Identification and characterization of homeobox (Hox) genes and conservation of the single Hox cluster (324.6 kb) in the water flea Daphnia magna.

We report the complete sequence analysis of the entire complement of eight typical homeobox (Hox) genes (Lab, Pb, Dfd, Scr, Antp, Ubx, Abd-A, and Abd-B) and two other genes (Hox3 and Ftz) in a 324.6-kb region in the water flea Daphnia magna. In the cluster of D. magna Hox genes, we found one long interspersed nuclear element (LINE)/R2-NeSL between Ubx and Abd-A that was not present in Daphnia pulex Hox genes. In basal expression of Hox genes at different developmental stages, biothorax complex genes (Ubx, Abd-A, and Abd-B) and some antennapedia complex genes (Lab, Scr, Antp) were moderately expressed, but the Hox3 gene was barely expressed. Three homeobox genes (Antp, Ubx, Abd-A) were highly expressed at 6-7 days after release from the brood chamber and/or in the adult stage. The structural array and transcribed orientation of Dm-Hox genes were identical to those of the sister species D. pulex (∼340 kb), indicating that the Hox gene structure in daphnids is highly conserved. However, Dm- and Dp-Hox3, -deformed (Dfd), and -fushi tarazu (Ftz) genes varied from orthologous genes in pancrustacean species.

Genome-wide identification of nuclear receptor (NR) genes and the evolutionary significance of the NR1O subfamily in the monogonont rotifer Brachionus spp.

Nuclear receptors (NRs) are a large family of transcription factors that are involved in many fundamental biological processes. NRs are considered to have originated from a common ancestor, and are highly conserved throughout the whole animal taxa. Therefore, the genome-wide identification of NR genes in an animal taxon can provide insight into the evolutionary tendencies of NRs. Here, we identified all the NR genes in the monogonont rotifer Brachionus spp., which are considered an ecologically key species due to their abundance and world-wide distribution. The NR family was composed of 40, 32, 29, and 32 genes in the genomes of the rotifers B. calyciflorus, B. koreanus, B. plicatilis, and B. rotundiformis, respectively, which were classified into seven distinct subfamilies. The composition of each subfamily was highly conserved between species, except for NR1O genes, suggesting that they have undergone sporadic evolutionary processes for adaptation to their different environmental pressures. In addition, despite the dynamics of NR evolution, the significance of the conserved endocrine system, particularly for estrogen receptor (ER)-signaling, in rotifers was discussed on the basis of phylogenetic analyses. The results of this study may help provide a better understanding the evolution of NRs, and expand our knowledge of rotifer endocrine systems.

Identification and conservation of gene loss events of Hox gene clusters in the marine medaka (Oryzias melastigma).

In this study, the identification of the whole Hox gene clusters (46 Hox genes) in the marine medaka Oryzias melastigma was investigated using genome assembly and RNA-seq information. Moreover, the gene loss events of Hox gene clusters, which may occur during fish evolution, were examined for a better understanding of the evolutionary status of the gene lost events of the Hox gene cluster across fish species, particularly in the genus Oryzias.

Adverse Effects, Expression of the Bk-CYP3045C1 Gene, and Activation of the ERK Signaling Pathway in the Water Accommodated Fraction-Exposed Rotifer.

To examine the deleterious effects of the water accommodated fraction (WAF) of crude oil, the growth curve, fecundity, and lifespan of the monogonont rotifer (Brachionus koreanus) were measured for 24 h in response to three different doses (0.2×, 0.4×, and 0.8×) of WAFs. A higher dose of WAFs significantly reduced the fecundity and lifespan. A rotifer 32K microarray chip showed that the Bk-CYP3045C1 gene had the highest expression. Of the 25 entire CYP genes, the Bk-CYP3045C1 gene showed a significant expression for different doses and times in response to WAFs and chemical components of WAFs (naphthalene and phenanthrene); also, glutathione S-transferase genes, ABC transporter, and other genes showed dose responses upon exposure to 80% WAF over time. Different doses of WAFs increased the oxidative stress with an induction of reactive oxygen species (ROS) and a depletion of glutathione (GSH). Exposure to WAFs did not show toxic effects on survivability in B. koreanus; however, toxicity to WAFs was shown when piperonyl butoxide, a potent inhibitor of cytochrome P450 (CYP) enzymes, was added. This toxicity was dose-dependent. After WAFs exposure, p-ERK was activated over time in response to WAFs, which suggests that WAFs can be activated by the p-ERK signaling pathway.

Microplastic Size-Dependent Toxicity, Oxidative Stress Induction, and p-JNK and p-p38 Activation in the Monogonont Rotifer (Brachionus koreanus).

In this study, we evaluated accumulation and adverse effects of ingestion of microplastics in the monogonont rotifer (Brachionus koreanus). The dependence of microplastic toxicity on particle size was investigated by measuring several in vivo end points and studying the ingestion and egestion using 0.05-, 0.5-, and 6-µm nonfunctionalized polystyrene microbeads. To identify the defense mechanisms activated in response to microplastic exposure, the activities of several antioxidant-related enzymes and the phosphorylation status of mitogen-activated protein kinases (MAPKs) were determined. Exposure to polystyrene microbeads of all sizes led to significant size-dependent effects, including reduced growth rate, reduced fecundity, decreased lifespan and longer reproduction time. Rotifers exposed to 6-µm fluorescently labeled microbeads exhibited almost no fluorescence after 24 h, while rotifers exposed to 0.05- and 0.5-µm fluorescently labeled microbeads displayed fluorescence until 48 h, suggesting that 6-µm microbeads are more effectively egested from B. koreanus than 0.05- or 0.5-µm microbeads. This observation provides a potential explanation for our findings that microbead toxicity was size-dependent and smaller microbeads were more toxic. In vitro tests revealed that antioxidant-related enzymes and MAPK signaling pathways were significantly activated in response to microplastic exposure in a size-dependent manner.

Genome-wide identification of nuclear receptor (NR) superfamily genes in the copepod Tigriopus japonicus.

BACKGROUND: Nuclear receptors (NRs) are a large superfamily of proteins defined by a DNA-binding domain (DBD) and a ligand-binding domain (LBD). They function as transcriptional regulators to control expression of genes involved in development, homeostasis, and metabolism. The number of NRs differs from species to species, because of gene duplications and/or lineage-specific gene losses during metazoan evolution. Many NRs in arthropods interact with the ecdysteroid hormone and are involved in ecdysone-mediated signaling in arthropods. The nuclear receptor superfamily complement has been reported in several arthropods, including crustaceans, but not in copepods. We identified the entire NR repertoire of the copepod Tigriopus japonicus, which is an important marine model species for ecotoxicology and environmental genomics. RESULTS: Using whole genome and transcriptome sequences, we identified a total of 31 nuclear receptors in the genome of T. japonicus. Nomenclature of the nuclear receptors was determined based on the sequence similarities of the DNA-binding domain (DBD) and ligand-binding domain (LBD). The 7 subfamilies of NRs separate into five major clades (subfamilies NR1, NR2, NR3, NR4, and NR5/6). Although the repertoire of NR members in, T. japonicus was similar to that reported for other arthropods, there was an expansion of the NR1 subfamily in Tigriopus japonicus. The twelve unique nuclear receptors identified in T. japonicus are members of NR1L. This expansion may be a unique lineage-specific feature of crustaceans. Interestingly, E78 and HR83, which are present in other arthropods, were absent from the genomes of T. japonicus and two congeneric copepod species (T. japonicus and Tigriopus californicus), suggesting copepod lineage-specific gene loss. CONCLUSIONS: We identified all NR receptors present in the copepod, T. japonicus. Knowledge of the copepod nuclear receptor repertoire will contribute to a better understanding of copepod- and crustacean-specific NR evolution.

Comparison of the Estimation Methods from Acute to Chronic Biotic Ligand Model-Based Predicted No-Effect Concentrations for Nickel in Freshwater Species.

Biotic ligand models (BLMs) and the sensitivities of indigenous species are used to assess the environmental risk considering the bioavailability of metals, such as nickel. However, the BLM-based acute-to-chronic ratio (ACR) is required if the predicted no-effect concentration (PNEC) cannot be derived from the chronic species sensitivity distribution (SSD). The applicability of the ACR approach for estimating BLM-based PNEC for nickel from acute toxicity data was evaluated in the present study. The BLM-based acute SSD for nickel was built using the sensitivities of 21 indigenous species and different taxon-specific BLMs for each taxonomic group. To predict the acute sensitivity of invertebrates, the chronic crustacean nickel BLM with pH effect term, which can account for nickel toxicity at high pH levels, was used. This was used instead of the existing acute BLM for crustacean, which has too narrow a pH range to cover the pH dependency of toxicity. The final BLM-based ACR of nickel, determined within a factor of 1.53 from the species-specific acute and chronic sensitivities of the six species, was more reliable than the typical ACR estimated within a factor of 1.84. A linear relationship (r2 = 0.95) was observed between the PNECs using BLM-based ACR and the PNECs derived from the BLM-based chronic SSD of the European Union Risk Assessment Reports. In conclusion, the BLM-based PNEC for nickel could be derived using the ACR approach, unlike when copper BLM was applied. The BLM-based ACR for nickel is the first result calculated by directly comparing acute and chronic species sensitivities, and will contribute to the application of BLM-based risk assessment in broader ecoregions. Environ Toxicol Chem 2023;42:914-927. © 2023 SETAC.

Estimation of divergence times in cnidarian evolution based on mitochondrial protein-coding genes and the fossil record.

The phylum Cnidaria is comprised of remarkably diverse and ecologically significant taxa, such as the reef-forming corals, and occupies a basal position in metazoan evolution. The origin of this phylum and the most recent common ancestors (MRCAs) of its modern classes remain mostly unknown, although scattered fossil evidence provides some insights on this topic. Here, we investigate the molecular divergence times of the major taxonomic groups of Cnidaria (27 Hexacorallia, 16 Octocorallia, and 5 Medusozoa) on the basis of mitochondrial DNA sequences of 13 protein-coding genes. For this analysis, the complete mitochondrial genomes of seven octocoral and two scyphozoan species were newly sequenced and combined with all available mitogenomic data from GenBank. Five reliable fossil dates were used to calibrate the Bayesian estimates of divergence times. The molecular evidence suggests that cnidarians originated 741 million years ago (Ma) (95% credible region of 686-819), and the major taxa diversified prior to the Cambrian (543 Ma). The Octocorallia and Scleractinia may have originated from radiations of survivors of the Permian-Triassic mass extinction, which matches their fossil record well.

Derivation of acute copper biotic ligand model-based predicted no-effect concentrations and acute-chronic ratio.

The copper biotic ligand model (BLM) can quantitatively describe the bioavailability depending on various environmental factors and has been used to derive the predicted no-effect concentrations (PNECs). The commonly employed acute BLM tool, HydroQual, which applies the biotic ligand constants of fathead minnow in the same model structure for all taxonomic groups, estimates lower acute copper toxicity values compared to the chronic copper PNECs of the European Union Risk Assessment Reports (EU-RAR), which are based on taxon-specific model structures and biotic ligand constants for vertebrates, invertebrates, and algae. In this study, the full-BLM approach was applied using an appropriate acute BLM for each taxonomic group to derive acute HC5s (fifth percentile value in the species sensitivity distribution [SSD]) and an acute-chronic ratio for copper. Two acute BLMs for vertebrates and invertebrates were used and validated against site waters using the new method to estimate the intrinsic sensitivity for each species across different environmental conditions. To derive acute copper full BLM-based HC5s in Korean freshwater, acute toxicity tests were performed with 10 indigenous species, which were used to build the acute BLM-based SSD at each site. The final estimated acute full-BLM HC5s were higher than the EU-RAR chronic PNECs within the BLM calibration range. Furthermore, a linear relationship was observed between the acute full-BLM HC5s and the EU-RAR chronic PNECs. This linear regression function was suggested as an acute to chronic transformation function that can be applied to calculate chronic PNEC values. In conclusion, if the chronic ecotoxicity database of indigenous aquatic organisms for copper is lacking, it may be more efficient to derive chronic PNECs using an acute-chronic ratio after deriving BLM-based acute copper SSDs for indigenous species within representative taxonomic groups. This study provides a scientific foundation for the derivation of water quality criteria for copper in freshwater.

A comparative analysis of the complete mitochondrial genome of the Eurasian otter Lutra lutra (Carnivora; Mustelidae).

Otter populations are declining throughout the world and most otter species are considered endangered. Molecular methods are suitable tools for population genetic research on endangered species. In the present study, we analyzed the complete mitochondrial genome (mitogenome) sequence of the Eurasian otter Lutra lutra. The mitochondrial DNA sequence of the Eurasian otter is 16,505 bp in length and consists of 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region (CR). The CR sequence of otters from Europe and Asia showed nearly identical numbers and nucleotide sequences of minisatellites. Phylogenetic analysis of Mustelidae mitogenomes, including individual genes, revealed that Lutrinae and Mustelinae form a clade, and that L. lutra and Enhydra lutris are sister taxa within the Lutrinae. Phylogenetic analyses revealed that of the 13 mitochondrial protein-coding genes, ND5 is the most reliable marker for analysis of phylogenetic relationships within the Mustelidae.

Effects of endocrine disruptors on Bombina orientalis P450 aromatase activity.

To assess the effects of endocrine-disrupting chemicals on the expression and activity of aromatase in the gonads of Bombina orientalis, a common amphibian, we intraperitoneally injected nonylphenol or bisphenol-A and then examined aromatase mRNA levels by RT-PCR as well as aromatase enzymatic activity by tritiated water release assays. To design primers for the RT-PCR, we cloned the B. orientalis aromatase gene using RT-PCR and degenerate primers. The full-length cDNA was obtained by 5'- and 3'-RACE PCR. The complete sequence of the B. orientalis aromatase gene revealed an open reading frame of 1500 bp encoding a deduced protein of 500 amino acids. Semi-quantitative RT-PCR indicated that nonylphenol or bisphenol-A injection did not significantly affect the expression of B. orientalis aromatase mRNA. However, a 48-hr treatment with nonyphenol or bisphenol A reduced aromatase activity to 47% and 32% of the control, respectively. These results suggest that endocrine disrupters can effectively modulate the activity of B. orientalis aromatase without affecting its mRNA levels.

Differential expression of metallothionein (MT) gene by trace metals and endocrine-disrupting chemicals in the hermaphroditic mangrove killifish, Kryptolebias marmoratus.

Metallothionein (MT) gene expression was studied in different tissues, development stages and gender types of the mangrove killifish (Kryptolebias marmoratus). MT expression was also studied in a time-series experiment after exposure to trace metals and endocrine-disrupting chemicals (EDCs). The brain showed the highest level of MT transcripts. Although all the development stage showed some level of MT expression, the adult hermaphrodites showed the highest expression which was significantly higher than the secondary males. In the trace metal-exposed fish, cadmium caused the strongest induction of MT. However, other trace metals such as copper and zinc also caused MT gene induction. All the EDCs suppressed the expression of MT gene, and the effect of EDCs were not gender-specific. K. marmoratus has previously shown its suitability as a model species for toxicity studies and cancer research. This study demonstrated utility of MT as biomarker in K. marmoratus. However, confounding factors such as age, gender, and tissue types appear to influence the MT expression. Response of trace and organic pollutants such as EDCs also varied greatly. These observations suggest that MT would be a specific biomarker of trace metal exposure in K. marmoratus and expression would be influenced by intrinsic factors.

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

The complete mitochondrial genome was sequenced from the calanoid copepod Eurytemora affinis. The sequenced total genome size was 18,553 bp. The mitochondrial genome of E. affinis has 13 protein-coding genes (PCGs), two rRNAs, and 22 tRNAs. Of 13 PCGs, ND1, ND5, and ATP6 genes had incomplete stop codons TA-, T-, and TA-, respectively. Furthermore, the stop codons of the remaining eleven PCGs were TAG or TAA while the start codon of 13 PCGs was ATG (Cytb, ATP8, ATP6, and CO3 genes), ATT (CO1, ND2, ND3, ND4L, ND5, and ND6 genes), and ATA (ND1, ND4, and CO2 genes), respectively. The ratio of A + T and G + C nucleotides of 13 PCGs of E. affinis mitogenome showed 63.9% and 36.1%, respectively while those ratio of the entire sequences were 65.5% and 34.5%, respectively.

Complete mitochondrial genome of the marine mysid Neomysis awatschensis (Mysida, Mysidae).

The complete mitochondrial genome was sequenced from the marine mysid Neomysis awatschensis. The sequenced total genome size was 19,135 bp. The mitochondrial genome of N. awatschensis contained 13 protein-coding genes (PCGs), two rRNAs, and 22 tRNAs. Of 13 PCGs, all the genes had complete stop codons TAA and TAG, respectively, while the start codon of 13 PCGs was ATG (CO1, Cytb, ND4L, ATP8, ATP6, and ND4 genes), ATT (CO3, ND2, and ND5 genes), and ATA (CO2, ND3, ND6, and ND1 genes), respectively. The ratio of A + T and G + C nucleotides of 13 PCGs of N. awatschensis mitogenome showed 68.8% and 31.2%, respectively, while those ratio of all the sequences were 70.8% and 29.2%, respectively.

Molecular cloning, phylogenetic analysis and developmental expression of a vitellogenin (Vg) gene from the intertidal copepod Tigriopus japonicus.

Vitellogenin (Vg) is the precursor of egg yolk protein vitellins, which serve as energy resource for embryonic development. Vg measurement has been used as a biomarker of exposure to endocrine-disrupting chemicals (EDCs). Therefore, Vg gene structure has been identified from several species used in environmental monitoring of EDCs. Among the copepods, except from the salmon louse, there is no report on Vg genes or their products. By using molecular cloning, we determined the full Vg gene sequence from the intertidal copepod, Tigriopus japonicus. The full cDNA sequence was of 5692 bp containing 5529 bp of open reading frame (ORF) encoding for 1842 amino acids. The phylogenetic analysis revealed that T. japonicus Vg is distinct from the other arthropods as it formed a clade with salmon louse only. The expression of Vg transcripts was negligible in nauplii; detectable only at the copepodid stage 3. Females expressed over 270 times more Vg transcripts than males. The promoter sequence of T. japonicus Vg gene revealed an estrogen receptor (ER) half site and a metal response element (MRE). When copepods were exposed to trace metals, cadmium after 96 h exposure caused significantly higher induction of Vg transcripts. Taken together, molecular analysis of T. japonicus Vg would be helpful in understanding its role in development. Previous studies have established T. japonicus as a potential model for testing of endocrine-disrupting chemicals (EDCs). The study of T. japonicus Vg will fuel momentum in using this species in comparative molecular endocrinology and biomonitoring of EDCs.

Expression of glutathione S-transferase (GST) genes in the marine copepod Tigriopus japonicus exposed to trace metals.

The intertidal copepod, Tigriopus japonicus has been recognized as a potential model species for marine pollution toxicity testing. Toxicity ranges of several biocides, endocrine-disrupting chemicals (EDCs), and trace metals are known in T. japonicus. A large number of expressed sequence tags (ESTs) and genomic DNA are also sequenced from T. japonicus. In this study, expression of ten glutathione S-transferase (GST) genes was studied in the copepods exposed to trace metals. Expression of these genes was also studied against exposure to hydrogen peroxide (H(2)O(2)) used as a positive control with prooxidant activity. Of all genes, expression of GST-Sigma (GSTS) was highly upregulated in H(2)O(2) as well as trace metal-exposed copepods. In the time-course study, expression of GSTS mRNA was more consistent compared to other GSTs such as GST-Omega, GST-Delta1, GST-Theta3 or microsomal GST1 (mGST1). GSTS is predominantly reported from the insects. Coupled with the previous study of the in vitro antioxidant role of T. japonicus GSTS, these findings imply an antioxidant role for GSTS and highlight its importance as a biomarker of exposure to trace metals in T. japonicus. However, further validation and field trials would be necessary to propose GSTS gene expression as biomarker of exposure to trace metals, as for some trace metals such as silver the response was not consistent in concentration and time-series exposure experiments.

Two-generation toxicity study on the copepod model species Tigriopus japonicus.

Previous studies on the intertidal copepod Tigriopus japonicus have demonstrated that it is a suitable model species for the assessment of acute toxicities of marine pollutants. In order to standardize T. japonicus for use in environmental risk assessment involving whole life cycle exposure, we tested nine pollutants for their effects on growth and reproduction during a two-generation life cycle exposure test. Nauplii (F 0) were exposed to a range of concentrations of each chemical in a static renewal culture system. Broods of the second generation (F1) were subsequently exposed to the same concentrations for one full life cycle. Of the seven traits (nauplius phase, development time, survival, sex ratio, number of clutch, nauplii per clutch and fecundity), only the length of the nauplius phase and development time showed a greater sensitivity to chemical exposure. Between the two sensitive traits, the period of the nauplius phase was more sensitive than cohort generation time. Biocides significantly increased the maturation period of nauplii as well as copepodids in F 0 generation. In this study, it was demonstrated that T. japonicus could also be used in reproduction and life cycle tests and it provides an opportunity for testing the chronic and subchronic toxic effects of marine pollutants. Further validation and harmonization in a multi-centric study involving other laboratories of the region will strengthen its use as a supplement to existing model species.

The genome of the marine medaka Oryzias melastigma.

Marine medaka (Oryzias melastigma) is considered to be a useful fish model for marine and estuarine ecotoxicology studies and has good potential for field-based population genomics because of its geographical distribution in Asian estuarine and coastal areas. In this study, we present the first whole-genome draft of O. melastigma. The genome assembly consists of 8,602 scaffolds (N50 = 23.737 Mb) and a total genome length of 779.4 Mb. A total of 23,528 genes were predicted, and 12,670 gene families shared with three teleost species (Japanese medaka, mangrove killifish and zebrafish) were identified. Genome analyses revealed that the O. melastigma genome is highly heterozygous and contains a large number of repeat sequences. This assembly represents a useful genomic resource for fish scientists.

The genome of the freshwater monogonont rotifer Brachionus calyciflorus.

Monogononta is the most speciose class of rotifers, with more than 2,000 species. The monogonont genus Brachionus is widely distributed at a global scale, and a few of its species are commonly used as ecological and evolutionary models to address questions related to aquatic ecology, cryptic speciation, evolutionary ecology, the evolution of sex and ecotoxicology. With the importance of Brachionus species in many areas of research, it is remarkable that the genome has not been characterized. This study aims to address this lacuna by presenting, for the first time, the whole-genome assembly of the freshwater species Brachionus calyciflorus. The total length of the assembled genome was 129.6 Mb, with 1,041 scaffolds. The N50 value was 786.6 kb, and the GC content was 24%. A total of 16,114 genes were annotated with repeat sequences, accounting for 21% of the assembled genome. This assembled genome may form a basis for future studies addressing key questions on the evolution of monogonont rotifers. It will also provide the necessary molecular resources to mechanistically investigate ecophysiological and ecotoxicological responses.

Mining of biomarker genes from expressed sequence tags and differential display reverse transcriptase-polymerase chain reaction in the self-fertilizing fish, Kryptolebias marmoratus and their expression patterns in response to exposure to an endocrine-disrupting alkylphenol, bisphenol A.

Expressed sequence tags (ESTs) and differentially expressed cDNAs from the self-fertilizing fish, Kryptolebias marmoratus were mined to develop alternative biomarkers for endocrine-disrupting chemicals (EDCs). 1,577 K. marmoratus cDNA clones were randomly sequenced from the 5'-end. These clones corresponded to 1,518 and 1,519 genes in medaka dbEST and zebrafish dbEST, respectively. Of the matched genes, 197 and 115 genes obtained Unigene IDs in medaka dbEST and zebrafish dbEST, respectively. Many of the annotated genes are potential biomarkers for environmental stresses. In a differential display reverse transcriptase-polymerase chain reaction (DD RT-PCR) study, 56 differential expressed genes were obtained from fish liver exposed to bisphenol A. Of these, 16 genes were identified after BLAST search to GenBank, and the annotated genes were mainly involved in catalytic activity and binding. The expression patterns of these 16 genes were validated by real-time RT-PCR of liver tissue from fish exposed to bisphenol A. Our findings suggest that expression of these 16 genes is modulated by endocrine disrupting chemicals, and therefore that they are potential biomarkers for environmental stress including EDCs exposure.