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Van Caenegem W, Haelewaters D. New insights into the DNA extraction and PCR amplification of minute ascomycetes in the genus Laboulbenia (Pezizomycotina, Laboulbeniales). IMA Fungus 2024; 15:14. [PMID: 38863065 PMCID: PMC11167896 DOI: 10.1186/s43008-024-00146-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 05/17/2024] [Indexed: 06/13/2024] Open
Abstract
Molecular studies of fungi within the order Laboulbeniales (Ascomycota, Pezizomycotina) have been hampered for years because of their minute size, inability to grow in axenic culture, and lack of reliable and cost-efficient DNA extraction protocols. In particular, the genus Laboulbenia is notorious for low success with DNA extraction and polymerase chain reaction (PCR) amplification. This is attributed to the presence of melanin, a molecule known to inhibit PCR, in the cells. We evaluated the efficacy of a standard single cell-based DNA extraction protocol by halving the recommended amount of reagents to reduce the cost per extraction and adding bovine serum albumin (BSA) during the multiple displacement amplification step to reverse the effect of melanin. A total of 196 extractions were made, 111 of which were successful. We found that halving the reagents used in the single cell-based extraction kit did not significantly affect the probability of successful DNA extraction. Using the halved protocol reduces cost and resource consumption. Moreover, there was no significant difference in the probability of successfully extracting DNA based on whether BSA was added or not, suggesting that the amount of melanin present in cells of the thallus has no major inhibitory effect on PCR. We generated 277 sequences from five loci, but amplification of the internal transcribed spacer region, the mitochondrial small subunit rDNA, and protein-coding genes remains challenging. The probability of successfully extracting DNA from Laboulbeniales was also impacted by specimen storage methods, with material preserved in > 95% ethanol yielding higher success rates compared to material stored in 70% ethanol and dried material. We emphasize the importance of proper preservation of material and propose the design of Laboulbeniales-specific primers to overcome the problems of primer mismatches and contaminants. Our new insights apply not only to the genus Laboulbenia; Laboulbeniales generally are understudied, and the vast majority of species remain unsequenced. New and approachable molecular developments will benefit the study of Laboulbeniales, helping to elucidate the true diversity and evolutionary relationships of these peculiar microfungi.
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Affiliation(s)
- Warre Van Caenegem
- Research Group Mycology, Department of Biology, Ghent University, Ghent, 9000, Belgium.
| | - Danny Haelewaters
- Research Group Mycology, Department of Biology, Ghent University, Ghent, 9000, Belgium.
- Meise Botanic Garden, Meise, 1860, Belgium.
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czech Republic.
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Lu N, Qiao Y, An P, Luo J, Bi C, Li M, Lu Z, Tu J. Exploration of whole genome amplification generated chimeric sequences in long-read sequencing data. Brief Bioinform 2023; 24:bbad275. [PMID: 37529913 DOI: 10.1093/bib/bbad275] [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] [Received: 03/20/2023] [Revised: 06/21/2023] [Accepted: 07/10/2023] [Indexed: 08/03/2023] Open
Abstract
MOTIVATION Multiple displacement amplification (MDA) has become the most commonly used method of whole genome amplification, generating a vast amount of DNA with higher molecular weight and greater genome coverage. Coupling with long-read sequencing, it is possible to sequence the amplicons of over 20 kb in length. However, the formation of chimeric sequences (chimeras, expressed as structural errors in sequencing data) in MDA seriously interferes with the bioinformatics analysis but its influence on long-read sequencing data is unknown. RESULTS We sequenced the phi29 DNA polymerase-mediated MDA amplicons on the PacBio platform and analyzed chimeras within the generated data. The 3rd-ChimeraMiner has been constructed as a pipeline for recognizing and restoring chimeras into the original structures in long-read sequencing data, improving the efficiency of using TGS data. Five long-read datasets and one high-fidelity long-read dataset with various amplification folds were analyzed. The result reveals that the mis-priming events in amplification are more frequently occurring than widely perceived, and the propor tion gradually accumulates from 42% to over 78% as the amplification continues. In total, 99.92% of recognized chimeric sequences were demonstrated to be artifacts, whose structures were wrongly formed in MDA instead of existing in original genomes. By restoring chimeras to their original structures, the vast majority of supplementary alignments that introduce false-positive structural variants are recycled, removing 97% of inversions on average and contributing to the analysis of structural variation in MDA-amplified samples. The impact of chimeras in long-read sequencing data analysis should be emphasized, and the 3rd-ChimeraMiner can help to quantify and reduce the influence of chimeras. AVAILABILITY AND IMPLEMENTATION The 3rd-ChimeraMiner is available on GitHub, https://github.com/dulunar/3rdChimeraMiner.
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Affiliation(s)
- Na Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yi Qiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Pengfei An
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
- Monash University-Southeast University Joint Research Institute, Suzhou 215123, China
| | - Jiajian Luo
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Changwei Bi
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China
| | - Musheng Li
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89511, USA
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
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Wang Z, Meng X, Du Z, Wang S, Qu C, Mo H, Jiang C, Wang J, Zang Y, Chen S. Zinc loaded amidoxime polyacrylonitrile porous resin microcapsules for uranium extraction from seawater. J Radioanal Nucl Chem 2023. [DOI: 10.1007/s10967-023-08851-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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Lu N, Qiao Y, Lu Z, Tu J. Chimera: The spoiler in multiple displacement amplification. Comput Struct Biotechnol J 2023; 21:1688-1696. [PMID: 36879882 PMCID: PMC9984789 DOI: 10.1016/j.csbj.2023.02.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 02/18/2023] [Accepted: 02/18/2023] [Indexed: 02/24/2023] Open
Abstract
Multiple displacement amplification (MDA) based on isothermal random priming and high fidelity phi29 DNA polymerase-mediated processive extension has revolutionized the field of whole genome amplification by enabling the amplification of minute amounts of DNA, such as from a single cell, generating vast amounts of DNA with high genome coverage. Despite its advantages, MDA has its own challenges, one of the grandest being the formation of chimeric sequences (chimeras), which presents in all MDA products and seriously disturbs the downstream analysis. In this review, we provide a comprehensive overview of current research on MDA chimeras. We first reviewed the mechanisms of chimera formation and chimera detection methods. We then systematically summarized the characteristics of chimeras, including overlap, chimeric distance, chimeric density, and chimeric rate, as found in independently published sequencing data. Finally, we reviewed the methods used to process chimeric sequences and their impacts on the improvement of data utilization efficiency. The information presented in this review will be useful for those interested in understanding the challenges with MDA and in improving its performance.
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Affiliation(s)
- Na Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yi Qiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
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Smith SE, Huang W, Tiamani K, Unterer M, Khan Mirzaei M, Deng L. Emerging technologies in the study of the virome. Curr Opin Virol 2022; 54:101231. [DOI: 10.1016/j.coviro.2022.101231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/16/2022] [Accepted: 04/19/2022] [Indexed: 11/03/2022]
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Xia Y, Gawad C. Bringing precision oncology to cellular resolution with single-cell genomics. Clin Exp Metastasis 2022; 39:79-83. [PMID: 34807338 PMCID: PMC8969191 DOI: 10.1007/s10585-021-10129-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/23/2021] [Indexed: 02/03/2023]
Abstract
Single-cell sequencing technologies have undergone rapid development and adoption by the scientific community in the past 5 years, fueling discoveries about the etiology, pathogenesis, and treatment responsiveness of individual tumor cells within cancer ecosystems. Most of the advancements in our understanding of cancer with these new technologies have focused on basic tumor biology. However, the knowledge produced by these and other studies are beginning to provide biomarkers and drug targets for clinically-relevant subpopulations within a tumor, creating opportunities for the development of biologically-informed, clone-specific combination treatment strategies. Here we provide an overview of the development of the field of single-cell cancer sequencing and provide a roadmap for shepherding these technologies from research tools to diagnostic instruments that provide high-resolution, treatment-directing details of tumors to clinical oncologists.
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Affiliation(s)
- Yuntao Xia
- Department of Pediatrics, Division of Hematology/Oncology, Stanford University, Stanford, USA
| | - Charles Gawad
- Department of Pediatrics, Division of Hematology/Oncology, Stanford University, Stanford, USA.
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Moon YJ, Lee SY, Oh SW. A Review of Isothermal Amplification Methods and Food-Origin Inhibitors against Detecting Food-Borne Pathogens. Foods 2022; 11:322. [PMID: 35159473 PMCID: PMC8833899 DOI: 10.3390/foods11030322] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 02/06/2023] Open
Abstract
The isothermal amplification method, a molecular-based diagnostic technology, such as loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA), is widely used as an alternative to the time-consuming and labor-intensive culture-based detection method. However, food matrices or other compounds can inhibit molecular-based diagnostic technologies, causing reduced detection efficiencies, and false-negative results. These inhibitors originating from food are polysaccharides and polyphenolic compounds in berries, seafood, and vegetables. Additionally, magnesium ions needed for amplification reactions can also inhibit molecular-based diagnostics. The successful removal of inhibitors originating from food and molecular amplification reaction is therefore proposed to enhance the efficiency of molecular-based diagnostics and allow accurate detection of food-borne pathogens. Among molecular-based diagnostics, PCR inhibitors have been reported. Nevertheless, reports on the mechanism and removal of isothermal amplification method inhibitors are insufficient. Therefore, this review describes inhibitors originating from food and some compounds inhibiting the detection of food-borne pathogens during isothermal amplification.
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Affiliation(s)
| | | | - Se-Wook Oh
- Department of Food and Nutrition, Kookmin University, Seoul 136-702, Korea; (Y.-J.M.); (S.-Y.L.)
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Parikh FR, Athalye AS, Kulkarni DK, Sanap RR, Dhumal SB, Warang DJ, Naik DJ, Madon PF. Evolution and Utility of Preimplantation Genetic Testing for Monogenic Disorders in Assisted Reproduction - A Narrative Review. J Hum Reprod Sci 2021; 14:329-339. [PMID: 35197677 PMCID: PMC8812395 DOI: 10.4103/jhrs.jhrs_148_21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/20/2021] [Accepted: 11/20/2021] [Indexed: 11/04/2022] Open
Abstract
Preimplantation genetic testing (PGT) for monogenic disorders and assisted reproductive technology have evolved and progressed in tandem. PGT started with single-cell polymerase chain reaction (PCR) followed by fluorescent in situ hybridisation for a limited number of chromosomes, later called 'preimplantation genetic diagnosis (PGD) version 1'. This review highlights the various molecular genetic techniques that have evolved to detect specific inherited monogenic disorders in the preimplantation embryo. Literature review in English was performed in PubMed from 1990 to 2021, using the term 'preimplantation genetic diagnosis'. With whole-genome amplification, multiple copies of embryonic DNA were created. This helped in avoiding misdiagnosis caused by allele dropout. Multiplex fluorescent PCR analysed informative short tandem repeats (STR) and detected mutations simultaneously on automated capillary electrophoresis sequencers by mini-sequencing. Comparative genomic hybridisation (CGH) and array CGH were used for 24 chromosome aneuploidy screening. Subsequently, aneuploidies were detected by next-generation sequencing using single-nucleotide polymorphism arrays, while STR markers were used for haplotyping. 'PGD version 2' included accurate marker-based diagnosis of most monogenic disorders and detection of aneuploidy of all chromosomes. Human leukocyte antigen matching of embryos has important implications in diagnosis and cure of haemoglobinopathies and immunodeficiencies in children by means of matched related haematopoietic stem cell transplantation from an unaffected 'saviour sibling' obtained by PGT.
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Affiliation(s)
- Firuza R. Parikh
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Fertility Centre, Jaslok Hospital and Research Centre, Mumbai, Maharashtra, India
| | - Arundhati S. Athalye
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Fertility Centre, Jaslok Hospital and Research Centre, Mumbai, Maharashtra, India
| | - Dhananjaya K. Kulkarni
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Fertility Centre, Jaslok Hospital and Research Centre, Mumbai, Maharashtra, India
| | - Rupesh R. Sanap
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Fertility Centre, Jaslok Hospital and Research Centre, Mumbai, Maharashtra, India
| | - Suresh B. Dhumal
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Fertility Centre, Jaslok Hospital and Research Centre, Mumbai, Maharashtra, India
| | - Dhanashree J. Warang
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Fertility Centre, Jaslok Hospital and Research Centre, Mumbai, Maharashtra, India
| | - Dattatray J. Naik
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Fertility Centre, Jaslok Hospital and Research Centre, Mumbai, Maharashtra, India
| | - Prochi F. Madon
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Fertility Centre, Jaslok Hospital and Research Centre, Mumbai, Maharashtra, India
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