Results 1 - 10 of 39

The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res 35: D883–887

by Shu Ouyang, Wei Zhu, John Hamilton, Haining Lin, Matthew Campbell, Kevin Childs, Renae L. Malek, An Lee, Li Zheng, Joshua Orvis, Brian Haas, Jennifer Wortman, C. Robin Buell , 2007
"... continued to update the rice genome sequence with new data and improve the quality of the annotation. In our current release of annotation (Release 4.0; January 12, 2006), we have identified 42 653 non-transposable element-related genes encoding 49 472 gene models as a result of the detection of alt ..."
Abstract - Cited by 161 (2 self) - Add to MetaCart
continued to update the rice genome sequence with new data and improve the quality of the annotation. In our current release of annotation (Release 4.0; January 12, 2006), we have identified 42 653 non-transposable element-related genes encoding 49 472 gene models as a result of the detection of alternative splicing. We have refined our identification methods for transposable element-related genes resulting in 13 237 genes that are related to transposable ele-ments. Through incorporation of multiple transcript and proteomic expression data sets, we have been able to annotate 24 799 genes (31 739 gene models), representing 50 % of the total gene models, as expressed in the rice genome. All structural and functional annotation is viewable through our Rice Genome Browser which currently supports 59 tracks. Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads.

Gramene: a growing plant comparative genomics resource

by Chengzhi Liang, Pankaj Jaiswal, Claire Hebbard, Shuly Avraham, Edward S. Buckler, Terry Casstevens, Bonnie Hurwitz, Susan Mccouch, Junjian Ni, Anuradha Pujar, Dean Ravenscroft, Liya Ren, William Spooner, Isaak Tecle, Jim Thomason, Chih-wei Tung, Xuehong Wei, Immanuel Yap - Nucleic Acids Res , 2008
"... doi:10.1093/nar/gkm968 Gramene: a growing plant comparative genomics resource ..."
Abstract - Cited by 32 (6 self) - Add to MetaCart
doi:10.1093/nar/gkm968 Gramene: a growing plant comparative genomics resource
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Type-B ARR transcription factors, ARR10 and ARR12, are implicated in cytokinin-mediated regulation of protoxylem differentiation in roots of Arabidopsis thaliana. Plant and Cell Physiology 48

by Akihiro Yokoyama, Takafumi Yamashino, Yu-ichiro Amano, Yoshinori Tajima, Aya Imamura, Hitoshi Sakakibara, Takeshi Mizuno , 2007
"... In the phosphorelay-mediated cytokinin signal transduction of Arabidopsis thaliana, certain members of the type-B authentic response regulator (ARR) family are implicated in the regulatory networks that are primarily propagated by the cytokinin-receptors [authentic histidine kinases (AHKs)]. Clarifi ..."
Abstract - Cited by 13 (5 self) - Add to MetaCart
In the phosphorelay-mediated cytokinin signal transduction of Arabidopsis thaliana, certain members of the type-B authentic response regulator (ARR) family are implicated in the regulatory networks that are primarily propagated by the cytokinin-receptors [authentic histidine kinases (AHKs)]. Clarification of the involvement of each type-B ARR transcription factor in cytokinin-responsive phenomena is still at a very early stage. Here we analyzed the redundant function of two type-B ARR genes, ARR10 and ARR12, by constructing an arr10/arr12 double mutant. The resulting mutant plants showed stronger phenotypes with special reference to the cytokinin action in roots (e.g. inhibition of root elongation, green callus formation from root explants) than those for each single mutant, suggesting that ARR10 and ARR12 redundantly play an

Sequencing and analysis of approximately 40,000 soybean cDNA clones from a full-lengthenriched cDNA library

by Taishi Umezawa, Tetsuya Sakurai, Yasushi Totoki, Atsushi Toyoda, Motoaki Seki, Atsushi Ishiwata, Kenji Akiyama, Atsushi Kurotani, Takuhiro Yoshida, Keiichi Mochida, Mie Kasuga, Daisuke Todaka, Kyonoshin Maruyama, Kazuo Nakashima, Akiko Enju, Saho Mizukado, Selina Ahmed, Kyoko Yoshiwara, Kyuya Harada, Yasutaka Tsubokura, Masaki Hayashi, Shusei Sato, Toyoaki Anai, Masao Ishimoto, Hideyuki Funatsuki, Masayoshi Teraishi, Mitsuru Osaki, Takuro Shinano, Ryo Akashi, Yoshiyuki Sakaki, Kazuko Yamaguchi-shinozaki, Kazuo Shinozaki - DNA Res , 2008
"... ..."
Abstract - Cited by 7 (3 self) - Add to MetaCart
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RiceXPro version 3.0: expanding the informatics resource for rice transcriptome

by Yutaka Sato, Hinako Takehisa, Kaori Kamatsuki, Hiroshi Minami, Nobukazu Namiki, Hiroshi Ikawa, Hajime Ohyanagi, Kazuhiko Sugimoto, Baltazar A. Antonio, Yoshiaki Nagamura - Nucleic Acids Res , 2013
"... A wide range of resources on gene expression profiling enhance various strategies in plant molecu-lar biology particularly in characterization of gene function. We have updated our gene expression profile database, RiceXPro ..."
Abstract - Cited by 6 (0 self) - Add to MetaCart
A wide range of resources on gene expression profiling enhance various strategies in plant molecu-lar biology particularly in characterization of gene function. We have updated our gene expression profile database, RiceXPro

Plant cytochrome P450s from moss to poplar

by David R. Nelson - Phytochem. Rev , 2006
"... This review represents the first attempt to define the origins of the major P450-containing pathways in plants. Comparative genomics with five complete P450 gene sets from Chlamydomonas reinhardtii with 39 sequences, Physcomitrella patens (moss) with 71 sequences, rice with 356 sequences, Arabidopsi ..."
Abstract - Cited by 5 (1 self) - Add to MetaCart
This review represents the first attempt to define the origins of the major P450-containing pathways in plants. Comparative genomics with five complete P450 gene sets from Chlamydomonas reinhardtii with 39 sequences, Physcomitrella patens (moss) with 71 sequences, rice with 356 sequences, Arabidopsis with 246 sequences and Populus with 312 sequences is used to estimate how old each gene family is and to identify the most ancient P450s and their pathways. The pathways included are the phenylpropanoid and lignin pathways, the gibberellin pathway, the oxylipin/jasmonate pathway, the basic flavonoid pathway, the brassinosteroid pathway, the abscisic acid pathway and the cutin synthesis pathway. An effort is made to identify at least some examples of P450s that have emerged at many different levels of the evolutionary bush, from the base to the tips.

Discovery of genome-wide DNA polymorphisms in a landrace cultivar of japonica rice by whole-genome sequencing. Plant Cell Physiol

by Yuko Arai-kichise, Yuh Shiwa, Hideki Nagasaki, Kaworu Ebana, Hirofumi Yoshikawa, Masahiro Yano, Kyo Wakasa
"... Molecular breeding approaches are of growing importance to crop improvement. However, closely related cultivars generally used for crossing material lack sufficient known DNA polymorphisms due to their genetic relatedness. Next-generation sequencing allows the identification of a massive number of D ..."
Abstract - Cited by 4 (2 self) - Add to MetaCart
Molecular breeding approaches are of growing importance to crop improvement. However, closely related cultivars generally used for crossing material lack sufficient known DNA polymorphisms due to their genetic relatedness. Next-generation sequencing allows the identification of a massive number of DNA polymorphisms such as single nu-cleotide polymorphisms (SNPs) and insertions–deletions (InDels) between highly homologous genomes. Using this technology, we performed whole-genome sequencing of a landrace of japonica rice, Omachi, which is used for sake brewing and is an important source for modern cultivars. A total of 229 million reads, each comprising 75 nucleotides of the Omachi genome, was generated with 45-fold coverage and uniquely mapped to 89.7 % of the Nipponbare genome, a closely related cultivar. We identified 132,462 SNPs, 16,448 insertions and 19,318 deletions between the Omachi and Nipponbare genomes. An SNP array was designed to validate 731 selected SNPs, resulting in validation rates of 95 and 88% for the Omachi and Nipponbare genomes, respectively. Among the 577 SNPs validated in both genomes, 532 are entirely new SNP markers not previously reported between related rice cultivars. We also validated InDels on a part of chromosome 2 as DNA markers and successfully genotyped five japonica rice cultivars. Our results present the method-ology and extensive data on SNPs and InDels available for whole-genome genotyping and marker-assisted breeding. The polymorphism information between Omachi and Nipponbare is available at NGRC_Rice_Omachi
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RiceFREND: a platform for retrieving coexpressed gene networks in rice

by Yutaka Sato, Nobukazu Namiki, Hinako Takehisa, Kaori Kamatsuki, Jun-ichi Itoh, Baltazar A. Antonio, Yoshiaki Nagamura , 2012
"... Similarity of gene expression across a wide range of biological conditions can be efficiently used in char-acterization of gene function. We have constructed a rice gene coexpression database, RiceFREND ..."
Abstract - Cited by 4 (0 self) - Add to MetaCart
Similarity of gene expression across a wide range of biological conditions can be efficiently used in char-acterization of gene function. We have constructed a rice gene coexpression database, RiceFREND

Large-Scale Collection and Analysis of Full-Length cDNAs from Brachypodium distachyon and Integration with Pooideae Sequence Resources

by Keiichi Mochida, Yukiko Uehara-yamaguchi, Fuminori Takahashi, Takuhiro Yoshida, Tetsuya Sakurai, Kazuo Shinozaki , 2013
"... A comprehensive collection of full-length cDNAs is essential for correct structural gene annotation and functional analyses of genes. We constructed a mixed full-length cDNA library from 21 different tissues of Brachypodium distachyon Bd21, and obtained 78,163 high quality expressed sequence tags (E ..."
Abstract - Cited by 3 (0 self) - Add to MetaCart
A comprehensive collection of full-length cDNAs is essential for correct structural gene annotation and functional analyses of genes. We constructed a mixed full-length cDNA library from 21 different tissues of Brachypodium distachyon Bd21, and obtained 78,163 high quality expressed sequence tags (ESTs) from both ends of ca. 40,000 clones (including 16,079 contigs). We updated gene structure annotations of Brachypodium genes based on full-length cDNA sequences in comparison with the latest publicly available annotations. About 10,000 non-redundant gene models were supported by full-length cDNAs; ca. 6,000 showed some transcription unit modifications. We also found ca. 580 novel gene models, including 362 newly identified in Bd21. Using the updated transcription start sites, we searched a total of 580 plant cis-motifs in the 23 kb promoter regions and determined a genome-wide Brachypodium promoter architecture. Furthermore, we integrated the Brachypodium full-length cDNAs and updated gene structures with available sequence resources in wheat and barley in a web-accessible database, the RIKEN Brachypodium FL cDNA database. The database represents a ‘‘one-stop’ ’ information resource for all genomic information in the Pooideae, facilitating functional analysis of genes in this model grass plant and
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W: Rate and polarity of gene fusion and fission in Oryza sativa and Arabidopsis thaliana. Mol Biol Evol 2007, 24(1):110–121. Comparison of the expression patterns of two small gene families of S gene family receptor kinase genes during the defence respons

by Yoji Nakamura, Takeshi Itoh, William Martin - Gene
"... Running head: Gene fusion and fission in rice and Arabidopsis This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ..."
Abstract - Cited by 3 (0 self) - Add to MetaCart
Running head: Gene fusion and fission in rice and Arabidopsis This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License
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