The complete nucleotide sequence of wild rice ( Oryza nivara) chloroplast genome: first genome wide comparative sequence analysis of wild and cultivated rice

We determined the complete nucleotide sequence of the chloroplast genome of wild rice, Oryza nivara and compared it with the corresponding published sequence of relative cultivated rice, Oryza sativa. The genome was 134,494 bp long with a large single-copy region of 80,544 bp, a small single-copy re...

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Bibliographic Details
Published in:Gene 2004-09, Vol.340 (1), p.133-139
Main Authors: Shahid Masood, M., Nishikawa, Tomotaro, Fukuoka, Shu-ichi, Njenga, Peter K., Tsudzuki, Takahiko, Kadowaki, Koh-ichi
Format: Article
Language:English
Subjects:
Cell Nucleus - genetics
Chloroplast
Comparative genome
DNA, Chloroplast - chemistry
DNA, Chloroplast - genetics
DNA, Plant - genetics
Evolution, Molecular
Gene Order
Genes, Plant - genetics
Genome, Plant
Molecular Sequence Data
Mutagenesis, Insertional
Oryza - genetics
Oryza nivara
Oryza sativa
Poaceae - genetics
Point Mutation
Sequence Analysis, DNA
Sequence Deletion
Species Specificity
Wild rice
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Summary:We determined the complete nucleotide sequence of the chloroplast genome of wild rice, Oryza nivara and compared it with the corresponding published sequence of relative cultivated rice, Oryza sativa. The genome was 134,494 bp long with a large single-copy region of 80,544 bp, a small single-copy region of 12,346 bp and two inverted repeats of 20,802 bp each. The overall A+T content was 61.0%. The O. nivara chloroplast genome encoded identical functional genes to O. sativa in the same order along the genome. On the other hand, detailed analysis revealed 57 insertion, 61 deletion and 159 base substitution events in the entire chloroplast genome of O. nivara. Among substitutions, transversions were much higher than transitions with the former even more frequent than the latter in the coding region. Most of the insertions/deletions were single-base but a few large length mutations were also detected. The frequency of insertion/deletion events was more in the coding region within inverted repeats. In contrast, a very few substitution events were identified in the coding region. Polymorphism was observed among rice cultivars at loci of large insertion/deletion events. This is the first report describing comparative and genome wide chloroplast analysis between a wild and cultivated crop.
ISSN:0378-1119
1879-0038
DOI:10.1016/j.gene.2004.06.008