RiceFOX: A Database of Arabidopsis Mutant Lines Overexpressing Rice Full-Length cDNA that Contains a Wide Range of Trait Information to Facilitate Analysis of Gene Function

Sakurai, Tetsuya; Kondou, Youichi; Akiyama, Kenji; Kurotani, Atsushi; Higuchi, Masakazu; Ichikawa, Takanari; Kawakubo, Hirofumi; Kusano, Miyako; Mori, Masaki; Saitou, Tsutomu; Sakakibara, Hitoshi; Sugano, Shoji; Suzuki, Makoto; Takahashi, Hideki; Takahashi, Shinya; Takatsuji, Hiroshi; Yokotani, Naoki; Yoshizumi, Takeshi; Saito, Kazuki; Shinozaki, Kazuo; Oda, Kazuhiro; Hirochika, Hirohiko; Matsui, Minami

doi:10.1093/pcp/pcq190

Cited by 58 publications

(44 citation statements)

References 56 publications

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“…We compared the appearance of any morphological effects with those that appeared in FOX lines (32). Lines overexpressing coding sORFs were associated with a higher proportion of growth rate or flowering timing differences compared with the FOX lines (Table 1).…”

Section: Resultsmentioning

confidence: 99%

Small open reading frames associated with morphogenesis are hidden in plant genomes

Hanada

Higuchi-Takeuchi

Okamoto

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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172

160

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It is likely that many small ORFs (sORFs; 30-100 amino acids) are missed when genomes are annotated. To overcome this limitation, we identified ∼8,000 sORFs with high coding potential in intergenic regions of the Arabidopsis thaliana genome. However, the question remains as to whether these coding sORFs play functional roles. Using a designed array, we generated an expression atlas for 16 organs and 17 environmental conditions among 7,901 identified coding sORFs. A total of 2,099 coding sORFs were highly expressed under at least one experimental condition, and 571 were significantly conserved in other land plants. A total of 473 coding sORFs were overexpressed; ∼10% (49/473) induced visible phenotypic effects, a proportion that is approximately seven times higher than that of randomly chosen known genes. These results indicate that many coding sORFs hidden in plant genomes are associated with morphogenesis. We believe that the expression atlas will contribute to further study of the roles of sORFs in plants.transcriptome | phenome | Agilent custom microarray | transgenic plant | peptide hormone I t has been revealed that small ORFs (sORFs; 30-100 amino acids) are translated into peptides that play essential roles in eukaryotes. For example, in yeast, 21 of 247 peptides encoded by sORFs are essential for viability, as identified by KO analyses (1). In Drosophila, several peptides encoded by sORFs are involved in activating transcription factors related to development (2). In plants, a number of peptides encoded by known small genes (<150 codons) play significant roles in various aspects of plant growth and development. Specific receptors for various peptides have been identified as receptor kinases (3-18). Although peptides translated from sORFs have important roles, a high rate of false-positive prediction affects the identification of coding sORFs in genome sequences (19,20). Therefore, in a representative plant species, Arabidopsis thaliana, many small genes had been manually identified using a restricted Markov model and similarity searching (21). To further explore the field of small genes, we developed a computational method to identify coding sORFs using the hexamer composition bias between coding sequences (CDSs) and noncoding sequences (NCDSs) (22, 23). Among available gene finders, this program package has the best performance for identifying true small genes (24).The model plant species A. thaliana has a high-quality genome, and more than 7,000 coding sORFs were identified in the intergenic regions that lacked annotated genes (22). The coding sORFs do not have any sequence similarities to annotated genes. In the present study, to examine the functional roles of these newly identified coding sORFs, we designed an array to generate an expression atlas under 16 developmental stages and 17 environmental conditions, with three replicates. Then, we looked for evidence of expression of coding sORFs. We also examined the signatures of selective constraints on the CDSs among the coding sORFs in 16 land plant sp...

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Section: Resultsmentioning

confidence: 99%

Small open reading frames associated with morphogenesis are hidden in plant genomes

Hanada

Higuchi-Takeuchi

Okamoto

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

172

160

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“…Using a normalized full-length cDNA library, Ichikawa et al 2006 have developed 30,000 independent Arabidopsis FOX lines which are available from RIKEN. As a further extension of this, full-length rice cDNA clones have been transformed into Arabidopsis with an aim of screening for rice functional genes in a high-throughput manner (Sakurai et al 2010 ).…”

Section: Gain-of-function Systems For Functional Analysismentioning

confidence: 99%

Arabidopsis thaliana: A Model for Plant Research

Sivasubramanian

Mukhi

Kaur

2015

Plant Biology and Biotechnology

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Arabidopsis thaliana , a small, fl owering, self-pollinating weed, has been developed into an elegant model system. Concerted effort from the plant research community has led to development of extensive genomic resources, tools, and techniques. Advances in high-throughput (omicsbased) approaches and their application in Arabidopsis research have provided ample understanding of basic biological processes in plants. Further, bioinformatics platforms allow for integration of the multiple "omics" data, thus, enhancing our appreciation of biological interactions at an organismal level. Taken together, A. thaliana has emerged as an excellent reference source for functional and comparative genomic analysis. In this chapter, we summarize advances made in the fi eld of Arabidopsis research and resources, tools, and technologies available to the plant scientifi c community. In addition, we briefl y discuss ways in which knowledge gained from this model system can be harnessed for effective deployment in crop improvement.

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“…From this library, more than 33,000 independent Arabidopsis transgenic lines (rice FOX Arabidopsis lines) expressing rice fl-cDNAs were obtained 520 M. Higuchi-Takeuchi et al . The screening results are available through the website (http://ricefox.psc.riken.jp; Sakurai et al, 2011). The functions of several rice genes investigated with the rice FOX Arabidopsis lines are summarized in Table 1.…”

Section: Rice Fox Arabidopsis Linesmentioning

confidence: 99%

“…The sequence analysis provided 6,501 fl-cDNAs from 13,018 (70.2%) of the tested lines, of which 3,309 fl-cDNAs were identified in more than two lines. The flcDNA information is available in the rice fl-cDNA overexpressed Arabidopsis mutant database (http://ricefox.psc.riken.jp; Sakurai et al, 2011).…”

Section: Rice Fox Arabidopsis Linesmentioning

confidence: 99%

High-throughput analysis of rice genes by means of the heterologous full-length cDNA overexpressor (FOX)-hunting system

Higuchi-Takeuchi¹,

Mori²,

Matsui³

2013

Int. J. Dev. Biol.

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Mutant populations are indispensable tools for investigating plant gene functions.Gain-of-function technology is one of the approaches used for the systematic production of mutant resources and activation tagging is a well-established method to generate gain-of-function mutants in plants. As an alternative approach for the systematic generation of a gain-of-function mutant population, we developed the Full-length cDNA OvereXpressor (FOX)-hunting system in which full-length cDNAs (fl-cDNAs) are overexpressed in plants to quickly identify candidate genes. The FOX-hunting system was used for high-throughput analysis of rice (Oryza sativa) genes heterologously expressed in Arabidopsis thaliana (rice FOX Arabidopsis lines). A large screening to identify and characterize rice genes with rice FOX Arabidopsis lines revealed that one of the isolated genes, BROAD-SPECTRUM RESISTANCE 1 (BSR1) conferred multiple or broad-spectrum disease resistance in both a dicotyledonous and monocotyledonous plant. We found that expression of rice fl-cDNAs without a homolog in Arabidopsis affected morphological traits. In addition, overexpression of homologous genes of rice and Arabidopsis led to a similar phenotype. Thus, we conclude that the FOX-hunting system is an excellent heterologous system and offers a new tool with which to explore gene function in rice.

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RiceFOX: A Database of Arabidopsis Mutant Lines Overexpressing Rice Full-Length cDNA that Contains a Wide Range of Trait Information to Facilitate Analysis of Gene Function

Cited by 58 publications

References 56 publications

Small open reading frames associated with morphogenesis are hidden in plant genomes

Small open reading frames associated with morphogenesis are hidden in plant genomes

Arabidopsis thaliana: A Model for Plant Research

High-throughput analysis of rice genes by means of the heterologous full-length cDNA overexpressor (FOX)-hunting system

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