De novo transcriptomes of six calanoid copepods (Crustacea): a resource for the discovery of novel genes
Abstract This study presents eight new high-quality de novo transcriptomes from six co-occurring species of calanoid copepods, the first published for Neocalanus plumchrus, N. cristatus, Eucalanus bungii and Metridia pacifica and additional ones for N. flemingeri and Calanus marshallae. They are eco...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-04-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-023-02130-1 |
| _version_ | 1797836616069283840 |
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| author | Daniel K. Hartline Matthew C. Cieslak Ann M. Castelfranco Brandon Lieberman Vittoria Roncalli Petra H. Lenz |
| author_facet | Daniel K. Hartline Matthew C. Cieslak Ann M. Castelfranco Brandon Lieberman Vittoria Roncalli Petra H. Lenz |
| author_sort | Daniel K. Hartline |
| collection | DOAJ |
| description | Abstract This study presents eight new high-quality de novo transcriptomes from six co-occurring species of calanoid copepods, the first published for Neocalanus plumchrus, N. cristatus, Eucalanus bungii and Metridia pacifica and additional ones for N. flemingeri and Calanus marshallae. They are ecologically-important members of sub-arctic North Pacific marine zooplankton communities. ‘Omics data for this diverse and numerous taxonomic group are sparse and difficult to obtain. Total RNA from single individuals was used to construct gene libraries that were sequenced on an Illumina Next-Seq platform. Quality filtered reads were assembled with Trinity software and validated using multiple criteria. The study’s primary purpose is to provide a resource for gene expression studies. The integrated database can be used for quantitative inter- and intra-species comparisons of gene expression patterns across biological processes. An example of an additional use is provided for discovering novel and evolutionarily-significant proteins within the Calanoida. A workflow was designed to find and characterize unannotated transcripts with homologies across de novo assemblies that have also been shown to be eco-responsive. |
| first_indexed | 2024-04-09T15:12:52Z |
| format | Article |
| id | doaj.art-695a8f8c99654737981045008db3c760 |
| institution | Directory Open Access Journal |
| issn | 2052-4463 |
| language | English |
| last_indexed | 2024-04-09T15:12:52Z |
| publishDate | 2023-04-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj.art-695a8f8c99654737981045008db3c7602023-04-30T11:07:10ZengNature PortfolioScientific Data2052-44632023-04-0110111410.1038/s41597-023-02130-1De novo transcriptomes of six calanoid copepods (Crustacea): a resource for the discovery of novel genesDaniel K. Hartline0Matthew C. Cieslak1Ann M. Castelfranco2Brandon Lieberman3Vittoria Roncalli4Petra H. Lenz5Pacific Biosciences Research Center, University of Hawai’i at MānoaPacific Biosciences Research Center, University of Hawai’i at MānoaPacific Biosciences Research Center, University of Hawai’i at MānoaPacific Biosciences Research Center, University of Hawai’i at MānoaIntegrative Marine Ecology Department, Stazione Zoologica Anton DohrnPacific Biosciences Research Center, University of Hawai’i at MānoaAbstract This study presents eight new high-quality de novo transcriptomes from six co-occurring species of calanoid copepods, the first published for Neocalanus plumchrus, N. cristatus, Eucalanus bungii and Metridia pacifica and additional ones for N. flemingeri and Calanus marshallae. They are ecologically-important members of sub-arctic North Pacific marine zooplankton communities. ‘Omics data for this diverse and numerous taxonomic group are sparse and difficult to obtain. Total RNA from single individuals was used to construct gene libraries that were sequenced on an Illumina Next-Seq platform. Quality filtered reads were assembled with Trinity software and validated using multiple criteria. The study’s primary purpose is to provide a resource for gene expression studies. The integrated database can be used for quantitative inter- and intra-species comparisons of gene expression patterns across biological processes. An example of an additional use is provided for discovering novel and evolutionarily-significant proteins within the Calanoida. A workflow was designed to find and characterize unannotated transcripts with homologies across de novo assemblies that have also been shown to be eco-responsive.https://doi.org/10.1038/s41597-023-02130-1 |
| spellingShingle | Daniel K. Hartline Matthew C. Cieslak Ann M. Castelfranco Brandon Lieberman Vittoria Roncalli Petra H. Lenz De novo transcriptomes of six calanoid copepods (Crustacea): a resource for the discovery of novel genes Scientific Data |
| title | De novo transcriptomes of six calanoid copepods (Crustacea): a resource for the discovery of novel genes |
| title_full | De novo transcriptomes of six calanoid copepods (Crustacea): a resource for the discovery of novel genes |
| title_fullStr | De novo transcriptomes of six calanoid copepods (Crustacea): a resource for the discovery of novel genes |
| title_full_unstemmed | De novo transcriptomes of six calanoid copepods (Crustacea): a resource for the discovery of novel genes |
| title_short | De novo transcriptomes of six calanoid copepods (Crustacea): a resource for the discovery of novel genes |
| title_sort | de novo transcriptomes of six calanoid copepods crustacea a resource for the discovery of novel genes |
| url | https://doi.org/10.1038/s41597-023-02130-1 |
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