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High-Throughput Sequencing Technologies

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Bioinformatics in Rice Research

Abstract

Optical and biochemical methods determine the sequence of nucleotide bases in a DNA macromolecule. Since 2010, considerable progress has been made on DNA sequencing technology. There are various high-throughput sequencing (HTS) technologies, such as Roche 454, Illumina dye sequencing, PacBio’s SMRT, Ion Torrent, Oxford Nanopore, SOLiD, and DNA nano-array sequencer, that have emerged with less cost and are time-saving. Sanger sequencing is the first-generation sequencing method. Subsequently, many next-generation sequencing (NGS) platforms are being used for genome sequencing. These DNA sequencing technologies have altered our view on understanding genomes and their analysis. This chapter presents a simple overview of the HTS technologies, their applications, and limitations. We aim to provide readers in the field with an easy and comprehensible description of HTS technologies to provide them with essential knowledge in full zeal.

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Abbreviations

ARE:

Parallel analysis of RNA ends

BAM:

Binary alignment map

CAGE:

Cap analysis of gene expression

ChIA-PET:

Chromatin interaction analysis by paired-end tag sequencing

DOE:

Department of Energy

HTS:

High-throughput sequencing

ISPs:

Ion Sphere Particles

NGS:

Next-Generation Sequencing

NHGRI:

National Human Genome Research Institute

NIH:

National Institute of Health

PCR:

Polymerase chain reaction

RIP-chip:

RNA immunoprecipitation chip

RNA-Map:

RNA on a massively parallel array

SBS:

Sequencing by synthesis

SMRT:

Single molecule real-time

SNVs:

Single nucleotide variants

SOLiD:

Sequencing by sequential ligation of oligonucleotide probes

Svs:

Structural variations

TADs:

Topological Associated Domains

XIAP:

X-lined inhibitor of apoptosis

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Authors and Affiliations

  1. School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamil Nadu, India

    Krishna Kant Gupta

  2. Centre for Bioinformatics, Pondicherry University, Pondicherry, India

    Elakkiya Elumalai

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  1. Elakkiya Elumalai
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  2. Krishna Kant Gupta
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Correspondence to Krishna Kant Gupta .

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  1. Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha, India

    Manoj Kumar Gupta

  2. Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha, India

    Lambodar Behera

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Fig. 13.1 (CC BY 4.0) [3] and Table 13.1 (CC BY 4.0) [6] have been used under the terms of the Creative Commons Attribution License.

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Elumalai, E., Gupta, K.K. (2021). High-Throughput Sequencing Technologies. In: Gupta, M.K., Behera, L. (eds) Bioinformatics in Rice Research. Springer, Singapore. https://doi.org/10.1007/978-981-16-3993-7_13

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