Annual Report 2006

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Analysis of Diversity in the Genus by Comparative Genomics Approach The high-quality sequence of the rice genome based on the japonica cultivar Nipponbare was revealed in 2004. Since then, the information derived from the genome sequence has been widely used in understanding the biology of rice including the identification and functional characterization of novel genes for agricultural traits. As a model cereal crop, the rice genome sequence could also be used in clarifying how the genus originated from the ancestral cereal genome, as well as how it evolved and diversified. This would not only elucidate the lineage between cultivated rice varieties from their wild relatives but would also be useful in searching for new beneficial alleles of the genes in the wild rice species that had been lost during the establishment of modern varieties. A comparative genomics approach is becoming more and more important because the wild rice has been recognized as one of the major source for novel gene alleles. Many agriculturally important genes such as disease resistance genes have been found in wild rice and introduced into the modern rice varieties. We investigated the nucleotide sequence variation among wild rice species using 900 ESTs mapped at intervals of approximately 500 kb throughout the genome. Primers were designed mainly from the 3-UTR region of the EST sequences and used for PCR amplification of DNA from 45 accessions belonging to 21 Oryza species from the germplasm collection of NIAS and the National Institute of Genetics (NIG). The overall efficiency of amplification for each species is shown in Fig. 1. Most of the regions were amplified in the AA genome ( complex, 94% in average for 15 accessions), suggesting that the genome sequence is conserved. On the other hand, the complex, which includes BB, BBCC, CC, CCDD and EE genomes, has 50-70% amplification efficiency. The other remote genomes (FF, GG and HHJJ) showed only 20-30% amplification. We have clearly shown here that the rice genome sequence has gradually changed in the course of evolution from the wild species. These results also indicate the utility of the standard genome sequence from the japonica cultivar Nipponbare for analysis of genome diversity as well as the evolutionary relationships between modern rice varieties and wild rice species. Moreover, the conserved regions across species could be good markers for comparative genomics among species. Fig. 1 Amplification of ssp. cv. Nipponbare EST markers in wild rice accessions The height of the bars represents the efficiency (%) of marker amplification.
The Rice Annotation Project Database (RAP-DB) and Comparative Genome Analysis Completion of the rice genome sequencing by the International Rice Genome Sequencing Project (IRGSP) enabled us to annotate all the rice genes. Automated annotations of the gene functions were manually curated in a jamboreestyle annotation meeting of the Rice Annotation Project (RAP). The annotation data is available in the RAP Database (RAP-DB, http://rapdb. lab.nig.ac.jp/) which was constructed in collaboration with the DNA Data Bank of Japan (DDBJ), National Institute of Genetics (Fig. 2). The RAP-DB provides two types of viewers (GBrowse and G-integra), BLAST/BLAT similarity searches, and keyword searches. Information about TIGR and NCBI annotations on the IRGSP genome assembly is also available. Additionally, the RAP genes are linked to other rice genomics data, such as fulllength cDNAs and insertion mutant lines. We expect that the RAP-DB will serve as a hub for rice genomics. The RAP annotation data was envisaged to elucidate the evolutionary process of flowering plants. We compared the genomes of two representative plant species, rice and First, our analysis revealed that the number and average length of exons in rice were quite similar to those in while the lengths of introns and intergenic regions varied between the two species. This may be because transposable elements had been inserted extensively in non-exonic regions of rice. Second, we found that 22% of the rice genes had no homologs in the gene set. Although this observation is consistent with the previous view that the rice genome possesses a number of unique genes, the majority of the rice-specific genes might be due to gene loss in the lineage or mispredictions of the protein coding regions. Lastly, despite independent gene duplication events after the speciation between the monocot and dicot plant species, the distribution of the paralogs and protein functions had been retained in a similar manner in both of rice and These data suggest that the rice and gene sets have shared a common feature for over 100 million years. The phenotypic difference between the two species may have been derived from changes of a small number of genes or the divergence of gene regulation. Fig. 2 The Rice Annotation Project Database (RAP-DB) with an overview of the two genome viewers, G-integra and GBrowse
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Page 3 and 4: Teruo Ishige, President The Nationa
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Page 9 and 10: studies. To construct a fully satur
Page 11 and 12: Fig. 2 Geographical distribution of
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Page 15 and 16: Mulberry latex defense mulberry tre
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Page 41 and 42: Expression patterns of two novel ge
Page 43 and 44: Fig. 5 PGC and EBC fused cells PGCs
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Page 61 and 62: Table 1 Menu of Commercial silkworm
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Page 73 and 74: B iochemistry Department Structural
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Proteomic analysis Based on the pro
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photoautotrophic medium (Fig. 1B).
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Fig. 4 Blast resistance of OsWRKY45
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phosphatase activity by SIPK depend
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the endosperm in co-operation with
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isolated genes in transgenic Anal
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Fig. 1 Gene structures and mutation
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cytochimera among the mulberries (
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15 G. Hariraj, Kinoshita Haruo, T.
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49 Kameda Tsunenori, Teramoto Hidet
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85 Matsuyama Shuichi, Ohkura Satosh
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120 Ozawa Kenjiro, Kawahigashi Hiro
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155 Taguchi-Shiobara Fumio, Yamamot
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192 Ueno Osamu, Agarie Sakae, (2005
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8 Murakami Ritsuko, Koyama Akio, Sh
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20 Todoroki Junichi, Kaneko Hiroyuk
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Executive Members and Research Staf
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Developmental Biology Department Di
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Research Leader Hayasaka Shoji Rese
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Mutation Genetics Laboratory Head N
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thousands of yen TOTAL BUDGET OPERA
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Annual Report 2006 (Apr. 2005Mar. 2
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Annual Report 2006

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