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Wang Q, Zhang S, Li Y. Efficient DNA Coding Algorithm for Polymerase Chain Reaction Amplification Information Retrieval. Int J Mol Sci 2024; 25:6449. [PMID: 38928155 PMCID: PMC11204281 DOI: 10.3390/ijms25126449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/02/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Polymerase Chain Reaction (PCR) amplification is widely used for retrieving information from DNA storage. During the PCR amplification process, nonspecific pairing between the 3' end of the primer and the DNA sequence can cause cross-talk in the amplification reaction, leading to the generation of interfering sequences and reduced amplification accuracy. To address this issue, we propose an efficient coding algorithm for PCR amplification information retrieval (ECA-PCRAIR). This algorithm employs variable-length scanning and pruning optimization to construct a codebook that maximizes storage density while satisfying traditional biological constraints. Subsequently, a codeword search tree is constructed based on the primer library to optimize the codebook, and a variable-length interleaver is used for constraint detection and correction, thereby minimizing the likelihood of nonspecific pairing. Experimental results demonstrate that ECA-PCRAIR can reduce the probability of nonspecific pairing between the 3' end of the primer and the DNA sequence to 2-25%, enhancing the robustness of the DNA sequences. Additionally, ECA-PCRAIR achieves a storage density of 2.14-3.67 bits per nucleotide (bits/nt), significantly improving storage capacity.
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Affiliation(s)
| | - Shufang Zhang
- School of Electrical Automation and Information Engineering, Tianjin University, Tianjin 300072, China
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Nishimura K, Kokaji H, Motoki K, Yamazaki A, Nagasaka K, Mori T, Takisawa R, Yasui Y, Kawai T, Ushijima K, Yamasaki M, Saito H, Nakano R, Nakazaki T. Degenerate oligonucleotide primer MIG-seq: an effective PCR-based method for high-throughput genotyping. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2296-2317. [PMID: 38459738 DOI: 10.1111/tpj.16708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/14/2024] [Accepted: 02/14/2024] [Indexed: 03/10/2024]
Abstract
Next-generation sequencing (NGS) library construction often involves using restriction enzymes to decrease genome complexity, enabling versatile polymorphism detection in plants. However, plant leaves frequently contain impurities, such as polyphenols, necessitating DNA purification before enzymatic reactions. To overcome this problem, we developed a PCR-based method for expeditious NGS library preparation, offering flexibility in number of detected polymorphisms. By substituting a segment of the simple sequence repeat sequence in the MIG-seq primer set (MIG-seq being a PCR method enabling library construction with low-quality DNA) with degenerate oligonucleotides, we introduced variability in detectable polymorphisms across various crops. This innovation, named degenerate oligonucleotide primer MIG-seq (dpMIG-seq), enabled a streamlined protocol for constructing dpMIG-seq libraries from unpurified DNA, which was implemented stably in several crop species, including fruit trees. Furthermore, dpMIG-seq facilitated efficient lineage selection in wheat and enabled linkage map construction and quantitative trait loci analysis in tomato, rice, and soybean without necessitating DNA concentration adjustments. These findings underscore the potential of the dpMIG-seq protocol for advancing genetic analyses across diverse plant species.
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Affiliation(s)
- Kazusa Nishimura
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama City, 700-8530, Okayama, Japan
| | - Hiroyuki Kokaji
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Ko Motoki
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama City, 700-8530, Okayama, Japan
| | - Akira Yamazaki
- Faculty of Agriculture, Kindai University, 3327-204, Nakamachi, Nara City, Nara, 631-8505, Japan
| | - Kyoka Nagasaka
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Takashi Mori
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Rihito Takisawa
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu City, Shiga, 520-2194, Japan
| | - Yasuo Yasui
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Takashi Kawai
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama City, 700-8530, Okayama, Japan
| | - Koichiro Ushijima
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama City, 700-8530, Okayama, Japan
| | - Masanori Yamasaki
- Graduate School of Science and Technology, Niigata University, 8050 Ikarashi 2 no-cho, Nishi-ku, Niigata City, Niigata, 950-2181, Japan
| | - Hiroki Saito
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences, 1091-1 Maezato-Kawarabaru, Ishigaki, Okinawa, 907-0002, Japan
| | - Ryohei Nakano
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Tetsuya Nakazaki
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
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Liu CW, Tsutsui H. Sample-to-answer sensing technologies for nucleic acid preparation and detection in the field. SLAS Technol 2023; 28:302-323. [PMID: 37302751 DOI: 10.1016/j.slast.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/16/2023] [Accepted: 06/06/2023] [Indexed: 06/13/2023]
Abstract
Efficient sample preparation and accurate disease diagnosis under field conditions are of great importance for the early intervention of diseases in humans, animals, and plants. However, in-field preparation of high-quality nucleic acids from various specimens for downstream analyses, such as amplification and sequencing, is challenging. Thus, developing and adapting sample lysis and nucleic acid extraction protocols suitable for portable formats have drawn significant attention. Similarly, various nucleic acid amplification techniques and detection methods have also been explored. Combining these functions in an integrated platform has resulted in emergent sample-to-answer sensing systems that allow effective disease detection and analyses outside a laboratory. Such devices have a vast potential to improve healthcare in resource-limited settings, low-cost and distributed surveillance of diseases in food and agriculture industries, environmental monitoring, and defense against biological warfare and terrorism. This paper reviews recent advances in portable sample preparation technologies and facile detection methods that have been / or could be adopted into novel sample-to-answer devices. In addition, recent developments and challenges of commercial kits and devices targeting on-site diagnosis of various plant diseases are discussed.
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Affiliation(s)
- Chia-Wei Liu
- Department of Mechanical Engineering, University of California, Riverside, CA 92521, USA
| | - Hideaki Tsutsui
- Department of Mechanical Engineering, University of California, Riverside, CA 92521, USA; Department of Bioengineering, University of California, Riverside, CA 92521, USA.
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Kinoshita Y, Motoki K, Hosokawa M. Upregulation of tandem duplicated BoFLC1 genes is associated with the non-flowering trait in Brassica oleracea var. capitata. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:41. [PMID: 36897379 DOI: 10.1007/s00122-023-04311-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Tandem duplicated BoFLC1 genes (BoFLC1a and BoFLC1b), which were identified as the candidate causal genes for the non-flowering trait in the cabbage mutant 'nfc', were upregulated during winter in 'nfc'. The non-flowering natural cabbage mutant 'nfc' was discovered from the breeding line 'T15' with normal flowering characteristics. In this study, we investigated the molecular basis underlying the non-flowering trait of 'nfc'. First, 'nfc' was induced to flower using the grafting floral induction method, and three F2 populations were generated. The flowering phenotype of each F2 population was widely distributed with non-flowering individuals appearing in two populations. QTL-seq analysis detected a genomic region associated with flowering date at approximately 51 Mb on chromosome 9 in two of the three F2 populations. Subsequent validation and fine mapping of the candidate genomic region using QTL analysis identified the quantitative trait loci (QTL) at 50,177,696-51,474,818 bp on chromosome 9 covering 241 genes. Additionally, RNA-seq analysis in leaves and shoot apices of 'nfc' and 'T15' plants identified 19 and 15 differentially expressed genes related to flowering time, respectively. Based on these results, we identified tandem duplicated BoFLC1 genes, which are homologs of the floral repressor FLOWERING LOCUS C, as the candidate genes responsible for the non-flowering trait of 'nfc'. We designated the tandem duplicated BoFLC1 genes as BoFLC1a and BoFLC1b. Expression analysis revealed that the expression levels of BoFLC1a and BoFLC1b were downregulated during winter in 'T15' but were upregulated and maintained during winter in 'nfc'. Additionally, the expression level of the floral integrator BoFT was upregulated in the spring in 'T15' but hardly upregulated in 'nfc'. These results suggest that the upregulated levels of BoFLC1a and BoFLC1b contributed to the non-flowering trait of 'nfc'.
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Affiliation(s)
- Yu Kinoshita
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto 606-8502, Japan
| | - Ko Motoki
- Graduate School of Agriculture, Kyoto University, Kizugawa, Kyoto 619-0218, Japan
| | - Munetaka Hosokawa
- Faculty of Agriculture, Kindai University, Nara, Nara 631-8505, Japan.
- Agricultural Technology and Innovation Research Institute (ATIRI), Kindai University, Nara, Nara 631-8505, Japan.
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Lynagh PG, Osuna-Kleist P, Wang B, Malagon E, Anleu Gil MX, Comai L. Letter to the Editor: Accurate Direct PCR with Arabidopsis and Rice. PLANT & CELL PHYSIOLOGY 2023; 64:1-3. [PMID: 36242565 DOI: 10.1093/pcp/pcac145] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 10/09/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Peter G Lynagh
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA
- Genome Center, University of California Davis, Davis, CA 95616, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94720, USA
| | - Paul Osuna-Kleist
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA
- Genome Center, University of California Davis, Davis, CA 95616, USA
| | - Bohai Wang
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA
- Genome Center, University of California Davis, Davis, CA 95616, USA
| | - Edgar Malagon
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA
- Genome Center, University of California Davis, Davis, CA 95616, USA
| | | | - Luca Comai
- Department of Plant Biology, University of California Davis, Davis, CA 95616, USA
- Genome Center, University of California Davis, Davis, CA 95616, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94720, USA
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Tsuda K. Editorial Feature: Meet the PCP Editor-Kenichi Tsuda. PLANT & CELL PHYSIOLOGY 2022; 63:1-3. [PMID: 34669965 DOI: 10.1093/pcp/pcab151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/12/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Kenichi Tsuda
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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Jia Z, Han X, Tsuda K. An Efficient Method for DNA Purification-Free PCR from Plant Tissue. Curr Protoc 2021; 1:e289. [PMID: 34748285 DOI: 10.1002/cpz1.289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Amplification of genomic DNA fragments by PCR is necessary for plant molecular biology approaches such as genotyping. While this is a routine molecular technique in a modern laboratory, there are still significant hurdles when analyzing a large number of samples or collecting and storing samples while in the field. Because PCR amplification directly from plant tissue is often unsuccessful due to various inhibitors, genomic DNA purification is usually required, which involves laborious and time-consuming procedures or costly materials, particularly when using commercial kits. These undermine scalability and use in less-equipped settings. In addition, plant tissues and purified DNA need to be stored under proper conditions to avoid degradation. Here, we describe a low-cost, high-throughput PCR method to amplify genomic DNA fragments from plant tissue pounded to cellulose-based filter paper without the need for DNA purification or special equipment for sample storage. In this protocol, a small punch of plant tissue is pounded to a commercially available or homemade DNA storage card and directly placed into a PCR mixture containing Tween-20, a non-ionic detergent, directly followed by PCR. We also describe the steps to prepare a homemade DNA storage card, which is easy to make and can be stored with plant tissue at room temperature for a long time without any special equipment, allowing us to test the same sample multiple times. We have used this method in at least eleven plant species, including arabidopsis, tomato, soybean, potato, cotton, and rice. Altogether, our method decreases labor and cost, thereby increasing throughput and making plant DNA-based molecular diagnostic assays accessible to resource-limited settings, including classrooms, and facilitating sample collection in the field. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Making a homemade cellulose-based DNA storage card Basic Protocol 2: Pounding plant tissue on a DNA storage card Basic Protocol 3: DNA-purification free PCR.
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Affiliation(s)
- Zhengnan Jia
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Xiaowei Han
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Kenichi Tsuda
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
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