Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era

Shangqian Xie; Amy Wing-Sze Leung; Zhenxian Zheng; Dake Zhang; Chuanle Xiao; Ruibang Luo; Ming Luo; Shoudong Zhang

doi:10.1016/j.xinn.2021.100153

Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era

Innovation (Camb). 2021 Aug 11;2(4):100153. doi: 10.1016/j.xinn.2021.100153. eCollection 2021 Nov 28.

Authors

Shangqian Xie¹, Amy Wing-Sze Leung², Zhenxian Zheng², Dake Zhang³, Chuanle Xiao⁴, Ruibang Luo², Ming Luo⁵, Shoudong Zhang^{6

7}

Affiliations

¹ Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Forestry, Hainan University, Haikou 570228, China.
² Department of Computer Science, The University of Hong Kong, Hong Kong 999077, China.
³ Beijing 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, China.
⁴ State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangzhou 510060, China.
⁵ Agriculture 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.
⁶ School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China.
⁷ Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China.

Abstract

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.

Keywords: base modification; base-calling; direct DNA sequencing; direct RNA sequencing; long-read sequencing; nanopore sequencing; tools and algorithms.

Publication types

Review