Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of <i>Penaeus monodon</i>
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...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-08-01
|
| Series: | Life |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2075-1729/11/8/862 |
| _version_ | 1797523178386358272 |
|---|---|
| author | Zulema Udaondo Kanchana Sittikankaew Tanaporn Uengwetwanit Thidathip Wongsurawat Chutima Sonthirod Piroon Jenjaroenpun Wirulda Pootakham Nitsara Karoonuthaisiri Intawat Nookaew |
| author_facet | Zulema Udaondo Kanchana Sittikankaew Tanaporn Uengwetwanit Thidathip Wongsurawat Chutima Sonthirod Piroon Jenjaroenpun Wirulda Pootakham Nitsara Karoonuthaisiri Intawat Nookaew |
| author_sort | Zulema Udaondo |
| collection | DOAJ |
| 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, <i>Penaeus monodon</i>. 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. |
| first_indexed | 2024-03-10T08:39:42Z |
| format | Article |
| id | doaj.art-139394c2d89b492a8871aeebbfc317b4 |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-03-10T08:39:42Z |
| publishDate | 2021-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-139394c2d89b492a8871aeebbfc317b42023-11-22T08:23:59ZengMDPI AGLife2075-17292021-08-0111886210.3390/life11080862Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of <i>Penaeus monodon</i>Zulema Udaondo0Kanchana Sittikankaew1Tanaporn Uengwetwanit2Thidathip Wongsurawat3Chutima Sonthirod4Piroon Jenjaroenpun5Wirulda Pootakham6Nitsara Karoonuthaisiri7Intawat Nookaew8Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USANational Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani 12120, ThailandNational Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani 12120, ThailandDepartment of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USANational Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, ThailandDepartment of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USANational Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, ThailandNational Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani 12120, ThailandDepartment of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USAWith 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, <i>Penaeus monodon</i>. 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.https://www.mdpi.com/2075-1729/11/8/862long read sequencingtranscriptomicsOxford Nanopore TechnologiesPacBio<i>Penaeus monodon</i> |
| spellingShingle | Zulema Udaondo Kanchana Sittikankaew Tanaporn Uengwetwanit Thidathip Wongsurawat Chutima Sonthirod Piroon Jenjaroenpun Wirulda Pootakham Nitsara Karoonuthaisiri Intawat Nookaew Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of <i>Penaeus monodon</i> Life long read sequencing transcriptomics Oxford Nanopore Technologies PacBio <i>Penaeus monodon</i> |
| title | Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of <i>Penaeus monodon</i> |
| title_full | Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of <i>Penaeus monodon</i> |
| title_fullStr | Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of <i>Penaeus monodon</i> |
| title_full_unstemmed | Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of <i>Penaeus monodon</i> |
| title_short | Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of <i>Penaeus monodon</i> |
| title_sort | comparative analysis of pacbio and oxford nanopore sequencing technologies for transcriptomic landscape identification of i penaeus monodon i |
| topic | long read sequencing transcriptomics Oxford Nanopore Technologies PacBio <i>Penaeus monodon</i> |
| url | https://www.mdpi.com/2075-1729/11/8/862 |
| work_keys_str_mv | AT zulemaudaondo comparativeanalysisofpacbioandoxfordnanoporesequencingtechnologiesfortranscriptomiclandscapeidentificationofipenaeusmonodoni AT kanchanasittikankaew comparativeanalysisofpacbioandoxfordnanoporesequencingtechnologiesfortranscriptomiclandscapeidentificationofipenaeusmonodoni AT tanapornuengwetwanit comparativeanalysisofpacbioandoxfordnanoporesequencingtechnologiesfortranscriptomiclandscapeidentificationofipenaeusmonodoni AT thidathipwongsurawat comparativeanalysisofpacbioandoxfordnanoporesequencingtechnologiesfortranscriptomiclandscapeidentificationofipenaeusmonodoni AT chutimasonthirod comparativeanalysisofpacbioandoxfordnanoporesequencingtechnologiesfortranscriptomiclandscapeidentificationofipenaeusmonodoni AT piroonjenjaroenpun comparativeanalysisofpacbioandoxfordnanoporesequencingtechnologiesfortranscriptomiclandscapeidentificationofipenaeusmonodoni AT wiruldapootakham comparativeanalysisofpacbioandoxfordnanoporesequencingtechnologiesfortranscriptomiclandscapeidentificationofipenaeusmonodoni AT nitsarakaroonuthaisiri comparativeanalysisofpacbioandoxfordnanoporesequencingtechnologiesfortranscriptomiclandscapeidentificationofipenaeusmonodoni AT intawatnookaew comparativeanalysisofpacbioandoxfordnanoporesequencingtechnologiesfortranscriptomiclandscapeidentificationofipenaeusmonodoni |