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Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of Penaeus monodon
- 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.
- Subjects :
- Science
Genomics
Computational biology
Biology
General Biochemistry, Genetics and Molecular Biology
Penaeus monodon
Transcriptome
03 medical and health sciences
transcriptomics
0302 clinical medicine
Ecology, Evolution, Behavior and Systematics
030304 developmental biology
Oxford Nanopore Technologies
PacBio
0303 health sciences
Black tiger shrimp
long read sequencing
Brief Report
Paleontology
biology.organism_classification
Space and Planetary Science
Identification (biology)
Nanopore sequencing
Pacific biosciences
030217 neurology & neurosurgery
Reference genome
Subjects
Details
- Language :
- English
- ISSN :
- 20751729
- Volume :
- 11
- Issue :
- 862
- Database :
- OpenAIRE
- Journal :
- Life
- Accession number :
- edsair.doi.dedup.....cdf76c305fa7d3f6db6faf38124f741b