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| 著者 | Tang,J., Xia,H., Cao,M., Zhang,X., Zeng,W., Hu,S., Tong,W., Wang,J., Wang,J., Yu,J., Yang,H. and Zhu,L. | |
| タイトル | A Comparison of Rice Chloroplast Genomes. | |
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Abstract: Using high quality sequence reads extracted from our whole genome shotgun repository, we assembled two chloroplast genome sequences from two rice (Oryza sativa) varieties, one from 93-11 (a typical indica variety) and the other from PA64S (an indica-like variety with maternal origin of japonica), which are both parental varieties of the super-hybrid rice, LYP9. Based on the patterns of high sequence coverage, we partitioned chloroplast sequence variations into two classes, intravarietal and intersubspecific polymorphisms. Intravarietal polymorphisms refer to variations within 93-11 or PA64S. Intersubspecific polymorphisms were identified by comparing the major genotypes of the two subspecies represented by 93-11 and PA64S, respectively. Some of the minor genotypes occurring as intravarietal polymorphisms in one variety existed as major genotypes in the other subspecific variety, thus giving rise to intersubspecific polymorphisms. In our study, we found that the intersubspecific variations of 93-11 (indica) and PA64S (japonica) chloroplast genomes consisted of 72 single nucleotide polymorphisms and 27 insertions or deletions. The intersubspecific polymorphism rates between 93-11 and PA64S were 0.05% for single nucleotide polymorphisms and 0.02% for insertions or deletions, nearly 8 and 10 times lower than their respective nuclear genomes. Based on the total number of nucleotide substitutions between the two chloroplast genomes, we dated the divergence of indica and japonica chloroplast genomes as occurring approximately 86,000 to 200,000 years ago. |
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| 掲載誌 | Plant Physiol. | |
| Country | China | |
| 刊数 | 135(1) | |
| ページ | 412-420 | |
| 発刊年 | 2004 | |
| PubMed ID | 15122023 | |
| PubMed Central ID | - | |
| DOI | 10.1104/pp.103.031245 | |
| URL | - | |
| 関連情報 | ||
| 遺伝子 | CLPP INFA NDHC NDHD NDHE NDHF NDHG NDHH NDHI NDHJ NDHK PETA PETD PETE PSAA PSAB PSAC PSBA PSBB PSBC PSBD PSBE PSBF PSBH PSBI PSBK PSBM PSBN RBCL RPL14 RPL16 RPL2 RPL2 RPL2 RPL22 RPL23 RPL23 RPL32 RPL33 RPL36 RPOA RPOB RPOC1 RPS11 RPS14 RPS15 RPS15 RPS18 RPS19 RPS2 RPS3 RPS3 RPS4 RPS7 RPS7 RPS8 YCF4 _ _ _ _ _ _ _ _ _ _ | |
| INSD | AY522330 AY522331 AY522329 | |
| 系統 |
野生イネ コアコレクション |
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| 突然変異系統(遺伝研 Collection) | - | |
| 種子不稔系統 | - | |
| 致死変異体系統 | - | |
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組織別発生段階 - 突然変異系統(遺伝子) |
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| 栽培イネ品種(遺伝研 Collection) | - | |
| 組織別発生段階 | - | |
