Dataset Information

The complete mitochondrial genome of the southern calanoid copepod Calanus simillimus Giesbrecht, 1902.

ABSTRACT: The complete mitochondrial genome of Calanus simillimus is 27,876 bp in length (GenBank accession OK500294) and containing 13 protein-coding genes (PCGs), 2 rRNA genes, 22 transfer RNA genes. The gene order is novel compared to other Calanus species and copepods with sequenced mitogenomes. Phylogenetic analysis suggests that C. simillimus represent a fourth group within Calanus genus in addition to C. hyperboreus, C. finmarchicus and C. helgolandicus groups. The complete mitochondrial genome of C. simillimus will be useful for species identification, population genetics, phylogenetic and evolutionary studies among copepods.

SUBMITTER: Smolina I

PROVIDER: S-EPMC9275497 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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The complete mitochondrial genome of the southern calanoid copepod Calanus simillimus Giesbrecht, 1902.

Smolina Irina I Espinasse Marina M Amundsen Cesilie Røtnes CR Espinasse Boris B

Mitochondrial DNA. Part B, Resources 20220707 7

The complete mitochondrial genome of Calanus simillimus is 27,876 bp in length (GenBank accession OK500294) and containing 13 protein-coding genes (PCGs), 2 rRNA genes, 22 transfer RNA genes. The gene order is novel compared to other Calanus species and copepods with sequenced mitogenomes. Phylogenetic analysis suggests that C. simillimus represent a fourth group within Calanus genus in addition to C. hyperboreus, C. finmarchicus and C. helgolandicus gro ...[more]

PMID: 35837496

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Project description:BackgroundCopepods are highly diverse and abundant, resulting in extensive ecological radiation in marine ecosystems. Calanus sinicus dominates continental shelf waters in the northwest Pacific Ocean and plays an important role in the local ecosystem by linking primary production to higher trophic levels. A lack of effective molecular markers has hindered phylogenetic and population genetic studies concerning copepods. As they are genome-level informative, mitochondrial DNA sequences can be used as markers for population genetic studies and phylogenetic studies.ResultsThe mitochondrial genome of C. sinicus is distinct from other arthropods owing to the concurrence of multiple non-coding regions and a reshuffled gene arrangement. Further particularities in the mitogenome of C. sinicus include low A + T-content, symmetrical nucleotide composition between strands, abbreviated stop codons for several PCGs and extended lengths of the genes atp6 and atp8 relative to other copepods. The monophyletic Copepoda should be placed within the Vericrustacea. The close affinity between Cyclopoida and Poecilostomatoida suggests reassigning the latter as subordinate to the former. Monophyly of Maxillopoda is rejected. Within the alignment of 11 C. sinicus mitogenomes, there are 397 variable sites harbouring three 'hotspot' variable sites and three microsatellite loci.ConclusionThe occurrence of the circular subgenomic fragment during laboratory assays suggests that special caution should be taken when sequencing mitogenomes using long PCR. Such a phenomenon may provide additional evidence of mitochondrial DNA recombination, which appears to have been a prerequisite for shaping the present mitochondrial profile of C. sinicus during its evolution. The lack of synapomorphic gene arrangements among copepods has cast doubt on the utility of gene order as a useful molecular marker for deep phylogenetic analysis. However, mitochondrial genomic sequences have been valuable markers for resolving phylogenetic issues concerning copepods. The variable site maps of C. sinicus mitogenomes provide a solid foundation for population genetic studies.

Project description:The copepod Calanus sinicus Brodsky dominates the zooplankton in the Yellow Sea, China, and undergoes over-summering within the Yellow Sea Cold Water Mass (YSCWM). Termination of over-summering and subsequent development are regarded as key processes in population recruitment, and are probably linked to environmental variations in the YSCWM. In this study, we examined the effects of temperature (9 and 18°C) and food conditions (0.1 μg C mL-1 and unfed) on metabolic rates, morphological characteristics, and relative gene expressions of six genes involved in molting, gonad development, lipid catabolism, and stress tolerance processes of C. sinicus during termination of over-summering and subsequent development. Both elevated temperature and external food supply rapidly ended over-summering of C. sinicus, accompanied by up-regulation of the ecdysteroid receptor (EcR) gene expression and increased metabolic rates. These environmental conditions resulted in irreversible termination of over-summering and ensure the success of molting. During subsequent development, the lipid reserve in oil sacs could permit only early gonad development. The food supply might be a trigger to activate the final maturity of gonad by up-regulating expression of the vitellogenin receptor (VgR) gene. Thus, food played an indispensable role in population recruitment after termination of over-summering, whereas the elevated temperature accelerated these physiological processes. This study revealed the first dynamic profiles of physiological processes involved in over-summering termination and the subsequent development of C. sinicus using morphological, physiological and molecular methods simultaneously, confirmed the quiescent state of over-summering C5 copepodites, detected the effects of environmental changes on over-summering termination and subsequent development, and provided a foundation for future investigations of the mechanisms involved in over-summering in YSCWM.

Dataset Information

The complete mitochondrial genome of the southern calanoid copepod Calanus simillimus Giesbrecht, 1902.

Publications

The complete mitochondrial genome of the southern calanoid copepod <i>Calanus simillimus</i> Giesbrecht, 1902.

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