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Hirose Y, Suda K, Liu YG, Sato S, Nakamura Y, Yokoyama K, Yamamoto N, Hanano S, Takita E, Sakurai N, Suzuki H, Nakamura Y, Kaneko T, Yano K, Tabata S, Shibata D. The Arabidopsis TAC Position Viewer: a high-resolution map of transformation-competent artificial chromosome (TAC) clones aligned with the Arabidopsis thaliana Columbia-0 genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:1114-1122. [PMID: 26227242 DOI: 10.1111/tpj.12949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 07/13/2015] [Accepted: 07/17/2015] [Indexed: 06/04/2023]
Abstract
We present a high-resolution map of genomic transformation-competent artificial chromosome (TAC) clones extending over all Arabidopsis thaliana (Arabidopsis) chromosomes. The Arabidopsis genomic TAC clones have been valuable genetic tools. Previously, we constructed an Arabidopsis genomic TAC library consisting of more than 10,000 TAC clones harboring large genomic DNA fragments extending over the whole Arabidopsis genome. Here, we determined 13,577 end sequences from 6987 Arabidopsis TAC clones and mapped 5937 TAC clones to precise locations, covering approximately 90% of the Arabidopsis chromosomes. We present the large-scale data set of TAC clones with high-resolution mapping information as a Java application tool, the Arabidopsis TAC Position Viewer, which provides ready-to-go transformable genomic DNA clones corresponding to certain loci on Arabidopsis chromosomes. The TAC clone resources will accelerate genomic DNA cloning, positional walking, complementation of mutants and DNA transformation for heterologous gene expression.
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Affiliation(s)
- Yoshitsugu Hirose
- Honda Research Institute Japan Co., Ltd., 8-1 Honcho, Wako-shi, Saitama, 351-0188, Japan
| | - Kunihiro Suda
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Yao-Guang Liu
- Laboratory of Genetic Engineering, South China Agricultural University, Gungzhou, 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Gungzhou, 510642, China
| | - Shusei Sato
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, 980-8577, Japan
| | - Yukino Nakamura
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama-ku, Kanagawa, Kawasaki, 214-8571, Japan
| | - Koji Yokoyama
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama-ku, Kanagawa, Kawasaki, 214-8571, Japan
| | - Naoki Yamamoto
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama-ku, Kanagawa, Kawasaki, 214-8571, Japan
| | - Shigeru Hanano
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Eiji Takita
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Nozomu Sakurai
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Hideyuki Suzuki
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Yasukazu Nakamura
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Takakazu Kaneko
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Kentaro Yano
- Bioinformatics Laboratory, Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama-ku, Kanagawa, Kawasaki, 214-8571, Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Daisuke Shibata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
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Bai SL, Zhong X, Ma L, Zheng W, Fan LM, Wei N, Deng XW. A simple and reliable assay for detecting specific nucleotide sequences in plants using optical thin-film biosensor chips. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 49:354-66. [PMID: 17156412 DOI: 10.1111/j.1365-313x.2006.02951.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Here we report the adaptation and optimization of an efficient, accurate and inexpensive assay that employs custom-designed silicon-based optical thin-film biosensor chips to detect unique transgenes in genetically modified (GM) crops and SNP markers in model plant genomes. Briefly, aldehyde-attached sequence-specific single-stranded oligonucleotide probes are arrayed and covalently attached to a hydrazine-derivatized biosensor chip surface. Unique DNA sequences (or genes) are detected by hybridizing biotinylated PCR amplicons of the DNA sequences to probes on the chip surface. In the SNP assay, target sequences (PCR amplicons) are hybridized in the presence of a mixture of biotinylated detector probes and a thermostable DNA ligase. Only perfect matches between the probe and target sequences, but not those with even a single nucleotide mismatch, can be covalently fixed on the chip surface. In both cases, the presence of specific target sequences is signified by a color change on the chip surface (gold to blue/purple) after brief incubation with an anti-biotin IgG horseradish peroxidase (HRP) to generate a precipitable product from an HRP substrate. Highly sensitive and accurate identification of PCR targets can be completed within 30 min. This assay is extremely robust, exhibits high sensitivity and specificity, and is flexible from low to high throughput and very economical. This technology can be customized for any nucleotide sequence-based identification assay and widely applied in crop breeding, trait mapping, and other work requiring positive detection of specific nucleotide sequences.
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Affiliation(s)
- Su-Lan Bai
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, and The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
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