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Comparative Genomics and Evolutionary Studies of Oryza Wild Species Using Expressed Sequences
https://ir.soken.ac.jp/records/1033
https://ir.soken.ac.jp/records/1033d30c904c-4d38-4b3f-9ef7-b27a10947e88
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要旨・審査要旨 (340.7 kB)
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本文 (13.4 MB)
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| Item type | 学位論文 / Thesis or Dissertation(1) | |||||
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| 公開日 | 2010-02-22 | |||||
| タイトル | ||||||
| タイトル | Comparative Genomics and Evolutionary Studies of Oryza Wild Species Using Expressed Sequences | |||||
| タイトル | ||||||
| タイトル | Comparative Genomics and Evolutionary Studies of Oryza Wild Species Using Expressed Sequences | |||||
| 言語 | en | |||||
| 言語 | ||||||
| 言語 | eng | |||||
| 資源タイプ | ||||||
| 資源タイプ識別子 | http://purl.org/coar/resource_type/c_46ec | |||||
| 資源タイプ | thesis | |||||
| 著者名 |
佐野, 幸恵
× 佐野, 幸恵 |
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| フリガナ |
サノ, ユキエ
× サノ, ユキエ |
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| 著者 |
SANO, Yukie
× SANO, Yukie |
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| 学位授与機関 | ||||||
| 学位授与機関名 | 総合研究大学院大学 | |||||
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| 学位名 | 博士（理学） | |||||
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| 内容記述タイプ | Other | |||||
| 内容記述 | 総研大甲第1062号 | |||||
| 研究科 | ||||||
| 値 | 生命科学研究科 | |||||
| 専攻 | ||||||
| 値 | 18 遺伝学専攻 | |||||
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| 学位授与年月日 | 2007-03-23 | |||||
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| 値 | 2006 | |||||
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| 内容記述タイプ | Other | |||||
| 内容記述 | The genus Oryza comprises 25 species in 10 different genome types (AA, BB, BBCC, CC, CCDD, EE, FF, GG HHJJ and HHKK). The AA genome species contain two cultivated rice species and others are wild relatives of rice. Wild relatives of rice are important as a genetic resource to resolve the questions about domestication, speciation, polyploidy, evolution and to identify useful traits such as resistance to Various stresses and vigorous growth characters those were missing from cultivated rice. 0ryza sativa, one of the cultivated rice has been analyzed well, and the sequencing of the O. sativa, japonica and indica genomes has been completed. Molecular and genetic analyses of the wild relatives have recently stated to show phylogenetic relationships among them, but not many studies have been carried out to date. ln this study, therefore, I examined the differences of gene sequences, and structure among three different genome types and the presence of the wild relatives of rice unique genes to gain an insight of the evolutional state in the genus Oryza. I have examined genome differences for expressed sequences between AA and BB, and between AA and CC by comparison of cDNA sequences. <br /> In chapter I, the divergence between O. sativa and O. punctata (BB genome) or O.officinalis (CC genome) was analyzed. cDNA libraries were constructed using mRNAs isolate from the shoots of O. punctata (BB) and the panicles of 0. officinalis (CC), and 3087 ESTs containing 973 clones of 0. punctata and 1425 clones of O. officinalis, were used for sequence comparison against O. sativa (AA), Nipponbare sequences. The results of BLASTN showed that 88-96% cDNA clones of the BB and CC genomes showed high similarity (90-100%) to the O. sativa sequence, and 8% of the O. punctata clones and 4% of the O. officinalis(CC) clones did not hit against the O. sativa cDNA and genome sequences. Substitution rate between japonica and O. punctata, and between japonica and O. officinalis were 31 and 36 bp/kb in the coding region and 44 and 44 bp/kb in the untranslated region, respectively. They were three or four times higher than those of japonica and indica. The number of nonsynonymous and synonymous substitutions per site (Ka and Ks) was calculated O.0018 and O.022 for Ka and O.091 and O.106 for Ks between japonica and O. punctata or O. offcinalis, respectively. These results together with in/del comparison indicate that the genetic structure of BB and CC genomes are very close with each other and in/dels are accumulated in the untranslated region. <br /> In chapter Ⅱ, the phylogenic relationships of the species in the genus Oryza were examined using seven nuclea DNA sequences; O. sativa full length cDNA (AK058507, AK059353 and AK098919), RAFTIN 1 (AJ575667), MAP kinase 5 (AF479884), fructokinase 1 (AF429948), teosinte branched 1 (tb1) and tryptophan synthase (orp), and one intron sequence of Adh1 3rd intron. The results showed that the phylogenetic relationships among O. brachyantha (FF genome), AA genome species (O. sativa japonica, O. rufipogon and O. barthii) and other oryza species was supported by high bootstrap values, while in the O.officinalis complex being composed of BB, CC, CCDD, and EE genomes, pylogenetic tree was entangled among genes used for the analysis. Estimation of the divergence time bage on a molecular clock approach was performed by assuming maize and rice diverged 50 million years ago [mya]. O. brachantha (FF) vs. remaining Oryza species revealed to be at 11.7-21.6 (mya) (average 17.2 mya). The divergence time within the 0. officinalis complex containing BB, CC, CCDD and EE genomes was estimated later than 9.5 mya (2.1～12.1 mya). AA genome was divenged from 0.officinalis complex at 2.2～14.9 mya (average 8.8 mya) and speciation within the AA genome was estimated to occur at O～5.6 mya These values can explain well the phylogenetic relationships and the estimatied divergence time of these species in relation to other evolutional evidences. Synonymous (Ks) and non-synonymous (Ka) substitution rates showed that RAFTlN 1 and tb showed higher Ka/Ks than other genes in ab genome types. These genes might connibute to speciation or phenotypic diversity. <br /> In chapter Ⅲ, 13 clones identified as unique to the wild relatives, but not to japonica rice, were analyzed. Full length cDNAs were obtained from four genes ofBB or CC genome. These genes encoded a ribosomal protein, a cyclin, a cold response protein and an unknown protein. One of the BB genomes clones, the BBS13D0I encodes a cyclin D2/4 like protein and its expression in yeast cells complemented cyclin mutations. This indicates that the BBS13DO1 encodes a functional cyclin unique to the wild relatives of rice. Another clone CCP17FO1 from CC genome has domains conserved among cold response proteins, and its expression was induced by a cold treatment. This suggests that CCP1701 encodes a cold response protein and is involved in the cold response of the wild relatives. The results suggest that wild relatives of rice have various unique genes which may be related to the characteristic features of the wild relatives in the morphogenesis and stress resistance. Unique genes of the wild relatives were devided into two categories: One was unique sequence present only in the wild relatives of rice, and the other has homologous genes in japanica, but its expression might be controlled differently. My approach to analyze molecular characteristics of the wild relatives genome species in rice revealed new infomiation about nucleotide substitution rate, in/del characteristics, urrique genes of the wild relatives, phylogenetic relationships and divergence time of the wild species of rice. Oryza is one of the most valuable species in. the studies of domestication, speciation polyploidization and evolutional analysis, due to the accumulation of fundamental knowledge of genomics and a plenty of genetic resources. Further analysis of the wild relatives of rice should provide us a lot of fundamental and valuable resources to resolve questions for evolution and speciation, and for practical application of the genomes in the genus Oryza. | |||||
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| 値 | 有 | |||||
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| 内容記述タイプ | Other | |||||
| 内容記述 | application/pdf | |||||
