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Author Masood,M.S., Nishikawa,T., Fukuoka,S., Njenga,P.K., Tsudzuki,T. and Kadowaki,K.
Title The complete nucleotide sequence of wild rice (Oryza nivara) chloroplast genome: first genome wide comparative sequence analysis of wild and cultivated rice
Abstract:
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.
Journal Gene
Country Japan
Volume 340(1)
Pages 133-139
Year 2004
PubMed ID 15556301
PubMed Central ID -
DOI 10.1016/j.gene.2004.06.008
URL -
Relation
Gene 16S rRNA 16S rRNA 23S rRNA 23S rRNA 3'RPS12 4.5S rRNA 4.5S rRNA 5S rRNA 5S rRNA CLPP INFA NDHA NDHB NDHB NDHC NDHD NDHE NDHF NDHG NDHH NDHI NDHJ NDHK PETA PETD PETE PSAA PSAB PSAC PSBA PSBC PSBD PSBE PSBF PSBH PSBI PSBK PSBL PSBM PSBN PSBZ RBCL RPL14 RPL16 RPL2 RPL2 RPL22 RPL23 RPL23 RPL32 RPL33 RPL36 RPOA RPOB RPOC1 RPOC2 RPS11 RPS12 RPS14 RPS15 RPS15 RPS16 RPS18 RPS19 RPS19 RPS2 RPS3 RPS4 RPS7 RPS7 RPS8 YCF4 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
INSD AP006728
Strain Wild Core Collection -
Sterile Seed Strain -
Lethal Embryo
Mutantion Strain
-
Stages in Each Organ
- Muant Lines (Gene)
-
Cultivated Varieties(NIG Collection) -
Stages in Each Organ -
/rice/oryzabase