genome annotation of Oryza sativa ssp . japonica and comparative genome analysis with Arabidopsis thaliana The Rice Annotation Project

Access the most recent version at doi: 2007 17: 175-183; originally published online Jan 8, 2007; Genome Res. Gojobori, Takuji Sasaki and for the Rice Annotation Project Yamamoto, Naoyuki Yamamoto, Yeisoo Yu, Hao Zhang, Qiang Zhao, Kenichi Higo, Benjamin Burr, Takashi Mika Tsugane, Akhilesh K. Tyagi, Apichart Vanavichit, Aihui Wang, Rod A. Wing, Kaori Yamaguchi, Mayu Smith-White, Jun-ichi Takeda, Motohiko Tanino, Tatiana Tatusova, Supat Thongjuea, Fusano Todokoro, Motoaki Seki, Michie Shibata, Yuji Shimizu, Kazuo Shinozaki, Yuji Shinso, Nagendra K. Singh, Brian Sakai, Yasumichi Sakai, Katsumi Sakata, Tetsuya Sakurai, Fumihiko Sato, Yoshiharu Sato, Heiko Schoof, Satoshi OOta, Naoki Osato, Lance E. Palmer, Francis Quetier, Saurabh Raghuvanshi, Naomi Saichi, Hiroaki Nobukazu Namiki, Hisataka Numa, Shin Nurimoto, Claire O’Donovan, Hajime Ohyanagi, Toshihisa Okido, Richard McCombie, Joachim Messing, Akio Miyao, Nicola Mulder, Yoshiaki Nagamura, Jongmin Nam, Kubooka, Damien Lieberherr, Yao-Cheng Lin, David Lonsdale, Takashi Matsumoto, Akihiro Matsuya, W. Hiroaki Kawashima, Jitendra P. Khurana, Shoshi Kikuchi, Setsuko Komatsu, Kanako O. Koyanagi, Hiromi Tadashi Imanishi, Yukiyo Ito, Pankaj Jaiswal, Masako Kanno, Yoshihiro Kawahara, Toshiyuki Kawamura, Hirohiko Hirochika, Douglas Hoen, Hiroki Hokari, Satomi Hosokawa, Yue Hsing, Hiroshi Ikawa, Kazuho Ikeo, Costa de Oliveira, Galina Fuks, Takuya Habara, Georg Haberer, Bin Han, Erimi Harada, Aiko T. Hiraki, Antonio Baltazar A. Antonio, Hideo Aono, Rolf Apweiler, Richard Bruskiewich, Thomas Bureau, Frances Burr, Takeshi Itoh, Tsuyoshi Tanaka, Roberto A. Barrero, Chisato Yamasaki, Yasuyuki Fujii, Phillip B. Hilton, Arabidopsis thaliana comparative genome analysis with and japonica ssp. Oryza sativa Curated genome annotation of

[1]  Yasuyuki Fujii,et al.  The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information , 2005, Nucleic Acids Res..

[2]  G. An,et al.  Functional Diversification of the Two C-Class MADS Box Genes OSMADS3 and OSMADS58 in Oryza sativa[W][OA] , 2005, The Plant Cell Online.

[3]  S. Salzberg,et al.  The Transcriptional Landscape of the Mammalian Genome , 2005, Science.

[4]  Takuji Sasaki,et al.  The map-based sequence of the rice genome , 2005, Nature.

[5]  Rolf Apweiler,et al.  InterProScan: protein domains identifier , 2005, Nucleic Acids Res..

[6]  N. Chua,et al.  MicroRNA Directs mRNA Cleavage of the Transcription Factor NAC1 to Downregulate Auxin Signals for Arabidopsis Lateral Root Development , 2005, The Plant Cell Online.

[7]  Thomas Girke,et al.  Cloning and Characterization of MicroRNAs from Ricew⃞ , 2005, The Plant Cell Online.

[8]  R. Dean,et al.  Large-Scale Identification of Expressed Sequence Tags Involved in Rice and Rice Blast Fungus Interaction1 , 2005, Plant Physiology.

[9]  A. Hüttenhofer,et al.  Non-coding RNAs: hope or hype? , 2005, Trends in genetics : TIG.

[10]  S. Komatsu,et al.  Rice proteome analysis: A step toward functional analysis of the rice genome , 2005, Proteomics.

[11]  Patrick S. Schnable,et al.  Evaluation of five ab initio gene prediction programs for the discovery of maize genes , 2005, Plant Molecular Biology.

[12]  Dawei Li,et al.  The Genomes of Oryza sativa: A History of Duplications , 2005, PLoS biology.

[13]  Jianxin Ma,et al.  Consistent over-estimation of gene number in complex plant genomes. , 2004, Current opinion in plant biology.

[14]  R. E. Miller,et al.  Construction and Evaluation of cDNA Libraries for Large-Scale Expressed Sequence Tag Sequencing in Wheat (Triticum aestivum L.) , 2004, Genetics.

[15]  B. Larkins,et al.  Characterization of the maize endosperm transcriptome and its comparison to the rice genome. , 2004, Genome research.

[16]  Qingpo Liu,et al.  Synonymous codon usage bias in Oryza sativa , 2004 .

[17]  G. Bernardi,et al.  The new genes of rice: a closer look. , 2004, Trends in plant science.

[18]  Kanako O. Koyanagi,et al.  Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones , 2004, PLoS Biology.

[19]  Steven G. Schroeder,et al.  Anchoring 9,371 Maize Expressed Sequence Tagged Unigenes to the Bacterial Artificial Chromosome Contig Map by Two-Dimensional Overgo Hybridization1 , 2004, Plant Physiology.

[20]  Wen-Hsiung Li,et al.  Dating the Monocot–Dicot Divergence and the Origin of Core Eudicots Using Whole Chloroplast Genomes , 2004, Journal of Molecular Evolution.

[21]  H. Leung,et al.  Rice Mutant Resources for Gene Discovery , 2004, Plant Molecular Biology.

[22]  A. Miyao,et al.  Target Site Specificity of the Tos17 Retrotransposon Shows a Preference for Insertion within Genes and against Insertion in Retrotransposon-Rich Regions of the Genome Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.012559. , 2003, The Plant Cell Online.

[23]  J. Kawai,et al.  Collection, Mapping, and Annotation of Over 28,000 cDNA Clones from japonica Rice , 2003, Science.

[24]  Ram Samudrala,et al.  Bioverse: functional, structural and contextual annotation of proteins and proteomes , 2003, Nucleic Acids Res..

[25]  M. Yano,et al.  Comparative biology comes into bloom: genomic and genetic comparison of flowering pathways in rice and Arabidopsis. , 2003, Current opinion in plant biology.

[26]  D. Barrell,et al.  The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. , 2003, Genome research.

[27]  Heiko Schoof,et al.  Comparison of rice and Arabidopsis annotation. , 2003, Current opinion in plant biology.

[28]  Michael Ashburner,et al.  Annotation of the Drosophila melanogaster euchromatic genome: a systematic review , 2002, Genome Biology.

[29]  T. Gojobori,et al.  The genome sequence and structure of rice chromosome 1 , 2002, Nature.

[30]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica) , 2002, Science.

[31]  V. Brendel,et al.  Comparison of RNA Expression Profiles Based on Maize Expressed Sequence Tag Frequency Analysis and Micro-Array Hybridization1 , 2002, Plant Physiology.

[32]  K. Waki,et al.  A Comprehensive Rice Transcript Map Containing 6591 Expressed Sequence Tag Sites , 2002, The Plant Cell Online.

[33]  P J Green,et al.  Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs. , 2001, Plant physiology.

[34]  Rolf Apweiler,et al.  InterProScan - an integration platform for the signature-recognition methods in InterPro , 2001, Bioinform..

[35]  Michael J. Stanhope,et al.  Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates , 2001, Nature.

[36]  J A Eisen,et al.  Microbial Genes in the Human Genome: Lateral Transfer or Gene Loss? , 2001, Science.

[37]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[38]  The Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[39]  M. Lynch,et al.  The evolutionary fate and consequences of duplicate genes. , 2000, Science.

[40]  M. Nei,et al.  Molecular Evolution and Phylogenetics , 2000 .

[41]  L. Duret,et al.  tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. , 2000, Trends in genetics : TIG.

[42]  Temple F. Smith,et al.  Biology's new Rosetta stone , 1997, Nature.

[43]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[44]  Masatoshi Nei,et al.  Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites , 1994, Journal of Molecular Evolution.

[45]  R. Cortese,et al.  Sequences of four tRNA genes from Caenorhabditis elegans and the expression of C. elegans tRNALeu (anticodon IAG) in Xenopus oocytes. , 1982, Nucleic acids research.

[46]  T. Ikemura Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. , 1981, Journal of molecular biology.

[47]  M. Gouy,et al.  Codon catalog usage and the genome hypothesis. , 1980, Nucleic acids research.

[48]  Jun Wang,et al.  Genome-wide transcription analyses in rice using tiling microarrays , 2006, Nature Genetics.

[49]  Kenichi Higo,et al.  Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003 , 2004, Nucleic Acids Res..

[50]  Hans-Werner Mewes,et al.  MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics , 2004, Nucleic Acids Res..

[51]  A. Oliphant,et al.  A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). , 2002, Science.

[52]  T. Ikemura Codon usage and tRNA content in unicellular and multicellular organisms. , 1985, Molecular biology and evolution.