTP. A total of 66 bands were obtained from all of the accessions. The total number of fragments per plant was higher in diploid A-genome species (an average of 35.3) than that in diploid B-and C-genome species and allotetraploid BC-and CDgenome species (an average of 28.2). The extent of the polymorphism in the RFLP patterns was various depending on the probes used. A diverse polymorphism was observed with most of the probes used, i.e. the cob, cox I, atp6, rrn18, rrn26 and atp9 regions, whereas, no polymorphic band was observed with a probe for the coxII region. The genus Oryza was separated into two large clusters. One cluster was comprised of A-genome species and the other cluster was comprised of B-, BC-, C-, and CD-genome species. Within A-genome species, the genetic variation was relatively high. Even in O. sativa species, the RFLP patterns of japonica and indica subspecies were clearly different from each other when three probes were used. However, there was no polymorphism between O. glaberrima and O. barthii. Within the genomes of B, BC, C, and CD, RFLP patterns were similar to each other and they showed a closer affinity except for O. minuta (BBCC). Within the BC genome species, the patterns of O. punctata and O. minuta were largely different from each other and separated into two different subclusters. Thus, the mitochondrial genomes of the two BC species (O. punctata and O. minuta) apparently evolved independently. Among CD genome species (O. latifolia and O. alta), the patterns of one accession, O. alta W0017 were largely different from those of the other accessions of CD genome species.

show abstract

“…The genomic clone containing the COX1 gene was used from our clone bank of rice mtDNA (Iwahashi et al, 1992). The nuclear-encoded COX5b gene from rice has already been identified by Kadowaki et al (1996).…”

mentioning

confidence: 99%