Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era
Summary: The Human Genome Project opened an era of (epi)genomic research, and also provided a platform for the development of new sequencing technologies. During and after the project, several sequencing technologies continue to dominate nucleic acid sequencing markets. Currently, Illumina (short-re...
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| Format: | Article |
| Language: | English |
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Elsevier
2021-11-01
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| Series: | The Innovation |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666675821000783 |
| _version_ | 1818683532822708224 |
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| author | Shangqian Xie Amy Wing-Sze Leung Zhenxian Zheng Dake Zhang Chuanle Xiao Ruibang Luo Ming Luo Shoudong Zhang |
| author_facet | Shangqian Xie Amy Wing-Sze Leung Zhenxian Zheng Dake Zhang Chuanle Xiao Ruibang Luo Ming Luo Shoudong Zhang |
| author_sort | Shangqian Xie |
| collection | DOAJ |
| description | Summary: The Human Genome Project opened an era of (epi)genomic research, and also provided a platform for the development of new sequencing technologies. During and after the project, several sequencing technologies continue to dominate nucleic acid sequencing markets. Currently, Illumina (short-read), PacBio (long-read), and Oxford Nanopore (long-read) are the most popular sequencing technologies. Unlike PacBio or the popular short-read sequencers before it, which, as examples of the second or so-called Next-Generation Sequencing platforms, need to synthesize when sequencing, nanopore technology directly sequences native DNA and RNA molecules. Nanopore sequencing, therefore, avoids converting mRNA into cDNA molecules, which not only allows for the sequencing of extremely long native DNA and full-length RNA molecules but also document modifications that have been made to those native DNA or RNA bases. In this review on direct DNA sequencing and direct RNA sequencing using Oxford Nanopore technology, we focus on their development and application achievements, discussing their challenges and future perspective. We also address the problems researchers may encounter applying these approaches in their research topics, and how to resolve them. Public summary: • Nanopore-seq can dissect native DNA/RNA molecules from any organisms at unlimited length • A wide variety of algorithms greatly increase the accuracy of signal decoding in Nanopore-Seq • Nanopore-Seq significantly facilitates genome assembly and structural variant calling, and can simultaneously detect base modifications • These advantages ensure its great potentials in future medical and agricultural practices |
| first_indexed | 2024-12-17T10:36:14Z |
| format | Article |
| id | doaj.art-fc8a9c0e6db04368846b6a076bd03baf |
| institution | Directory Open Access Journal |
| issn | 2666-6758 |
| language | English |
| last_indexed | 2024-12-17T10:36:14Z |
| publishDate | 2021-11-01 |
| publisher | Elsevier |
| record_format | Article |
| series | The Innovation |
| spelling | doaj.art-fc8a9c0e6db04368846b6a076bd03baf2022-12-21T21:52:23ZengElsevierThe Innovation2666-67582021-11-0124100153Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome eraShangqian Xie0Amy Wing-Sze Leung1Zhenxian Zheng2Dake Zhang3Chuanle Xiao4Ruibang Luo5Ming Luo6Shoudong Zhang7Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Forestry, Hainan University, Haikou 570228, ChinaDepartment of Computer Science, The University of Hong Kong, Hong Kong 999077, ChinaDepartment of Computer Science, The University of Hong Kong, Hong Kong 999077, ChinaBeijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, ChinaState Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangzhou 510060, China; Corresponding authorDepartment of Computer Science, The University of Hong Kong, Hong Kong 999077, China; Corresponding authorAgriculture and Biotechnology Research Center, Guangdong Provincial Key Laboratory of Applied Botany, Center of Economic Botany, Core Botanical Gardens, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; Corresponding authorSchool of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China; Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China; Corresponding authorSummary: The Human Genome Project opened an era of (epi)genomic research, and also provided a platform for the development of new sequencing technologies. During and after the project, several sequencing technologies continue to dominate nucleic acid sequencing markets. Currently, Illumina (short-read), PacBio (long-read), and Oxford Nanopore (long-read) are the most popular sequencing technologies. Unlike PacBio or the popular short-read sequencers before it, which, as examples of the second or so-called Next-Generation Sequencing platforms, need to synthesize when sequencing, nanopore technology directly sequences native DNA and RNA molecules. Nanopore sequencing, therefore, avoids converting mRNA into cDNA molecules, which not only allows for the sequencing of extremely long native DNA and full-length RNA molecules but also document modifications that have been made to those native DNA or RNA bases. In this review on direct DNA sequencing and direct RNA sequencing using Oxford Nanopore technology, we focus on their development and application achievements, discussing their challenges and future perspective. We also address the problems researchers may encounter applying these approaches in their research topics, and how to resolve them. Public summary: • Nanopore-seq can dissect native DNA/RNA molecules from any organisms at unlimited length • A wide variety of algorithms greatly increase the accuracy of signal decoding in Nanopore-Seq • Nanopore-Seq significantly facilitates genome assembly and structural variant calling, and can simultaneously detect base modifications • These advantages ensure its great potentials in future medical and agricultural practiceshttp://www.sciencedirect.com/science/article/pii/S2666675821000783nanopore sequencingdirect DNA sequencingdirect RNA sequencingbase modificationbase-callinglong-read sequencing |
| spellingShingle | Shangqian Xie Amy Wing-Sze Leung Zhenxian Zheng Dake Zhang Chuanle Xiao Ruibang Luo Ming Luo Shoudong Zhang Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era The Innovation nanopore sequencing direct DNA sequencing direct RNA sequencing base modification base-calling long-read sequencing |
| title | Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era |
| title_full | Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era |
| title_fullStr | Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era |
| title_full_unstemmed | Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era |
| title_short | Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era |
| title_sort | applications and potentials of nanopore sequencing in the epi genome and epi transcriptome era |
| topic | nanopore sequencing direct DNA sequencing direct RNA sequencing base modification base-calling long-read sequencing |
| url | http://www.sciencedirect.com/science/article/pii/S2666675821000783 |
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