Dataset Information

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.

ABSTRACT: We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is approximately 32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene.

SUBMITTER: Rice Annotation Project

PROVIDER: S-EPMC1781349 | biostudies-literature | 2007 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.

Itoh Takeshi T Tanaka Tsuyoshi T Barrero Roberto A RA Yamasaki Chisato C Fujii Yasuyuki Y Hilton Phillip B PB Antonio Baltazar A BA Aono Hideo H Apweiler Rolf R Bruskiewich Richard R Bureau Thomas T Burr Frances F Costa de Oliveira Antonio A Fuks Galina G Habara Takuya T Haberer Georg G Han Bin B Harada Erimi E Hiraki Aiko T AT Hirochika Hirohiko H Hoen Douglas D Hokari Hiroki H Hosokawa Satomi S Hsing Yue-ie YI Ikawa Hiroshi H Ikeo Kazuho K Imanishi Tadashi T Ito Yukiyo Y Jaiswal Pankaj P Kanno Masako M Kawahara Yoshihiro Y Kawamura Toshiyuki T Kawashima Hiroaki H Khurana Jitendra P JP Kikuchi Shoshi S Komatsu Setsuko S Koyanagi Kanako O KO Kubooka Hiromi H Lieberherr Damien D Lin Yao-Cheng YC Lonsdale David D Matsumoto Takashi T Matsuya Akihiro A McCombie W Richard WR Messing Joachim J Miyao Akio A Mulder Nicola N Nagamura Yoshiaki Y Nam Jongmin J Namiki Nobukazu N Numa Hisataka H Nurimoto Shin S O'Donovan Claire C Ohyanagi Hajime H Okido Toshihisa T Oota Satoshi S Osato Naoki N Osato Naoki N Palmer Lance E LE Quetier Francis F Raghuvanshi Saurabh S Saichi Naomi N Sakai Hiroaki H Sakai Yasumichi Y Sakata Katsumi K Sakurai Tetsuya T Sato Fumihiko F Sato Yoshiharu Y Schoof Heiko H Seki Motoaki M Shibata Michie M Shimizu Yuji Y Shinozaki Kazuo K Shinso Yuji Y Singh Nagendra K NK Smith-White Brian B Takeda Jun-ichi J Tanino Motohiko M Tatusova Tatiana T Thongjuea Supat S Todokoro Fusano F Tsugane Mika M Tyagi Akhilesh K AK Vanavichit Apichart A Wang Aihui A Wing Rod A RA Yamaguchi Kaori K Yamamoto Mayu M Yamamoto Naoyuki N Yu Yeisoo Y Zhang Hao H Zhao Qiang Q Higo Kenichi K Burr Benjamin B Gojobori Takashi T Sasaki Takuji T

Genome research 20070108 2

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experi ...[more]

PMID: 17210932

Similar Datasets

Project description:BackgroundCalcium signaling plays a prominent role in plants for coordinating a wide range of developmental processes and responses to environmental cues. Stimulus-specific generation of intracellular calcium transients, decoding of calcium signatures, and transformation of the signal into cellular responses are integral modules of the transduction process. Several hundred proteins with functions in calcium signaling circuits have been identified, and the number of downstream targets of calcium sensors is expected to increase. We previously identified a novel, calmodulin-binding nuclear protein, IQD1, which stimulates glucosinolate accumulation and plant defense in Arabidopsis thaliana. Here, we present a comparative genome-wide analysis of a new class of putative calmodulin target proteins in Arabidopsis and rice.ResultsWe identified and analyzed 33 and 29 IQD1-like genes in Arabidopsis thaliana and Oryza sativa, respectively. The encoded IQD proteins contain a plant-specific domain of 67 conserved amino acid residues, referred to as the IQ67 domain, which is characterized by a unique and repetitive arrangement of three different calmodulin recruitment motifs, known as the IQ, 1-5-10, and 1-8-14 motifs. We demonstrated calmodulin binding for IQD20, the smallest IQD protein in Arabidopsis, which consists of a C-terminal IQ67 domain and a short N-terminal extension. A striking feature of IQD proteins is the high isoelectric point (approximately 10.3) and frequency of serine residues (approximately 11%). We compared the Arabidopsis and rice IQD gene families in terms of gene structure, chromosome location, predicted protein properties and motifs, phylogenetic relationships, and evolutionary history. The existence of an IQD-like gene in bryophytes suggests that IQD proteins are an ancient family of calmodulin-binding proteins and arose during the early evolution of land plants.ConclusionComparative phylogenetic analyses indicate that the major IQD gene lineages originated before the monocot-eudicot divergence. The extant IQD loci in Arabidopsis primarily resulted from segmental duplication and reflect preferential retention of paralogous genes, which is characteristic for proteins with regulatory functions. Interaction of IQD1 and IQD20 with calmodulin and the presence of predicted calmodulin binding sites in all IQD family members suggest that IQD proteins are a new class of calmodulin targets. The basic isoelectric point of IQD proteins and their frequently predicted nuclear localization suggest that IQD proteins link calcium signaling pathways to the regulation of gene expression. Our comparative genomics analysis of IQD genes and encoded proteins in two model plant species provides the first step towards the functional dissection of this emerging family of putative calmodulin targets.

Project description:BACKGROUND AND AIMS:Salt stress leads to attenuated growth and productivity in rice. Transcription factors like heat shock factors (HSFs) represent central regulators of stress adaptation. Heat shock factors of the classes A and B are well established as regulators of thermal and non-thermal stress responses in plants; however, the role of class C HSFs is unknown. Here we characterized the function of the OsHsfC1b (Os01g53220) transcription factor from rice. METHODOLOGY:We analysed the expression of OsHsfC1b in the rice japonica cultivars Dongjin and Nipponbare exposed to salt stress as well as after mannitol, abscisic acid (ABA) and H(2)O(2) treatment. For functional characterization of OsHsfC1b, we analysed the physiological response of a T-DNA insertion line (hsfc1b) and two artificial micro-RNA (amiRNA) knock-down lines to salt, mannitol and ABA treatment. In addition, we quantified the expression of small Heat Shock Protein (sHSP) genes and those related to signalling and ion homeostasis by quantitative real-time polymerase chain reaction in roots exposed to salt. The subcellular localization of OsHsfC1b protein fused to green fluorescent protein (GFP) was determined in Arabidopsis mesophyll cell protoplasts. PRINCIPAL RESULTS:Expression of OsHsfC1b was induced by salt, mannitol and ABA, but not by H(2)O(2). Impaired function of OsHsfC1b in the hsfc1b mutant and the amiRNA lines led to decreased salt and osmotic stress tolerance, increased sensitivity to ABA, and temporal misregulation of salt-responsive genes involved in signalling and ion homeostasis. Furthermore, sHSP genes showed enhanced expression in knock-down plants under salt stress. We observed retarded growth of hsfc1b and knock-down lines in comparison with control plants under non-stress conditions. Transient expression of OsHsfC1b fused to GFP in protoplasts revealed nuclear localization of the transcription factor. CONCLUSIONS:OsHsfC1b plays a role in ABA-mediated salt stress tolerance in rice. Furthermore, OsHsfC1b is involved in the response to osmotic stress and is required for plant growth under non-stress conditions.

Dataset Information

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.

Publications

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets