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Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of Penaeus monodon
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 sequenci...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8399832/ https://www.ncbi.nlm.nih.gov/pubmed/34440606 http://dx.doi.org/10.3390/life11080862 |
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author | Udaondo, Zulema Sittikankaew, Kanchana Uengwetwanit, Tanaporn Wongsurawat, Thidathip Sonthirod, Chutima Jenjaroenpun, Piroon Pootakham, Wirulda Karoonuthaisiri, Nitsara Nookaew, Intawat |
author_facet | Udaondo, Zulema Sittikankaew, Kanchana Uengwetwanit, Tanaporn Wongsurawat, Thidathip Sonthirod, Chutima Jenjaroenpun, Piroon Pootakham, Wirulda Karoonuthaisiri, Nitsara Nookaew, Intawat |
author_sort | Udaondo, Zulema |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-8399832 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-83998322021-08-29 Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of Penaeus monodon Udaondo, Zulema Sittikankaew, Kanchana Uengwetwanit, Tanaporn Wongsurawat, Thidathip Sonthirod, Chutima Jenjaroenpun, Piroon Pootakham, Wirulda Karoonuthaisiri, Nitsara Nookaew, Intawat Life (Basel) Brief Report 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. MDPI 2021-08-23 /pmc/articles/PMC8399832/ /pubmed/34440606 http://dx.doi.org/10.3390/life11080862 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Brief Report Udaondo, Zulema Sittikankaew, Kanchana Uengwetwanit, Tanaporn Wongsurawat, Thidathip Sonthirod, Chutima Jenjaroenpun, Piroon Pootakham, Wirulda Karoonuthaisiri, Nitsara Nookaew, Intawat Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of Penaeus monodon |
title | Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of Penaeus monodon |
title_full | Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of Penaeus monodon |
title_fullStr | Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of Penaeus monodon |
title_full_unstemmed | Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of Penaeus monodon |
title_short | Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of Penaeus monodon |
title_sort | comparative analysis of pacbio and oxford nanopore sequencing technologies for transcriptomic landscape identification of penaeus monodon |
topic | Brief Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8399832/ https://www.ncbi.nlm.nih.gov/pubmed/34440606 http://dx.doi.org/10.3390/life11080862 |
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