First De Novo Transcriptome of the Copepod Rhincalanus gigas from Antarctic Waters

Lauritano, Chiara; Roncalli, Vittoria; Ambrosino, Luca; Cieslak, Matthew; Ianora, Adrianna

doi:10.3390/biology9110410

Cited by 6 publications

(3 citation statements)

References 49 publications

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“…We also found that 24.3% of the protein families among seven species have patterns of annotated transcripts similar to previously sequenced and here re-assembled C. finmarchicus (Tarrant et al, 2014), C. sinicus (Yang et al, 2014), and other recently investigated copepods, for example, Labidocera madurae (Roncalli et al, 2017) and Rhincalanus gigas (Lauritano et al, 2020).…”

Section: Conserved Protein Functions Across Speciessupporting

confidence: 83%

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Insights into the species evolution of Calanus copepods in the northern seas revealed by de novo transcriptome sequencing

Lizano

Smolina

Choquet

et al. 2022

Ecology and Evolution

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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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Section: Conserved Protein Functions Across Speciessupporting

confidence: 83%

“…finmarchicus (Tarrant et al, 2014 ), C . sinicus (Yang et al, 2014 ), and other recently investigated copepods, for example, Labidocera madurae (Roncalli et al, 2017 ) and Rhincalanus gigas (Lauritano et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Insights into the species evolution of Calanus copepods in the northern seas revealed by de novo transcriptome sequencing

Lizano

Smolina

Choquet

et al. 2022

Ecology and Evolution

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“…Query sequences from the fruit fly Drosophila melanogaster (NP_524873, AAF07876, NP_572854) were used to mine the transcriptome shotgun assembly (TSA) database on the National Center for Biotechnology Information (NCBI), limiting the searches (tblastn algorithm) to Copepoda (taxid:6830) (search February 2023). For Rhincalanus gigas, raw reads were downloaded from NCBI [25] and assembled as described in [26]. Additional mining was performed using queries from the copepod Lepeophtheirus salmonis (order Siphonostomatoida) (BT121711, BT121232, MK887318, BT077723, BT121164) [14].…”

Section: In Silico Workflowmentioning

confidence: 99%

The Distribution of Ferritins in Marine Copepods

Roncalli

Uttieri

Carotenuto

2023

JMSE

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Iron is an essential element for the functioning of cellular processes. Ferritins, the major intracellular iron storage proteins, convert the free Fe2+ into the nontoxic Fe3+ which can be stored and transported where needed. To date, little is known about the iron metabolism in copepods; however, in these crustaceans, ferritins have been used as biomarkers of stress and diapause. A limiting factor of these studies has been the use of a single ferritin transcript as a biomarker. In this paper, we in silico mined the publicly available copepod transcriptomes to characterize the multiplicity of the ferritin transcripts in different orders and families. We also examined the expression of ferritin in three ecologically important copepods—Calanus finmarchicus, C. helgolandicus and Temora stylifera—during development and under stress conditions. A full-length transcript encoding ferritin heavy chain has been identified in all 27 mined transcriptomes, with 50% of the species possessing multiple transcripts. Ferritin expression increased in C. finmarchicus during the early–late development transition, and in T. stylifera females exposed to oxylipins at sea. Overall, our results suggest that copepod ferritins can be involved in iron storage, larval development and stress response, thus representing potential biomarker genes for ocean health status monitoring.

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De novo transcriptome assembly of the Southern Ocean copepod Rhincalanus gigas sheds light on developmental changes in gene expression

et al. 2021

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First De Novo Transcriptome of the Copepod Rhincalanus gigas from Antarctic Waters

Cited by 6 publications

References 49 publications

Insights into the species evolution of Calanus copepods in the northern seas revealed by de novo transcriptome sequencing

Insights into the species evolution of Calanus copepods in the northern seas revealed by de novo transcriptome sequencing

The Distribution of Ferritins in Marine Copepods

De novo transcriptome assembly of the Southern Ocean copepod Rhincalanus gigas sheds light on developmental changes in gene expression

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