Third-Generation Sequencing: Recent Advances and Applications in the Era of Genomics, Transcriptomics and Epitranscriptomics

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Genetics and Genomics".

Deadline for manuscript submissions: closed (10 December 2021) | Viewed by 29920

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Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
Interests: genomics; molecular biology; epitranscriptomics; biochemistry
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Dear Colleagues,

The last few years, third generation sequencing (TGS), also known as long-read sequencing, has caused a new revolution in the scientific field of genomics as it provides a way to study genomes, transcriptomes, and metagenomes at an unprecedented resolution. While NGS methods lead to the production of short reads (approximately 600 bp), long-read sequencing enables the generation of reads of up to several tens of kilobases or even up to 1 Mb, thus addressing serious limitations of previous technologies, including de novo genome assembly, structural variation analysis and haplotype phasing. Besides the newly introduced capability of real-time sequencing analysis as well as the significantly increased throughput, TGS also exhibits decreased sequencing costs, run times and error rates. In addition, TGS requires minimal input material, thus eliminating biases inherent to previous sequencing technologies, such as the PCR amplification step that was needed during the NGS library preparation. This enormous technological progress has not only led to the superior investigation of genomes and transcriptomes, but also has offered new capabilities beyond nucleic acid sequencing. Notably, TGS approaches have allowed the identification of specific DNA and RNA modifications, highlighting their key roles in pre-mRNA splicing, nuclear export, mRNA stability and localization, and translation efficiency. In any case, we are only witnessing the beginning of the third-generation sequencing era, and the coming years promise to bring significant developments, discoveries, and breakthroughs. The present Special Issue entitled “Third-Generation sequencing: Recent advances and applications in the era of genomics, transcriptomics and epitranscriptomics” may provide a thorough overview of the scientific progress that TGS has achieved in the last few years.

Dr. Panagiotis G. Adamopoulos
Guest Editor

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Keywords

  • massive parallel sequencing
  • single-molecule DNA/RNA sequencing
  • post-transcriptional modifications
  • genome research
  • non-coding RNAs
  • gene expression and regulation

Published Papers (2 papers)

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22 pages, 1918 KiB  
Review
Third-Generation Sequencing: The Spearhead towards the Radical Transformation of Modern Genomics
by Konstantina Athanasopoulou, Michaela A. Boti, Panagiotis G. Adamopoulos, Paraskevi C. Skourou and Andreas Scorilas
Life 2022, 12(1), 30; https://doi.org/10.3390/life12010030 - 26 Dec 2021
Cited by 91 | Viewed by 21552
Abstract
Although next-generation sequencing (NGS) technology revolutionized sequencing, offering a tremendous sequencing capacity with groundbreaking depth and accuracy, it continues to demonstrate serious limitations. In the early 2010s, the introduction of a novel set of sequencing methodologies, presented by two platforms, Pacific Biosciences (PacBio) [...] Read more.
Although next-generation sequencing (NGS) technology revolutionized sequencing, offering a tremendous sequencing capacity with groundbreaking depth and accuracy, it continues to demonstrate serious limitations. In the early 2010s, the introduction of a novel set of sequencing methodologies, presented by two platforms, Pacific Biosciences (PacBio) and Oxford Nanopore Sequencing (ONT), gave birth to third-generation sequencing (TGS). The innovative long-read technologies turn genome sequencing into an ease-of-handle procedure by greatly reducing the average time of library construction workflows and simplifying the process of de novo genome assembly due to the generation of long reads. Long sequencing reads produced by both TGS methodologies have already facilitated the decipherment of transcriptional profiling since they enable the identification of full-length transcripts without the need for assembly or the use of sophisticated bioinformatics tools. Long-read technologies have also provided new insights into the field of epitranscriptomics, by allowing the direct detection of RNA modifications on native RNA molecules. This review highlights the advantageous features of the newly introduced TGS technologies, discusses their limitations and provides an in-depth comparison regarding their scientific background and available protocols as well as their potential utility in research and clinical applications. Full article
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20 pages, 2861 KiB  
Brief Report
Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of Penaeus monodon
by Zulema Udaondo, Kanchana Sittikankaew, Tanaporn Uengwetwanit, Thidathip Wongsurawat, Chutima Sonthirod, Piroon Jenjaroenpun, Wirulda Pootakham, Nitsara Karoonuthaisiri and Intawat Nookaew
Life 2021, 11(8), 862; https://doi.org/10.3390/life11080862 - 23 Aug 2021
Cited by 7 | Viewed by 7112
Abstract
With the advantages that long-read sequencing platforms such as Pacific Biosciences (Menlo Park, CA, USA) (PacBio) and Oxford Nanopore Technologies (Oxford, UK) (ONT) can offer, various research fields such as genomics and transcriptomics can exploit their benefits. Selecting an appropriate sequencing platform is [...] Read more.
With the advantages that long-read sequencing platforms such as Pacific Biosciences (Menlo Park, CA, USA) (PacBio) and Oxford Nanopore Technologies (Oxford, UK) (ONT) can offer, various research fields such as genomics and transcriptomics can exploit their benefits. Selecting an appropriate sequencing platform is undoubtedly crucial for the success of the research outcome, thus there is a need to compare these long-read sequencing platforms and evaluate them for specific research questions. This study aims to compare the performance of PacBio and ONT platforms for transcriptomic analysis by utilizing transcriptome data from three different tissues (hepatopancreas, intestine, and gonads) of the juvenile black tiger shrimp, Penaeus monodon. We compared three important features: (i) main characteristics of the sequencing libraries and their alignment with the reference genome, (ii) transcript assembly features and isoform identification, and (iii) correlation of the quantification of gene expression levels for both platforms. Our analyses suggest that read-length bias and differences in sequencing throughput are highly influential factors when using long reads in transcriptome studies. These comparisons can provide a guideline when designing a transcriptome study utilizing these two long-read sequencing technologies. Full article
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