Complete mitochondrial genome of the calanoid copepod Eurytemora affinis (Calanoida, Temoridae)

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

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.

The Complete Mitochondrial Genome of Pennella sp. Parasitizing Thunnus albacares

In the study, the parasite from the yellowfin tuna (Thunnus albacares) was separated, and morphological observation and molecular identification were carried out. Our results showed that the parasite was similar to Pennella sp. Its cephalothorax was covered by spherical to spherical non-branched nipples of almost the same size, which were very similar in shape and arrangement. A pair of slightly larger, the unbranched antenna was present on the outer margin of the small papillae-covered area. The gene sequence of COX1 with a length of 1,558 bp in the mitochondria of the parasite was 100% similar to Pennella sp. (MZ934363). The mitochondrial genome had a total length of 14,620 bp. It consisted of 36 genes (12 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs) and a dummy control region, but the mitochondrial genome had no ATP8 gene. Morphological observation showed that Pennella sp. was dark red, with a convex cephalothorax, with a total length of 8.42 cm, parasitic on the dorsal side of yellowfin tuna. Pennella sp. included the cephalothorax, neck, trunk, abdomen and egg belt. This study was the first report on the mitochondrial genome of Pennella sp. The results provide basic data for further identifying the parasites of Pennella genus.

Identification and characterization of homeobox gene clusters in harpacticoid and calanoid copepods

In this study, we have identified the entire complement of typical homeobox (Hox) genes (Lab, Pb, Dfd, Scr, Antp, Ubx, Abd-A, and Abd-B) in harpacticoid and calanoid copepods and compared them with the cyclopoid copepod Paracyclopina nana. The harpacticoid copepods Tigriopus japonicus and Tigriopus kingsejongensis have seven Hox genes (Lab, Dfd, Scr, Antp, Ubx, Abd-A, and Abd-B) and the Pb and Ftz genes are also present in the cyclopoid copepod P. nana. In the Hox gene cluster of the calanoid copepod Eurytemora affinis, all the Hox genes were present linearly in the genome but the Antp gene was duplicated. Of the three representative copepods, the P. nana Hox gene cluster was the most compact due to its small genome size. The Hox gene expression profile patterns in the three representative copepods were stage-specific. The Lab, Dfd, Scr, Pb, Ftz, and Hox3 genes showed a high expression in early developmental stages but Antp, Ubx, Abd-A, and Abd-B genes were mostly expressed in later developmental stages, implying that these Hox genes may be closely associated with the development of segment identity during early development.

Genome-wide identification of heat shock proteins in harpacticoid, cyclopoid, and calanoid copepods: Potential application in marine ecotoxicology

Constant evolution of omics-technologies has provided access to identification of various important gene families. Recently, genome assemblies on widely used ecotoxicological model species, including rotifers and copepods have been completed and representative detoxification-related gene families have been discovered for biomarker genes. However, despite ubiquitous presence of stress-response proteins, limited information on full genome-wide report on heat shock proteins (Hsps) is available. Various studies have demonstrated multiple cellular functions of Hsps in living organisms as an important biomarker in response to abiotic and biotic stressors, however, full genome-wide identification of Hsps, particularly in aquatic invertebrates, has not been reported. This is the first study to report the entire Hsps and basal gene expression levels in three regional-specific copepods: Tigriopus japonicus and kingsejongensis, Paracyclopina nana, and Eurytemora affnis, and how each Hsp family gene is regulated at a basal level.

Promotion of the Development of Sentinel Species in the Water Column: Example Using Body Size and Fecundity of the Egg-Bearing Calanoid Copepod Eurytemora affinis

The development of sentinel species in aquatic ecosystems is mostly based on benthic organisms; however, organisms living in water column such as zooplankton have received less attention, except for some cladocerans. In this paper, a new ecological indicator based on simple measurements of the size and fecundity of egg-bearing calanoid copepods is developed. The well-studied estuarine copepod Eurytemora affinis is used to illustrate this new framework. A large database obtained from laboratory experiments developed under different conditions is used to define a reference regression line between clutch size (CS) and prosome length (PL). The same database allowed one to confirm that the coefficient of variation (CV) of CS is an adequate estimator of the accumulated stress at population level. The CV of PL shows very little variability in all experimental and field conditions. The values of CS and PL obtained from the Seine, Loire, Gironde, Scheldt and Elbe estuaries in Europe are compared to the reference regression line. A quality index (QI) is calculated as a percentage of difference between the observed and the predicted CS. The QI classified 19 samples collected in the Seine estuary between 2004 and 2010 into four classes according to the physiological condition of the copepod female. A single sampling from June 2004 (5.26%) showed a very good condition, whereas 57.9% of the sampling dates confirmed good conditions. On the other hand, four sampling dates were associated to very bad conditions and three sampling dates indicated bad conditions. Seven additional samples obtained from other European estuaries between 2006 and 2009 were also used. Females showing poor conditions were observed in the early spring of 2005 and 2008 as well as during the month of November. These years were characterized by very strong climatic anomalies with a very cold late winter in 2005 and a warm winter in 2008. Therefore, it seems that the QI perfectly reflected the strong stress caused by the sudden change in hydro-climatic conditions that have certainly affected the physiology of copepod females and probably the availability of food. The new indicator is very simple to calculate and can be generalised to several aquatic ecosystems (fresh water and brackish water) by targeting the dominating egg-bearing calanoid copepods. As in the case of E. affinis, the development of sentinel species based on copepods or cladocerans can enrich ecological and ecotoxicological studies given their capacity to integrate the variability of their habitats’ quality at the individual and population levels.