Annual Report 2003

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DDBJ (DNA Data Bank of Japan). Thesequence data can also be accessed throughRGP’s website (http://rgp.dna.affrc.go.jp)together with the map position data andannotation data. As a whole, IRGSP hassubmitted 465 Mb of sequence data (or 366Mb total sequence data excluding overlaps)of the entire genome to public databases.This corresponds to about 92% of the estimatedsize of the rice genome and coversalmost all of the euchromatic regions foreach chromosome. The progress of sequencesubmission to the public databases by RGPand IRGSP is shown in Fig. 1.The sequencing initiative attained a significantachievement with the completion ofthe high-quality draft sequence of the entiregenome last year. A commemorative ceremonyto celebrate the occasion was held inTokyo on Dec. 18, 2002, with Prime MinisterJunichiro Koizumi of Japan declaring thecompletion of the rice phase 2 draft sequence.The initial attempt for annotation of theentire genome using RiceGAAS revealed62,435 protein-coding genes. Although thesequence has not yet been completed to finished-qualitylevel, it has already been usefulfor map-based gene cloning, elucidation ofgene functions and comparative studies withother species. IRGSP is currently shiftinggears into the finishing phase of sequencingto fill sequence gaps within the PAC/BACclones and to resolve the sequence of ambiguousregions with the goal of finishing thegenome before the end of 2004. Acquiringthe complete blueprint of the rice plant willfacilitate discovery of all rice genes that willprovide a critical foundation for crop improvementbeneficial to all mankind.Fig. 1Progress of the genome sequencing by IRGSP.The cumulative nucleotide sequence submission by IRGSP members tothe public database is shown. The red region correspond RGP contributionand the hatched region corresponds other IRGSP members.Fig. 2A snapshot from the commemorative ceremony.Dr. Benjamin Burr, a co-chairman of IRGSP, ismaking a speech. Other IRGSP representativesare sitting behind him.2 Annual Report 2003
Elucidation of genomic structure around joiningsegments of the swine T cell antigenicreceptor (TCR) / chain geneHirohide UenishiGenome Research DepartmentRecent developments in technology fortransplantation and regenerative medicinehave focused much attention on pigs. Inaddition, intensive investigation of immunemolecules of livestock has come to be indispensablefor understanding of animal infectiousdiseases and zoonosis. Studies inrecent years have implied that there aremany differences in the expression and functionof molecules in immune cells of artiodactyls,humans and mice, so that intensiveanalyses of swine immunology are required.T cell antigenic receptor (TCR) genes ingermline possess many V (some D in and genes) and J segments, and one or several Cregion(s). In the lineage process of T cells,V(D)J segments connect upon the genomicsequence and specificity to antigens of thereceptors is obtained by selection of the segmentsand insertion/deletion at the junctions.There are four types (, , and ) inTCR molecules, and the gene is locatedwithin the gene. We clarified the genomicstructure around J segments and C regionencoding TCR and genes in the presentstudy.The complete genomic region, 131.2kb inlength, including the swine T cell receptor/ constant region (TRAC/TRDC) and joiningsegments (TRAJ/TRDJ) was sequenced.The structure of this region was strikinglyconserved in comparison with that of thehuman or mouse. All of the TRAJ segmentsdetected in the human genomic sequencewere also detected in the swine sequence andthe sequence of the protein-binding site of Tearly alpha (TEA) and enhancer elementwas highly conserved. Insertion of the repetitivesequences that were interspersed afterthe differentiation of the species in mammalssuch as LINE and SINE are markedly suppressedin comparison with other genomicregions, while locations of the mammalianwideinterspersed sequences (MIRs) are wellconserved between humans and pigs. Thisfinding suggests the existence of highlyselective pressure to conserve this genomicregion around TRAJ throughout the evolutionprocess in mammals. Intensive analysisof the repertoire and the rearrangementmachinery of swine TRA/TRD based on theresults presented here will be a clue tounderstanding the function of / T cellsin artiodactyls, which have a relativelyhigher ratio of T cells in total peripheral Tcells than humans or mice.Fig. 1Genomic structure of the region including all of the swine TCR / J segmentsand C regions. Four J (TRDJ), 62 J (TRAJ) segments, one V (TRDV) segment,C (TRAC) and C (TRDC) regions were detected. Putative enhancerelements for TRA and TRD, and the TEA promotor were also observed.Annual Report 2003 3
Page 3 and 4: Message from the PresidentIn cooper
Page 5 and 6: ¡X-ray crystallographic studies of
Page 7: Topics of Research in This YearComp
Page 11 and 12: the total library) were mapped onto
Page 13 and 14: observed among the ribosomal protei
Page 15 and 16: molecular analyses and morphologica
Page 17 and 18: with 5 IU equine chorionic gonadotr
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Page 21 and 22: exogenous genes into a hymenopteran
Page 23 and 24: Isolation and characterization of B
Page 25 and 26: oids could be regenerated from endo
Page 27 and 28: Quantitative trait locus analyses o
Page 29 and 30: ion, induces hypercholesterolemia,
Page 31 and 32: is an important source for amino ac
Page 33 and 34: In this study, 1.4 and 1.6 kb-long
Page 35 and 36: aqueous solution using cyanuric chl
Page 37 and 38: Developing a waste selection device
Page 39 and 40: decreased every five days by 5˚C,
Page 41 and 42: ticides. If the viral dose that kil
Page 43 and 44: In addition, the number of crown ro
Page 45 and 46: Molecular structure of the GARP fam
Page 47 and 48: X-ray crystallographic studies ofSt
Page 49 and 50: Rapid and high resolution QTL analy
Page 51 and 52: Plant regeneration system through m
Page 53 and 54: Table 1 Transformation Efficiency a
Page 55 and 56: from the tissues of mutants. The In
Page 57 and 58: the regenerated plants were transpl
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plants and fungi, and RNA interfere
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eeding, classification of microbes
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efforts are made to obtain single m
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was carried out by shotgun sequenci
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epetitive sequence specific to Oryz
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75 µM of ABA at 25ºC. More than 8
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Change of the molecular weightforms
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A unique landrace group recognizedb
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eaction (PCR) primer pairs to detec
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This was the first successful case
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to disappear by degradation or dilu
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tained 1933 independent genes and b
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that antigen-specific regulatory T
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neural activity patterns evoked by
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considerable effect on the suscepti
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Insect Genetics and Evolution Depar
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activity, which was found to detoxi
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Insect Biomaterial and Technology D
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peptides obtained from sericin a re
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DNA markers for Nid-1, a resistance
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or carotenoid pigment. When sericin
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Plant Science DivisionThe Plant Sci
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mutants have been studied in relati
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have verified that candidate genes
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and C, connected by a distorted typ
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mammalian cells, respectively, inhi
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undle sheath cells (BSCs), the land
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(OsNHX1), barley (HvNHX1) and baril
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nation rates. However, in our attem
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Yeast two-hybrid assay showed inter
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and a few NADPH-cytochrome P450 oxi
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the R0(53%).Foreign genes (35S + np
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gamma ray from 44 TBq 60 Co was use
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List of PublicationOriginal Papers1
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35 Fujisaki S, Mizoguchi Y, Takahas
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71 Imai K, Khandoker MY, Yonai M, T
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107 Kiuchi S, Inage Y, Hiraiwa H, U
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147 Miyamoto Y, Sakumoto R, Sakabe
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184 Ochi A, Hossain KS, Magoshi J,
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219 Takahashi M, Nagai T, Okamura N
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258 Watanabe H, Nakashima K, Saito
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Author Department Paper.No.Yasushi
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Author Department Paper.No.Sadao Wa
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Monograph1 Magoshi J, Nakamura S (2
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on Lepidopteran Genomics”.NIAS-CO
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tion of the high-quality draft sequ
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Executive Members andResearch Staff
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Insect Growth Regulation Laboratory
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Sericultural Science LaboratoryMole
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Members of NIAS EvaluationComittee(
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Annual Report 2003 153
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Annual Report 2003

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