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Palomba M, Libro P, Di Martino J, Roca-Geronès X, Macali A, Castrignanò T, Canestrelli D, Mattiucci S. De novo transcriptome assembly of an Antarctic nematode for the study of thermal adaptation in marine parasites. Sci Data 2023; 10:720. [PMID: 37857654 PMCID: PMC10587230 DOI: 10.1038/s41597-023-02591-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
Understanding the genomic underpinnings of thermal adaptation is a hot topic in eco-evolutionary studies of parasites. Marine heteroxenous parasites have complex life cycles encompassing a free-living larval stage, an ectothermic intermediate host and a homeothermic definitive host, thus representing compelling systems for the study of thermal adaptation. The Antarctic anisakid Contracaecum osculatum sp. D is a marine parasite able to survive and thrive both at very cold and warm temperatures within the environment and its hosts. Here, a de novo transcriptome of C. osculatum sp. D was generated for the first time, by performing RNA-Seq experiments on a set of individuals exposed to temperatures experienced by the nematode during its life cycle. The analysis generated 425,954,724 reads, which were assembled and then annotated. The high-quality assembly was validated, achieving over 88% mapping against the transcriptome. The transcriptome of this parasite will represent a valuable genomic resource for future studies aimed at disentangling the genomic architecture of thermal tolerance and metabolic pathways related to temperature stress.
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Affiliation(s)
- Marialetizia Palomba
- Department of Ecological and Biological Sciences, Tuscia University, Viale dell'Università s/n, 01100, Viterbo, Italy
| | - Pietro Libro
- Department of Ecological and Biological Sciences, Tuscia University, Viale dell'Università s/n, 01100, Viterbo, Italy
| | - Jessica Di Martino
- Department of Ecological and Biological Sciences, Tuscia University, Viale dell'Università s/n, 01100, Viterbo, Italy
| | - Xavier Roca-Geronès
- Department of Biology, Health and Environment, Section of Parasitology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Joan XXIII Avenue, 27-31, 08028, Barcelona, Spain
| | - Armando Macali
- Department of Ecological and Biological Sciences, Tuscia University, Viale dell'Università s/n, 01100, Viterbo, Italy
| | - Tiziana Castrignanò
- Department of Ecological and Biological Sciences, Tuscia University, Viale dell'Università s/n, 01100, Viterbo, Italy.
| | - Daniele Canestrelli
- Department of Ecological and Biological Sciences, Tuscia University, Viale dell'Università s/n, 01100, Viterbo, Italy
| | - Simonetta Mattiucci
- Department of Public Health and Infectious Diseases, Section of Parasitology, Sapienza University of Rome, P.le Aldo Moro, 5, 00185, Rome, Italy
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Hartline DK, Cieslak MC, Castelfranco AM, Lieberman B, Roncalli V, Lenz PH. De novo transcriptomes of six calanoid copepods (Crustacea): a resource for the discovery of novel genes. Sci Data 2023; 10:242. [PMID: 37105953 PMCID: PMC10140051 DOI: 10.1038/s41597-023-02130-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
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.
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Affiliation(s)
- Daniel K Hartline
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, 1993 East-West Rd., Honolulu, HI, 96822, USA
| | - Matthew C Cieslak
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, 1993 East-West Rd., Honolulu, HI, 96822, USA
| | - Ann M Castelfranco
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, 1993 East-West Rd., Honolulu, HI, 96822, USA
| | - Brandon Lieberman
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, 1993 East-West Rd., Honolulu, HI, 96822, USA
| | - Vittoria Roncalli
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Naples, Italy.
| | - Petra H Lenz
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, 1993 East-West Rd., Honolulu, HI, 96822, USA
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Lizano AM, Smolina I, Choquet M, Kopp M, Hoarau G. Insights into the species evolution of Calanus copepods in the northern seas revealed by de novo transcriptome sequencing. Ecol Evol 2022; 12:e8606. [PMID: 35228861 PMCID: PMC8861592 DOI: 10.1002/ece3.8606] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/14/2022] [Accepted: 01/19/2022] [Indexed: 01/07/2023] Open
Abstract
Copepods of the zooplankton genus Calanus play a key role in marine ecosystems in the northern seas. Although being among the most studied organisms on Earth, due to their ecological importance, genomic resources for Calanus spp. remain scarce, mostly due to their large genome size (from 6 to 12 Gbps). As an alternative to whole-genome sequencing in Calanus spp., we sequenced and de novo assembled transcriptomes of five Calanus species: Calanus glacialis, C. hyperboreus, C. marshallae, C. pacificus, and C. helgolandicus. Functional assignment of protein families based on clusters of orthologous genes (COG) and gene ontology (GO) annotations showed analogous patterns of protein functions across species. Phylogenetic analyses using maximum likelihood (ML) of 191 protein-coding genes mined from RNA-seq data fully resolved evolutionary relationships among seven Calanus species investigated (five species sequenced for this study and two species with published datasets), with gene and site concordance factors showing that 109 out of 191 protein-coding genes support a separation between three groups: the C. finmarchicus group (including C. finmarchicus, C. glacialis, and C. marshallae), the C. helgolandicus group (including C. helgolandicus, C. sinicus, and C. pacificus) and the monophyletic C. hyperboreus group. The tree topology obtained in ML analyses was similar to a previously proposed phylogeny based on morphological criteria and cleared certain ambiguities from past studies on evolutionary relationships among Calanus species.
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Affiliation(s)
| | - Irina Smolina
- Faculty of Biosciences and AquacultureNord UniversityBodøNorway
| | - Marvin Choquet
- Faculty of Biosciences and AquacultureNord UniversityBodøNorway
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Martina Kopp
- Faculty of Biosciences and AquacultureNord UniversityBodøNorway
| | - Galice Hoarau
- Faculty of Biosciences and AquacultureNord UniversityBodøNorway
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Berger CA, Steinberg DK, Copley NJ, Tarrant AM. De novo transcriptome assembly of the Southern Ocean copepod Rhincalanus gigas sheds light on developmental changes in gene expression. Mar Genomics 2021; 58:100835. [PMID: 33526377 DOI: 10.1016/j.margen.2021.100835] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/30/2020] [Accepted: 12/30/2020] [Indexed: 11/18/2022]
Abstract
Copepods are small crustaceans that dominate most zooplankton communities in terms of both abundance and biomass. In the polar oceans, a subset of large lipid-storing copepods occupy central positions in the food web because of their important role in linking phytoplankton and microzooplankton with higher trophic levels. In this paper, we generated a high-quality de novo transcriptome for Rhincalanus gigas, the largest-and among the most abundant-of the Southern Ocean copepods. We then conducted transcriptional profiling to characterize the developmental transition between late-stage juveniles and adult females. We found that juvenile R. gigas substantially upregulate lipid synthesis and glycolysis pathways relative to females, as part of a developmental gene expression program that also implicates processes such as muscle growth, chitin formation, and ion transport. This study provides the first transcriptional profile of a developmental transition within Rhincalanus gigas or any endemic Southern Ocean copepod, thereby extending our understanding of copepod molecular physiology.
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Affiliation(s)
- Cory A Berger
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States; MIT-WHOI Joint Program in Oceanography/Applied Ocean Science & Engineering, Cambridge and Woods Hole, MA, USA
| | - Deborah K Steinberg
- Virginia Institute of Marine Science, William & Mary, Gloucester Pt, VA 23062, United States
| | - Nancy J Copley
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Ann M Tarrant
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States.
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