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Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of Penaeus monodon

Authors :
Nitsara Karoonuthaisiri
Kanchana Sittikankaew
Piroon Jenjaroenpun
Tanaporn Uengwetwanit
Thidathip Wongsurawat
Intawat Nookaew
Zulema Udaondo
Wirulda Pootakham
Chutima Sonthirod
Source :
Life, Vol 11, Iss 862, p 862 (2021), Life
Publication Year :
2021
Publisher :
MDPI AG, 2021.

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 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.

Details

Language :
English
ISSN :
20751729
Volume :
11
Issue :
862
Database :
OpenAIRE
Journal :
Life
Accession number :
edsair.doi.dedup.....cdf76c305fa7d3f6db6faf38124f741b