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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...

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Autores principales: Udaondo, Zulema, Sittikankaew, Kanchana, Uengwetwanit, Tanaporn, Wongsurawat, Thidathip, Sonthirod, Chutima, Jenjaroenpun, Piroon, Pootakham, Wirulda, Karoonuthaisiri, Nitsara, Nookaew, Intawat
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
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.
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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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