The genome of the freshwater monogonont rotifer Brachionus calyciflorus

Is there potential for estradiol receptor signaling in lophotrochozoans?

Estrogen receptors (ERs) are thought to be the ancestor of all steroid receptors and are present in most lophotrochozoans studied to date, including molluscs, annelids, and rotifers. A number of studies have investigated the functional role of estrogen receptors in invertebrate species, although most are in molluscs, where the receptor is constitutively active. In vitro experiments provided evidence for ligand-activated estrogen receptors in annelids, raising important questions about the role of estrogen signalling in lophotrochozoan lineages. Here, we review the concordant and discordant evidence of estradiol receptor signalling in lophotrochozoans, with a focus on annelids and rotifers. We explore the de novo synthesis of estrogens, the evolution and expression of estrogen receptors, and physiological responses to activation of estrogen receptors in the lophotrochozoan phyla Annelida and Rotifera. Key data are missing to determine if de novo biosynthesis of estradiol in non-molluscan lophotrochozoans is likely. For example, an ortholog for the CYP11 gene is present, but confirmation of substrate conversion and measured tissue products is lacking. Orthologs CYP17 and CYP19 are lacking, yet intermediates or products (e.g. estradiol) in tissues have been measured. Estrogen receptors are present in multiple species, and for a limited number, in vitro data show agonist binding of estradiol and/or transcriptional activation. The expression patterns of the lophotrochozoan ERs suggest developmental, reproductive, and digestive roles but are highly species dependent. E2 exposures suggest that lophotrochozoan ERs may play a role in reproduction, but no strong dose-response relationship has been established. Therefore, we expect most lophotrochozoan species, outside of perhaps platyhelminths, to have an ER but their physiological role remains elusive. Mining genomes for orthologs gene families responsible for steroidogenesis, coupled with in vitro and in vivo studies of the steroid pathway are needed to better assess whether lophotrochozoans are capable of estradiol biosynthesis. One major challenge is that much of the data are divided across a diversity of species. We propose that the polychaetes Capitella teleta or Platyneris dumerilii, and rotifer Brachionus manjavacas may be strong species choices for studies of estrogen receptor signalling, because of available genomic data, established laboratory culture techniques, and gene knockout potential.

Highly efficient CRISPR-mediated gene editing in a rotifer

Rotifers have been studied in the laboratory and field for over 100 years in investigations of microevolution, ecological dynamics, and ecotoxicology. In recent years, rotifers have emerged as a model system for modern studies of the molecular mechanisms of genome evolution, development, DNA repair, aging, life history strategy, and desiccation tolerance. However, a lack of gene editing tools and transgenic strains has limited the ability to link genotype to phenotype and dissect molecular mechanisms. To facilitate genetic manipulation and the creation of reporter lines in rotifers, we developed a protocol for highly efficient, transgenerational, CRISPR-mediated gene editing in the monogonont rotifer Brachionus manjavacas by microinjection of Cas9 protein and synthetic single-guide RNA into the vitellaria of young amictic (asexual) females. To demonstrate the efficacy of the method, we created knockout mutants of the developmental gene vasa and the DNA mismatch repair gene mlh3. More than half of mothers survived injection and produced offspring. Genotyping these offspring and successive generations revealed that most carried at least 1 CRISPR-induced mutation, with many apparently mutated at both alleles. In addition, we achieved precise CRISPR-mediated knock-in of a stop codon cassette in the mlh3 locus, with half of injected mothers producing F2 offspring with an insertion of the cassette. Thus, this protocol produces knockout and knock-in CRISPR/Cas9 editing with high efficiency, to further advance rotifers as a model system for biological discovery.

Draft genome assembly for the colombian freshwater bocachico fish, Prochilodus magdalenae

We report the first draft genome assembly for Prochilodus magdalenae, the leading representative species of the Prochilodontidae family in Colombia. This 1.2-Gb assembly, with a GC content of 42.0% and a repetitive content of around 31.0%, is in the range of previously reported characid species genomes. Annotation identified 34,725 nuclear genes, and BUSCO completeness value was 94.9%. Gene ontology and primary metabolic pathway annotations indicate similar gene profiles for P. magdalenae and the closest species with annotated genomes: blind cave fish (Astyanax mexicanus) and red piranha (Pygocentrus nattereri). A comparative analysis showed similar genome traits to other characid species. The fully sequenced and annotated mitochondrial genome reproduces the taxonomic classification of P. magdalenae and confirms the low mitochondrial genetic divergence inside the Prochilodus genus. Phylogenomic analysis, using nuclear single-copy orthologous genes, also confirmed the evolutionary position of the species. This genome assembly provides a high-resolution genetic resource for sustainable P. magdalenae management in Colombia and, as the first genome assembly for the Prochilodontidae family, will contribute to fish genomics throughout South America.

Comparative genome analysis of the monogonont marine rotifer Brachionus manjavacas Australian strain: Potential application for ecotoxicology and environmental genomics

This is the first study to analyze the whole-genome sequence of B. manjavacas Australian (Aus.) strain through combination of Oxford Nanopore long-read seq, resulting in a total length of 108.1 Mb and 75 contigs. Genome-wide detoxification related gene families in B. manjavacas Aus. strain were comparatively analyzed with those previously identified in other Brachionus spp., including B. manjavacas German (Ger.) strain. Most of the subfamilies in detoxification related families (CYPs, GSTs, and ABCs) were highly conserved and confirmed orthologous relationship with Brachionus spp., and with accumulation of genome data, clear differences between genomic repertoires were demonstrated the marine and the freshwater species. Furthermore, strain-specific genetic variations were present between the Aus. and Ger. strains of B. manjavacas. This whole-genome analysis provides in-depth review on the genomic structural differences for detoxification-related gene families and further provides useful information for comparative ecotoxicological studies and evolution of detoxification mechanisms in Brachionus spp.

G protein-coupled receptors (GPCRs) in rotifers and cladocerans: Potential applications in ecotoxicology, ecophysiology, comparative endocrinology, and pharmacology

The G protein-coupled receptor (GPCR) superfamily plays a fundamental role in both sensory functions and the regulation of homeostasis, and is highly conserved across the eukaryote taxa. Its functional diversity is related to a conserved seven-transmembrane core and invariant set of intracellular signaling mechanisms. The interplay between these properties is key to the evolutionary success of GPCR. As this superfamily originated from a common ancestor, GPCR genes have evolved via lineage-specific duplications through the process of adaptation. Here we summarized information on GPCR gene families in rotifers and cladocerans based on their evolutionary position in aquatic invertebrates and their potential application in ecotoxicology, ecophysiology, comparative endocrinology, and pharmacology. Phylogenetic analyses were conducted to examine the evolutionary significance of GPCR gene families and to provide structural insight on their role in aquatic invertebrates. In particular, most GPCR gene families have undergone sporadic evolutionary processes, but some GPCRs are highly conserved across species despite the dynamics of GPCR evolution. Overall, this review provides a better understanding of GPCR evolution in aquatic invertebrates and expand our knowledge of the potential application of these receptors in various fields.

The genome of the freshwater monogonont rotifer Brachionus rubens: Identification of phase I, II, and III detoxification genes

Monogonont rotifers are common species in aquatic environments and make model species for ecotoxicology studies. Whole genomes of several species of the genus Brachionus have been assembled, but no information on the freshwater rotifer Brachionus rubens has been reported. In this study, the whole-genome sequence of B. rubens was successfully assembled using NextDenovo. The total length of the genome was 132.7 Mb (N50 = 2.51 Mb), including 122 contigs. The GC contents accounted for 29.96% of the genome. Aquatic organisms are always exposed to various external stresses, and a comprehensive genomic analysis is needed to better understand the adverse effects on organisms. This paper focuses on the ecotoxicological aspect and conducted genome analysis of representative gene families involved in detoxification mechanisms against environmental stressors. Specifically, we identified cytochrome P450 genes (CYPs) of phase I, glutathione S-transferase genes (GSTs) of phase II, and ATP-binding cassette transporter genes (ABCs) of phase III in the genome of B. rubens. Gene duplications were found in CYP, GST, and ABC genes, as is the case for other Brachionus rotifers. Our results suggest that these detoxification-related gene families have evolved in a species-specific and/or lineage-specific manner. This paper improves our understanding of how the freshwater Brachionus rotifers respond to environmental stressors in a molecular ecotoxicology context.

The Genome of the Marine Rotifer Brachionus manjavacas: Genome-Wide Identification of 310 G Protein-Coupled Receptor (GPCR) Genes

The marine rotifer Brachionus manjavacas is widely used in ecological, ecotoxicological, and ecophysiological studies. The reference genome of B. manjavacas is a good starting point to uncover the potential molecular mechanisms of responses to various environmental stressors. In this study, we assembled the whole-genome sequence (114.1 Mb total, N50 = 6.36 Mb) of B. manjavacas, consisting of 61 contigs with 18,527 annotated genes. To elucidate the potential ligand-receptor signaling pathways in marine Brachionus rotifers in response to environmental signals, we identified 310 G protein-coupled receptor (GPCR) genes in the B. manjavacas genome after comparing them with three other species, including the minute rotifer Proales similis, Drosophila melanogaster, and humans (Homo sapiens). The 310 full-length GPCR genes were categorized into five distinct classes: A (262), B (26), C (7), F (2), and other (13). Most GPCR gene families showed sporadic evolutionary processes, but some classes were highly conserved between species as shown in the minute rotifer P. similis. Overall, these results provide potential clues for in silico analysis of GPCR-based signaling pathways in the marine rotifer B. manjavacas and will expand our knowledge of ligand-receptor signaling pathways in response to various environmental signals in rotifers.

First Insights into the Repertoire of Secretory Lectins in Rotifers

Due to their high biodiversity and adaptation to a mutable and challenging environment, aquatic lophotrochozoan animals are regarded as a virtually unlimited source of bioactive molecules. Among these, lectins, i.e., proteins with remarkable carbohydrate-recognition properties involved in immunity, reproduction, self/nonself recognition and several other biological processes, are particularly attractive targets for biotechnological research. To date, lectin research in the Lophotrochozoa has been restricted to the most widespread phyla, which are the usual targets of comparative immunology studies, such as Mollusca and Annelida. Here we provide the first overview of the repertoire of the secretory lectin-like molecules encoded by the genomes of six target rotifer species: Brachionus calyciflorus, Brachionus plicatilis, Proales similis (class Monogononta), Adineta ricciae, Didymodactylos carnosus and Rotaria sordida (class Bdelloidea). Overall, while rotifer secretory lectins display a high molecular diversity and belong to nine different structural classes, their total number is significantly lower than for other groups of lophotrochozoans, with no evidence of lineage-specific expansion events. Considering the high evolutionary divergence between rotifers and the other major sister phyla, their widespread distribution in aquatic environments and the ease of their collection and rearing in laboratory conditions, these organisms may represent interesting targets for glycobiological studies, which may allow the identification of novel carbohydrate-binding proteins with peculiar biological properties.

Comparative analysis reveals within-population genome size variation in a rotifer is driven by large genomic elements with highly abundant satellite DNA repeat elements

BACKGROUND

Eukaryotic genomes are known to display an enormous variation in size, but the evolutionary causes of this phenomenon are still poorly understood. To obtain mechanistic insights into such variation, previous studies have often employed comparative genomics approaches involving closely related species or geographically isolated populations within a species. Genome comparisons among individuals of the same population remained so far understudied-despite their great potential in providing a microevolutionary perspective to genome size evolution. The rotifer Brachionus asplanchnoidis represents one of the most extreme cases of within-population genome size variation among eukaryotes, displaying almost twofold variation within a geographic population.

RESULTS

Here, we used a whole-genome sequencing approach to identify the underlying DNA sequence differences by assembling a high-quality reference genome draft for one individual of the population and aligning short reads of 15 individuals from the same geographic population including the reference individual. We identified several large, contiguous copy number variable regions (CNVs), up to megabases in size, which exhibited striking coverage differences among individuals, and whose coverage overall scaled with genome size. CNVs were of remarkably low complexity, being mainly composed of tandemly repeated satellite DNA with only a few interspersed genes or other sequences, and were characterized by a significantly elevated GC-content. CNV patterns in offspring of two parents with divergent genome size and CNV patterns in several individuals from an inbred line differing in genome size demonstrated inheritance and accumulation of CNVs across generations.

CONCLUSIONS

By identifying the exact genomic elements that cause within-population genome size variation, our study paves the way for studying genome size evolution in contemporary populations rather than inferring patterns and processes a posteriori from species comparisons.

Genomics and transcriptomics of epizoic Seisonidea (Rotifera, syn. Syndermata) reveal strain formation and gradual gene loss with growing ties to the host

Background

Seisonidea (also Seisonacea or Seisonidae) is a group of small animals living on marine crustaceans (Nebalia spec.) with only four species described so far. Its monophyletic origin with mostly free-living wheel animals (Monogononta, Bdelloidea) and endoparasitic thorny-headed worms (Acanthocephala) is widely accepted. However, the phylogenetic relationships inside the Rotifera-Acanthocephala clade (Rotifera sensulato or Syndermata) are subject to ongoing debate, with consequences for our understanding of how genomes and lifestyles might have evolved. To gain new insights, we analyzed first drafts of the genome and transcriptome of the key taxon Seisonidea.

Results

Analyses of gDNA-Seq and mRNA-Seq data uncovered two genetically distinct lineages in Seison nebaliae Grube, 1861 off the French Channel coast. Their mitochondrial haplotypes shared only 82% sequence identity despite identical gene order. In the nuclear genome, distinct linages were reflected in different gene compactness, GC content and codon usage. The haploid nuclear genome spans ca. 46 Mb, of which 96% were reconstructed. According to ~ 23,000 SuperTranscripts, gene number in S. nebaliae should be within the range published for other members of Rotifera-Acanthocephala. Consistent with this, numbers of metazoan core orthologues and ANTP-type transcriptional regulatory genes in the S. nebaliae genome assembly were between the corresponding numbers in the other assemblies analyzed. We additionally provide evidence that a basal branching of Seisonidea within Rotifera-Acanthocephala could reflect attraction to the outgroup. Accordingly, rooting via a reconstructed ancestral sequence led to monophyletic Pararotatoria (Seisonidea+Acanthocephala) within Hemirotifera (Bdelloidea+Pararotatoria).

Conclusion

Matching genome/transcriptome metrics with the above phylogenetic hypothesis suggests that a haploid nuclear genome of about 50 Mb represents the plesiomorphic state for Rotifera-Acanthocephala. Smaller genome size in S. nebaliae probably results from subsequent reduction. In contrast, genome size should have increased independently in monogononts as well as bdelloid and acanthocephalan stem lines. The present data additionally indicate a decrease in gene repertoire from free-living to epizoic and endoparasitic lifestyles. Potentially, this reflects corresponding steps from the root of Rotifera-Acanthocephala via the last common ancestors of Hemirotifera and Pararotatoria to the one of Acanthocephala. Lastly, rooting via a reconstructed ancestral sequence may prove useful in phylogenetic analyses of other deep splits.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07857-y.

The genome of the minute marine rotifer Proales similis: Genome-wide identification of 401 G protein-coupled receptor (GPCR) genes

The minute marine rotifer Proales similis is a potential model species for ecotoxicological and ecophysiological studies. Therefore, the provision of whole-genome data for P. similis is an easy way to deepen understanding of the molecular mechanisms involved in response to various environmental stressors. In this research, we assembled the whole-genome sequence (32.7 Mb total, N50 = 2.42 Mb) of P. similis, consisting of 15 contigs with 10,785 annotated genes. To understand the ligand-receptor signaling pathway in rotifers in response to environmental cues, we identified 401 G protein-coupled receptor (GPCR) genes in the P. similis genome and compared them with those from other species. The 401 full-length GPCR genes were classified into five distinct classes: A (363), B (18), C (7), F (2), and other (11). Most GPCR gene families have undergone sporadic evolutionary processes. However, some classes were highly conserved between species. Overall, this result provides new information about GPCR-based signaling pathways and the evolution of GPCRs in the minute rotifer P. similis, and it expands our knowledge of ligand-receptor signaling pathways in response to various environmental cues.

Linking genome size variation to population phenotypic variation within the rotifer, Brachionus asplanchnoidis

Eukaryotic organisms usually contain much more genomic DNA than expected from their biological complexity. In explaining this pattern, selection-based hypotheses suggest that genome size evolves through selection acting on correlated life history traits, implicitly assuming the existence of phenotypic effects of (extra) genomic DNA that are independent of its information content. Here, we present conclusive evidence of such phenotypic effects within a well-mixed natural population that shows heritable variation in genome size. We found that genome size is positively correlated with body size, egg size, and embryonic development time in a population of the monogonont rotifer Brachionus asplanchnoidis. The effect on embryonic development time was mediated partly by an indirect effect (via egg size), and a direct effect, the latter indicating an increased replication cost of the larger amounts of DNA during mitosis. Our results suggest that selection-based change of genome size can operate in this population, provided it is strong enough to overcome drift or mutational change of genome size.

The genome of the euryhaline rotifer Brachionus paranguensis: Potential use in molecular ecotoxicology

Brachionus spp. rotifers have been proposed as model organisms for ecotoxicological studies. We analyzed the whole-genome sequence of B. paranguensis through NextDenovo, resulting in a total length of 106.2 Mb and 71 contigs. The N50 and the GC content were 4.13 Mb and 28%, respectively. A total of 18,501 genes were predicted within the genome of B. paranguensis. Prominent detoxification-related gene families of phase I and II detoxifications have been investigated. In parallel with other Brachionus rotifers, high gene expansion was observed in CYP clan 3 and GST sigma class in B. paranguensis. Moreover, species-specific expansion of sulfotransferase (SULTs) and gain of UDP-glucuronosyltransferases (UGTs) through horizontal gene transfer has been specifically found within B. plicatilis complex. This whole-genome analysis of B. paranguensis provides a basis for molecular ecotoxicological studies and provides useful information for comparative studies of the evolution of detoxification mechanisms in Brachionus spp.

The genome of the freshwater monogonont rotifer Brachionus angularis: Identification of phase I, II, and III detoxification genes and their roles in molecular ecotoxicology

Brachionus spp. rotifers, which are widely distributed in aquatic environments, have been proposed as model organisms for ecotoxicological studies. Although the genomes of several rotifers belonging to the genus Brachionus have been assembled, the genome for the freshwater rotifer Brachionus angularis remains unknown. In this study, we analyzed the whole-genome sequence of B. angularis, which revealed a total length of 56.5 Mb and 21 contigs. The N50 and the GC content were 5.42 Mb and 23.66%, respectively. A total of 13,952 genes were predicted. Of them, we identified the main detoxification-related gene families, including those for cytochrome P450, glutathione S-transferase (GST), and the ATP-binding cassette transporter. In comparison with other Brachionus rotifers, massive species-specific expansion in GST sigma genes was found in B. angularis. This whole-genome analysis of B. angularis provides a basis for molecular ecotoxicological studies and provides useful biological tools for comparative studies of the evolution of detoxification mechanisms in Brachionus spp.

Application of heavy-ion-beam irradiation to breeding large rotifer

In larviculture facilities, rotifers are generally used as an initial food source, while a proper size of live feeds to connect rotifer and Artemia associated with fish larval growth is needed. The improper management of feed size and density induces mass mortality and abnormal development of fish larvae. To improve the survival and growth of target larvae, this study applied carbon and argon heavy-ion-beam irradiation in mutation breeding to select rotifer mutants with larger lorica sizes. The optimal irradiation conditions of heavy-ion beam were determined with lethality, reproductivity, mutant frequency, and morphometric characteristics. Among 56 large mutants, TYC78, TYC176, and TYA41 also showed active population growth. In conclusion, (1) heavy-ion-beam irradiation was defined as an efficient tool for mutagenesis of rotifers and (2) the aforementioned 3 lines that have larger lorica length and active population growth may be used as a countermeasure of live feed size gap during fish larviculcure.

Evolutionary dynamics of transposable elements in bdelloid rotifers

Transposable elements (TEs) are selfish genomic parasites whose ability to spread autonomously is facilitated by sexual reproduction in their hosts. If hosts become obligately asexual, TE frequencies and dynamics are predicted to change dramatically, but the long-term outcome is unclear. Here, we test current theory using whole-genome sequence data from eight species of bdelloid rotifers, a class of invertebrates in which males are thus far unknown. Contrary to expectations, we find a variety of active TEs in bdelloid genomes, at an overall frequency within the range seen in sexual species. We find no evidence that TEs are spread by cryptic recombination or restrained by unusual DNA repair mechanisms. Instead, we find that that TE content evolves relatively slowly in bdelloids and that gene families involved in RNAi-mediated TE suppression have undergone significant expansion, which might mitigate the deleterious effects of active TEs and compensate for the consequences of long-term asexuality.

Brachionus rotifers as a model for investigating dietary and metabolic regulators of aging

Because every species has unique attributes relevant to understanding specific aspects of aging, using a diversity of study systems and a comparative biology approach for aging research has the potential to lead to novel discoveries applicable to human health. Monogonont rotifers, a standard model for studies of aquatic ecology, evolutionary biology, and ecotoxicology, have also been used to study lifespan and healthspan for nearly a century. However, because much of this work has been published in the ecology and evolutionary biology literature, it may not be known to the biomedical research community. In this review, we provide an overview of Brachionus rotifers as a model to investigate nutritional and metabolic regulators of aging, with a focus on recent studies of dietary and metabolic pathway manipulation. Rotifers are microscopic, aquatic invertebrates with many advantages as a system for studying aging, including a two-week lifespan, easy laboratory culture, direct development without a larval stage, sexual and asexual reproduction, easy delivery of pharmaceuticals in liquid culture, and transparency allowing imaging of cellular morphology and processes. Rotifers have greater gene homology with humans than do established invertebrate models for aging, and thus rotifers may be used to investigate novel genetic mechanisms relevant to human lifespan and healthspan. The research on caloric restriction; dietary, pharmaceutical, and genetic interventions; and transcriptomics of aging using rotifers provide insights into the metabolic regulators of lifespan and health and suggest future directions for aging research. Capitalizing on the unique biology of Brachionus rotifers, referencing the vast existing literature about the influence of diet and drugs on rotifer lifespan and health, continuing the development of genetic tools for rotifers, and growing the rotifer research community will lead to new discoveries a better understanding of the biology of aging.

Genome-wide identification and transcriptional modulation of histone variants and modification related genes in the low pH-exposed marine rotifer Brachionus koreanus

Histone modification is considered to be a major epigenetic control mechanism. These modifications (e.g. acetylation, phosphorylation, and methylation) may affect the interaction of histones with DNA and/or regulate DNA-based processes (e.g., recombination, repair, replication, and transcription) and chromatin remodeling complexes. Despite their significance in metazoan life and evolution, few studies have been conducted to identify genes undergoing epigenetic control modification in aquatic invertebrates. In this study, we identified whole core histones (70 total genes) and post-translational modification (PTM) histone genes (63 total genes) in the marine rotifer Brachionus koreanus through whole-genome analysis, and annotated them according to the human nomenclature. Notably, upon comparative analysis of cis-regulatory motif sequences, we found that B. koreanus core histone protein structures were similar to those of mammals. Furthermore, to examine the effect of parental low pH stress on the offspring's epigenetic regulation, we investigated the expression of PTM genes in two generations of B. koreanus exposed to low pH conditions. Given that the B. koreanus genome does not possess DNA methyltransferase 1 and 3 genes, we concluded that histone genes could be involved as an important epigenetic mechanism in B. koreanus. Therefore, the histone-associated genes identified in this study could be useful for ecotoxicological studies and facilitate the application of chromatin immunoprecipitation sequencing using high-throughput DNA sequencing based on the genome-wide identification of transcription factor binding sites in rotifers.

Genome-wide identification of DNA double-strand break repair genes and transcriptional modulation in response to benzo[α]pyrene in the monogonont rotifer Brachionus spp

The DNA repair system has evolved from the common ancestor of all life forms and its function is highly conserved within eukaryotes. In this study, to reveal the role of DNA double-strand break repair (DSB) genes in response to benzo[α]pyrene (B[α]P), we first identified DSB genes in relation to homologous recombination and non-homologous end joining events in four Brachionus rotifer spp.: B. calyciflorus, B. koreanus, B. plicatilis, and B. rotundiformis. In all the Brachionus spp., 39 orthologous genes to human DSB repair genes were identified. Furthermore, three genes in B. koreanus, two genes in B. plicatilis, and one gene in B. calyciflorus and B. rotundiformis were present as duplicated genes, indicating that these genes were diversified over speciation in the genus Brachionus. Moreover, we compared DSB repair genes on the gene structures in four monogonont Brachionus rotifers and the bdelloid rotifer Adineta vaga, which possesses highly efficient DNA repair ability. The transcriptional responses of four monogonont Brachionus rotifers in response to B[α]P exposure showed how B[α]P exposure led to DSBs and subsequently recruited DNA DSB repair pathways in the rotifer B. koreanus. Taken together, this study provides a better understanding of the potential role of DSB repair genes in the monogonont rotifer Brachionus spp. in response to B[α]P.

The genome of the marine monogonont rotifer Brachionus rotundiformis and insight into species-specific detoxification components in Brachionus spp

The monogonont rotifer Brachionus spp. have been widely used for ecotoxicological studies because of their advantages as one of the most suitable laboratory experimental species. In the present study, we obtained and assembled the whole genome sequence of the rotifer Brachionus rotundiformis, consisting of 13,612 annotated genes with 213 scaffolds and 58 Mb in total length. Focusing on ecotoxicological aspects, we conducted a comparative genome analysis on the gene families involved in detoxification, including four to six sulfotransferase gene families, seven uridine 5'-diphospho-glucuronosyltransferase gene families, and 58, 61, or 70 ATP-binding cassette genes in the genus Brachionus including Brachionus koreanus and Brachionus plicatilis. Our results suggest that these gene families have undergone a species- and/or lineage-specific evolution in response to the surrounding environmental pressure. Our genome resource for B. rotundiformis would be highly useful for future ecotoxicological studies and also provides a better understanding on the view of evolutionary mechanism of detoxification in the genus Brachionus spp.

Temperature-dependent life history and transcriptomic responses in heat-tolerant versus heat-sensitive Brachionus rotifers

Thermal stress response is an essential physiological trait that determines occurrence and temporal succession in nature, including response to climate change. We compared temperature-related demography in closely related heat-tolerant and heat-sensitive Brachionus rotifer species. We found significant differences in heat response, with the heat-sensitive species adopting a strategy of long survival and low population growth, while the heat-tolerant followed the opposite strategy. In both species, we examined the genetic basis of physiological variation by comparing gene expression across increasing temperatures. Comparative transcriptomic analyses identified shared and opposing responses to heat. Interestingly, expression of heat shock proteins (hsps) was strikingly different in the two species and mirrored differences in population growth rates, showing that hsp genes are likely a key component of a species' adaptation to different temperatures. Temperature induction caused opposing patterns of expression in further functional categories including energy, carbohydrate and lipid metabolism, and in genes related to ribosomal proteins. In the heat-sensitive species, elevated temperatures caused up-regulation of genes related to meiosis induction and post-translational histone modifications. This work demonstrates the sweeping reorganizations of biological functions that accompany temperature adaptation in these two species and reveals potential molecular mechanisms that might be activated for adaptation to global warming.

3 tera-basepairs as a fundamental limit for robust DNA replication

In order to maintain functional robustness and species integrity, organisms must ensure high fidelity of the genome duplication process. This is particularly true during early development, where cell division is often occurring both rapidly and coherently. By studying the extreme limits of suppressing DNA replication failure due to double fork stall errors, we uncover a fundamental constant that describes a trade-off between genome size and architectural complexity of the developing organism. This constant has the approximate value N U ≈ 3 × 1012 basepairs, and depends only on two highly conserved molecular properties of DNA biology. We show that our theory is successful in interpreting a diverse range of data across the Eukaryota.

The genome, transcriptome, and proteome of the fish parasite Pomphorhynchus laevis (Acanthocephala)

Thorny-headed worms (Acanthocephala) are endoparasites exploiting Mandibulata (Arthropoda) and Gnathostomata (Vertebrata). Despite their world-wide occurrence and economic relevance as a pest, genome and transcriptome assemblies have not been published before. However, such data might hold clues for a sustainable control of acanthocephalans in animal production. For this reason, we present the first draft of an acanthocephalan nuclear genome, besides the mitochondrial one, using the fish parasite Pomphorhynchus laevis (Palaeacanthocephala) as a model. Additionally, we have assembled and annotated the transcriptome of this species and the proteins encoded. A hybrid assembly of long and short reads resulted in a near-complete P. laevis draft genome of ca. 260 Mb, comprising a large repetitive portion of ca. 63%. Numbers of transcripts and translated proteins (35,683) were within the range of other members of the Rotifera-Acanthocephala clade. Our data additionally demonstrate a significant reorganization of the acanthocephalan gene repertoire. Thus, more than 20% of the usually conserved metazoan genes were lacking in P. laevis. Ontology analysis of the retained genes revealed many connections to the incorporation of carotinoids. These are probably taken up via the surface together with lipids, thus accounting for the orange coloration of P. laevis. Furthermore, we found transcripts and protein sequences to be more derived in P. laevis than in rotifers from Monogononta and Bdelloidea. This was especially the case in genes involved in energy metabolism, which might reflect the acanthocephalan ability to use the scarce oxygen in the host intestine for respiration and simultaneously carry out fermentation. Increased plasticity of the gene repertoire through the integration of foreign DNA into the nuclear genome seems to be another underpinning factor of the evolutionary success of acanthocephalans. In any case, energy-related genes and their proteins may be considered as candidate targets for the acanthocephalan control.

The genome of the marine rotifer Brachionus koreanus sheds light on the antioxidative defense system in response to 2-ethyl-phenanthrene and piperonyl butoxide

BRACHIONUS: spp. (Rotifera: Monogononta) have been introduced as ecotoxicological model-organisms that are widely distributed in aquatic environments. Among the Brachionus spp., the monogonont rotifer Brachionus koreanus has been widely used for ecology, ecotoxicology, and evolution, thus, providing the whole genome data of B. koreanus is important for further understandings of in-depth molecular mechanisms. In this study, the completed assembly and characterization of the B. koreanus genome resulted in a total length of 85.7 Mb with 14,975 annotated genes. The final number of scaffolds was 567 with an N50 value and a GC content of 1.86 Mb and 24.35 %, respectively. Based on the fully constructed genome database, a total of 24 CYPs, 23 GSTs, two SODs, and a single CAT genes were identified and analyzed antioxidant activities (CAT, SOD, and GST), and transcriptional regulation of the entire CYPs, GSTs, SODs, and CAT in response to 2-ethyl-phenanthrene (2-ethyl-PHE) and piperonyl butoxide (PBO), to demonstrate the usefulness of the whole genome library of B. koreanus in response xenobiotic-induced oxidative stress. The assembled B. koreanus genome will provide a better understanding on the molecular ecotoxicology in the view of molecular mechanisms underlying toxicological responses, particularly on xenobiotic detoxification processes in the rotifer B. koreanus.

Embryo bioassays with aquatic animals for toxicity testing and hazard assessment of emerging pollutants: A review

This review article gathers the available information on the use of embryo-tests as high-throughput tools for toxicity screening, hazard assessment and prioritization of new and existing chemical compounds. The approach is contextualized considering the new legal trends for animal experimentation, fostering the 3R policy, with reduction of experimental animals, addressing the potential of embryo-tests as high-throughput toxicity screening and prioritizing tools. Further, the current test guidelines, such as the ones provided by OECD and EPA, focus mainly in a limited number of animal lineages, particularly vertebrates and arthropods. To extrapolate hazard assessment to the ecosystem scale, a larger diversity of taxa should be tested. The use of new experimental animal models in toxicity testing, from a representative set of taxa, was thoroughly revised and discussed in this review. Here, we critically review current tools and the main advantages and drawbacks of different animal models and set researcher priorities.

Review of resistance to chronic ionizing radiation exposure under environmental conditions in multicellular organisms

Ionizing radiation resistance occurs among many phylogenetic groups and its mechanisms remain incompletely understood. Tolerances to acute and chronic irradiation do not always correlate because different mechanisms may be involved. The radioresistance phenomenon becomes even more complex in the field than in the laboratory because the effects of radioactive contamination on natural populations are intertwined with those of other factors, such as bioaccumulation of radionuclides, interspecific competition, seasonal variations in environmental conditions, and land use changes due to evacuation of humans from contaminated areas. Previous reviews of studies performed in radioactive sites like the Kyshtym, Chernobyl, and Fukushima accident regions, and of protracted irradiation experiments, often focused on detecting radiation effects at low doses in radiosensitive organisms. Here we review the literature with a different purpose: to identify organisms with high tolerance to chronic irradiation under environmental conditions, which maintained abundant populations and/or outcompeted more radiosensitive species at high dose rates. Taxa for which consistent evidence for radioresistance came from multiple studies conducted in different locations and at different times were found among plants (e.g. willow and birch trees, sedges), invertebrate and vertebrate animals (e.g. rotifers, some insects, crustaceans and freshwater fish). These organisms are not specialized "extremophiles", but tend to tolerate broad ranges of environmental conditions and stresses, have small genomes, reproduce quickly and/or disperse effectively over long distances. Based on these findings, resistance to radioactive contamination can be examined in a more broad context of chronic stress responses.

Two antidepressants fluoxetine and sertraline cause growth retardation and oxidative stress in the marine rotifer Brachionus koreanus

To understand effects of two widely used antidepressant on the antioxidant defense mechanism in the marine rotifer Brachionus koreanus, we assessed acute toxicity and measured population growth, reactive oxygen species (ROS) levels, glutathione (GSH) levels, and antioxidant enzymatic activities (GST, GR, and SOD) in response to fluoxetine hydrochloride (FLX) and sertraline hydrochloride (SER). The no observed effect concentration-24 h of fluoxetine and sertraline were 1000 μg/L and 450 μg/L, respectively, whereas the median lethal concentration (LC50)-24 h of fluoxetine and sertraline were 1560 μg/L and 507 μg/L, respectively. Both fluoxetine and sertraline caused significant reduction (P < 0.05) in the population growth rate indicating that both antidepressants have a potential adverse effect on life cycle parameters of B. koreanus. The intracellular ROS level and GSH level were significantly modulated (P < 0.05) in response to fluoxetine and sertraline. In addition, antioxidant enzymatic activities have shown significant modulation (P < 0.05) in response to FLX and SER in B. koreanus. Furthermore, transcriptional profiles of antioxidant genes (GSTs, SODs, and GR) have shown modulation in response to FLX compared to SER-exposed B. koreanus. Our results indicate that fluoxetine and sertraline induce oxidative stress, leading to reduction in the population density and modulation of antioxidant defense mechanism in the marine rotifer B. koreanus.

Genome size and lifestyle in gnesiotrochan rotifers

Gnesiotrochan rotifers display a variety of life styles ranging from taxa with free-swimming larval and sessile adult stages to those with motile adult stages and colonial habits. Several explanations for the C- value enigma posits that genome size is correlated with lifestyle. To investigate this, 13 gnesiotrochan species representing nine genera were measured by flow cytometry. Genome sizes (1C) within Gnesiotrocha ranged from 0.05 pg (Hexarthra mira and Hexarthra fennica) to 0.25 pg (Sinantherina ariprepes). Genome sizes varied within genera and species; e.g., H. fennica (El Huérfano, Mexico) was estimated to be 15% larger than that of H. mira and H. fennica (Keystone Wetland, TX, USA). Gnesiotrochan genome sizes are similar to those reported within Ploima, which range from 0.06 pg (Brachionus rotundiformis, B. dimidiatus) to 0.46 pg (B. asplanchnoidis). Within Gnesiotrocha, genome size was found to be significantly smaller in sessile versus motile species as well as in solitary versus colonial species. To account for phylogenetic background, Linear Mixed Models with hierarchical taxonomic ranks showed that there is a taxonomic component underlying genome size. This study provides the first estimates of genome size within the superorder, providing a baseline for genomic and evolutionary studies within the group.

Effects of metal-polluted seawater on life parameters and the induction of oxidative stress in the marine rotifer Brachionus koreanus

Metal pollution is one of the major threats to the aquatic environment due to its high bio-concentrations and toxicity. Although numerous studies have been conducted to understand detoxification and toxicity mechanisms in aquatic invertebrates, most of them were limited in laboratory study. Here, we investigated adverse effects of the contaminated-natural seawater on the marine rotifer Brachionus koreanus. Field seawater was collected from five different sites of Youngil Bay, South Korea where pollution by metals is predicted due to industrial discharges from nearby steel industry complexes. The marine rotifer B. koreanus was exposed to different seawater samples, and we found decreased population growth rates with highly induced transcriptional level of detoxification-related genes. Our finding shows a link between the induction of metal-mediated regulation of detoxification genes in B. koreanus and concentration of heavy metals present in various seawater samples, implying those biomarker genes can be useful to assess the toxicity of metal polluted natural seawaters. Our results are helpful to validate and establish biomarker genes for early risk assessment of metal contamination in the natural sea water.

Complete mitochondrial genome of the freshwater monogonont rotifer Brachionus calyciflorus (Rotifera, Brachionidae)

The two complete mitochondrial genomes were sequenced from the Netherlands strain of the freshwater monogonont rotifer Brachionus calyciflorus. The mitochondrial genome sequences were 27,698 bp and 9,906 bp in size, respectively. The gene order and contents of the two B. calyciflorus strains were mostly identical to one another, except for the additional identification and translocation of several tRNAs in mitochondrial DNA I and II. Of 13 protein-coding genes (PCGs), three genes (ND1, ND5, and ND3) had incomplete stop codons. Furthermore, the start codon of ND2, CO2, and CO3 and ND4 genes was ATT, GTG, and ATA, respectively, while the start codon of other PCGs was ATG. The base composition of 13 PCGs of B. calyciflorus (the Netherlands strain) mitogenome showed 31.1% for A, 37.6% for T, 16.5% for C, and 14.8% for G, respectively.

The genome of the marine monogonont rotifer Brachionus plicatilis: Genome-wide expression profiles of 28 cytochrome P450 genes in response to chlorpyrifos and 2-ethyl-phenanthrene

Brachionus spp. (Rotifera: Monogononta) are globally distributed in aquatic environments and play important roles in the aquatic ecosystem. The marine monogonont rotifer Brachionus plicatilis is considered a suitable model organism for ecology, evolution, and ecotoxicology. In this study, we assembled and characterized the B. plicatilis genome. The total length of the assembled genome was 106.9 Mb and the number of final scaffolds was 716 with an N50 value of 1.15 Mb and a GC content of 26.75%. A total of 20,154 genes were annotated after manual curation. To demonstrate the use of whole genome data, we targeted one of the main detoxifying enzyme of phase I detoxification system and identified in a total of 28 cytochrome P450 s (CYPs). Based on the phylogenetic analysis using the maximum likelihood, 28 B. plicatilis-CYPs were apparently separated into five different clans, namely, 2, 3, 4, mitochondrial (MT), and 46 clans. To better understand the CYPs-mediated xenobiotic detoxification, we measured the mRNA expression levels of 28 B. plicatilis CYPs in response to chlorpyrifos and 2-ethyl-phenanthrene. Most B. plicatilis CYPs were significantly modulated (P < 0.05) in response to chlorpyrifos and 2-ethyl-phenanthrene. In addition, xenobiotic-sensing nuclear receptor (XNR) response element sequences were identified in the 5 kb upstream of promoter regions of 28 CYPs from the genome of B. plicatilis, indicating that these XNR can be associated with detoxification of xenobiotics. Overall, the assembled B. plicatilis genome presented here will be a useful resource for a better understanding the molecular ecotoxicology in the view of molecular mechanisms underlying toxicological responses, particularly on xenobiotic detoxification in this species.

Protective Role of Freshwater and Marine Rotifer Glutathione S-Transferase Sigma and Omega Isoforms Transformed into Heavy Metal-Exposed Escherichia coli

Glutathione S-transferases (GSTs) play an important role in phase II of detoxification to protect cells in response to oxidative stress generated by exogenous toxicants. Despite their important role in defense, studies on invertebrate GSTs have mainly focused on identification and characterization. Here, we isolated omega and sigma classes of GSTs from the freshwater rotifer Brachionus calyciflorus and the marine rotifer Brachionus koreanus and explored their antioxidant function in response to metal-induced oxidative stress. The recombinant Bc- and Bk-GSTs were successfully transformed and expressed in Escherichia coli. Their antioxidant potential was characterized by measuring kinetic properties and enzymatic activity in response to pH, temperature, and chemical inhibitor. In addition, a disk diffusion assay, reactive oxygen species assay, and morphological analysis revealed that GST transformed into E. coli significantly protected cells from oxidative stress induced by H₂O₂ and metals (Hg, Cd, Cu, and Zn). Stronger antioxidant activity was exhibited by GST-S compared to GST-O in both rotifers, suggesting that GST-S plays a prominent function as an antioxidant defense mechanism in Brachionus spp. Overall, our study clearly shows the antioxidant role of Bk- and Bc-GSTs in E. coli and provides a greater understanding of GST class-specific and interspecific detoxification in rotifer Brachionus spp.

Small, but surprisingly repetitive genomes: transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex

BACKGROUND

The causes and consequences of genome size variation across Eukaryotes, which spans five orders of magnitude, have been hotly debated since before the advent of genome sequencing. Previous studies have mostly examined variation among larger taxonomic units (e.g., orders, or genera), while comparisons among closely related species are rare. Rotifers of the Brachionus plicatilis species complex exhibit a seven-fold variation in genome size and thus represent a unique opportunity to study such changes on a relatively short evolutionary timescale. Here, we sequenced and analysed the genomes of four species of this complex with nuclear DNA contents spanning 110-422 Mbp. To establish the likely mechanisms of genome size change, we analysed both sequencing read libraries and assemblies for signatures of polyploidy and repetitive element content. We also compared these genomes to that of B. calyciflorus, the closest relative with a sequenced genome (293 Mbp nuclear DNA content).

RESULTS

Despite the very large differences in genome size, we saw no evidence of ploidy level changes across the B. plicatilis complex. However, repetitive element content explained a large portion of genome size variation (at least 54%). The species with the largest genome, B. asplanchnoidis, has a strikingly high 44% repetitive element content, while the smaller B. plicatilis genomes contain between 14 and 25% repetitive elements. According to our analyses, the B. calyciflorus genome contains 39% repetitive elements, which is substantially higher than previously reported (21%), and suggests that high repetitive element load could be widespread in monogonont rotifers.

CONCLUSIONS

Even though the genome sizes of these species are at the low end of the metazoan spectrum, their genomes contain substantial amounts of repetitive elements. Polyploidy does not appear to play a role in genome size variations in these species, and these variations can be mostly explained by changes in repetitive element content. This contradicts the naïve expectation that small genomes are streamlined, or less complex, and that large variations in nuclear DNA content between closely related species are due to polyploidy.

Adverse effects, expression of defense-related genes, and oxidative stress-induced MAPK pathway in the benzo[α]pyrene-exposed rotifer Brachionus rotundiformis

To examine the adverse effects of the benzo[α]pyrene (B[α]P), the monogonont rotifer Brachionus rotundiformis was exposed to various concentration of B[α]P (0 [control], 1, 10, and 100 μg/L) and measured life cycle parameters (e.g., mortality, fecundity [cumulated number of offspring], and lifespan), reactive oxygen species (ROS), antioxidant enzymatic activity of glutathione S-transferase (GST). In addition, defense-related transcripts (e.g., glutathione S-transferases [GSTs], ATP binding cassette [ABCs] transporters) and Western blot analysis of mitogen-activated protein kinase (MAPK) signaling pathway were investigated in B[α]P-exposed rotifer. In this study, the total intracellular ROS level and GST activity were significantly increased (P < 0.05), while fecundity and lifespan were also significantly (P < 0.05) reduced in a concentration dependent manner in B[α]P-exposed B. rotundiformis. In addition, transcriptional regulation of GSTs and ABC transporters were significantly upregulated and downregulated (P < 0.05), respectively, suggesting that B[α]P can induce oxidative stress leading to induction of antioxidant system and detoxification mechanism. In addition to detoxification-related genes, B[α]P-exposed B. rotundiformis showed the increased levels of the p-JNK and p-p38, suggesting that B[α]P can activate MAPK signaling pathway in B. rotundiformis.

Genome-wide characterization and expression of the elongation of very long chain fatty acid (Elovl) genes and fatty acid profiles in the alga (Tetraselmis suecica) fed marine rotifer Brachionus koreanus

To understand the lipid metabolism in invertebrate species, identification of the fatty acid (FA) synthesis gene families in invertebrate species is important, since some FA are unable to be synthesized in the organisms by themselves. In the study, to identify the elongation of very long chain fatty acid (Elovl) genes in the marine rotifer Brachionus koreanus, the genome-wide identification and phylogenetic analysis of Elovl genes have been conducted with the expression profile of Elovl genes on the alga Tetraslemis suecica-fed B. koreanus. A total 10 Elovl genes have been identified from the genome of B. koreanus, with conserved HXXHH motif. Synteny analysis showed that tandem duplication event has occurred (Elovl3/6a and b, Elovl9a and b, and Elovl9c and d) in the ancestor. Phylogenetic analysis have clearly revealed that Brachionus spp. has only 2/5 and 3/6 subfamilies, and two novel Elovl classes have been revealed, namely Elovl9 and 10. Transcriptional data showed that the 10 Elovl genes were differently expressed and their expression could be regulated by feeding the alga T. suecica. From fatty acid (FA) profile data of the alga Tetraslemis suecica-fed B. koreanus, we revealed that the marine rotifer B. koreanus may synthesize very long chain fatty acid (VLCFA; >22 carbons) by themselves, as VLCFA was hardly detected in the alga T. suecica. The study provides a better understanding of FA metabolism of the marine rotifer B. koreanus after feeding the T. suecica.

Identification of the full 26 cytochrome P450 (CYP) genes and analysis of their expression in response to benzo[α]pyrene in the marine rotifer Brachionus rotundiformis

Cytochrome P450s (CYPs) are a large gene superfamily that are found in all living organisms. CYPs have a key role in detoxification of xenobiotics and endogenous chemicals. Although aquatic invertebrate CYPs and their detoxification mechanisms have been reported, little is known about interspecific comparison of CYPs and their detoxification mechanism in the rotifer Brachionus spp. The aim of this study was to identify the entire CYPs in the rotifer Brachionus rotundiformis (B. rotundiformis) and compare B. rotundiformis-CYPs to the previously reported CYPs in other model Brachionus spp. (B. koreanus, B. plicatilis, and B. calyciflorus). To validate the model, the rotifer, specifically Brachionus rotundiformis was exposed to various concentrations of B[α]P, which is widely used PAH xenobiotic, and analyzed gene expression in response to B[α]P. Here, in silico analysis results showed the total of 26 CYPs from the rotifer B. rotundiformis. Based on the phylogenetic analysis, the 26 B. rotundiformis-CYPs were separated into five different clans: 2, 3, 4, mitochondrial, and 46 clans in comparison to three rotifers species, B. koreanus, B. plicatilis, and B. calyciflorus. To understand the detoxification mechanisms of 26 B. rotundiformis-CYPs, we investigated transcriptional expression of 26 CYPs and found that five CYPs (CYP3045A2, CYP3045B4, CYP3045C10, CYP3049A5, and CYP3049E8) were significantly increased (P < 0.05) in response to 10 and 100 μg B[α]P. In addition, we identified the aryl hydrocarbon receptor (AhR) and aryl hydrocarbon receptor nuclear translocator (ARNT) and observed slight up-regulation of B. rotundiformis-AhR and -ARNT, indicating that these CYPs are likely associated with detoxification mechanism and could be used as potential molecular biomarkers of B[α]P in B. rotundiformis. Overall, this study will be helpful for expanding our knowledge of invertebrate CYPs on detoxification mechanisms associated with AhR signaling pathway in rotifers.

Congeneric variability in lifespan extension and onset of senescence suggest active regulation of aging in response to low temperature

Lifespan extension under low temperature is well conserved across both endothermic and exothermic taxa, but the mechanism underlying this change in aging is poorly understood. Low temperature is thought to decrease metabolic rate, thus slowing the accumulation of cellular damage from reactive oxygen species, although recent evidence suggests involvement of specific cold-sensing biochemical pathways. We tested the effect of low temperature on aging in 11 strains of Brachionus rotifers, with the hypothesis that if the mechanism of lifespan extension is purely thermodynamic, all strains should have a similar increase in lifespan. We found differences in change in median lifespan ranging from a 6% decrease to a 100% increase, as well as differences in maximum and relative lifespan extension and in mortality rate. Low temperature delays reproductive senescence in most strains, suggesting an extension of healthspan, even in strains with little to no change in lifespan. The combination of low temperature and caloric restriction in one strain resulted in an additive lifespan increase, indicating these interventions may work via non- or partially-overlapping pathways. The known low temperature sensor TRPA1 is present in the rotifer genome, but chemical TRPA1 agonists did not affect lifespan, suggesting that this gene may be involved in low temperature sensation but not in chemoreception in rotifers. The congeneric variability in response to low temperature suggests that the mechanism of low temperature lifespan extension is an active genetic process rather than a passive thermodynamic one and is dependent upon genotype.

Adverse effects of two pharmaceuticals acetaminophen and oxytetracycline on life cycle parameters, oxidative stress, and defensome system in the marine rotifer Brachionus rotundiformis

To investigate the adverse effect of two widely used pharmaceuticals, paracetamol (acetaminophen [APAP]) and oxytetracycline (OTC) on the marine rotifer Brachionus rotundiformis (B. rotundiformis), the animals were exposed to various environmentally-relevant concentrations. Up to date, acetaminophen and oxytetracycline have been considered as toxic, if used above threshold concentration, i.e. overdosed. However, this study demonstrated these two pharmaceuticals even at low concentration (i.e., μg/L scale) elicited oxidative stress through the generation of reactive oxygen species (ROS) along with the increased glutathione S-transferase activity, despite no-observed effect in in-vivo population growth. To validate the adverse effects of the two pharmaceuticals at relatively low concentrations, mRNA expression analysis was performed of the entire set of genes encoding 26 cytochrome P450s (CYPs) of phase I and 19 glutathione S-transferases (GSTs) of phase II of the rotifer B. rotundiformis. The mRNA expression analysis suggested specific genes CYP3045A2 and GSTσ1, GSTσ4, and GSTω1 take part in detoxification of APAP and OTC, resulting in no significant changes in the population growth and undetermined no observed effect concentration (NOEC) in the marine rotifer B. rotundiformis.

Genomic signatures of local adaptation to the degree of environmental predictability in rotifers

Environmental fluctuations are ubiquitous and thus essential for the study of adaptation. Despite this, genome evolution in response to environmental fluctuations —and more specifically to the degree of environmental predictability– is still unknown. Saline lakes in the Mediterranean region are remarkably diverse in their ecological conditions, which can lead to divergent local adaptation patterns in the inhabiting aquatic organisms. The facultatively sexual rotifer Brachionus plicatilis shows diverging local adaptation in its life-history traits in relation to estimated environmental predictability in its habitats. Here, we used an integrative approach —combining environmental, phenotypic and genomic data for the same populations– to understand the genomic basis of this diverging adaptation. Firstly, a novel draft genome for B. plicatilis was assembled. Then, genome-wide polymorphisms were studied using genotyping by sequencing on 270 clones from nine populations in eastern Spain. As a result, 4,543 high-quality SNPs were identified and genotyped. More than 90 SNPs were found to be putatively under selection with signatures of diversifying and balancing selection. Over 140 SNPs were correlated with environmental or phenotypic variables revealing signatures of local adaptation, including environmental predictability. Putative functions were associated to most of these SNPs, since they were located within annotated genes. Our results reveal associations between genomic variation and the degree of environmental predictability, providing genomic evidence of adaptation to local conditions in natural rotifer populations.

Genome-wide identification of the entire 90 glutathione S-transferase (GST) subfamily genes in four rotifer Brachionus species and transcriptional modulation in response to endocrine disrupting chemicals

Genome-wide identification of glutathione S-transferase (GST), a major phase II detoxification enzyme, was investigated in four different aquatic model rotifer species Brachionus koreanus, B. plicatilis, B. rotundiformis, and B. calyciflorus. GSTs are ubiquitous antioxidant enzymes that play versatile function including cellular detoxification, stress alleviation, and production of the radical conjugates. Among the four rotifers, B. rotundiformis was found with the least number of GST genes (total 19 GST genes), whereas the other three species shared 23 to 24 GST genes. Among the identified GST genes, belonging to the cytosolic GST superfamily, the expansion of GST sigma classes mainly occurs through tandem duplication, resulting in tandem-arrayed gene clusters on the chromosomes. Overall, the number of genes discovered in this study was highest in the sigma class, zeta, alpha, and omega in descending order. With integration of phylogenetic analysis and xenobiotic-mediated GST mRNA expression patterns along with previous enzymatic activities, the functional divergence among species-specific GST genes was clearly observed. This study covers full identification of GST classes in three marine rotifer and one fresh-water rotifer species and their important role in marine environmental ecotoxicology.

Nanoplastic Ingestion Enhances Toxicity of Persistent Organic Pollutants (POPs) in the Monogonont Rotifer Brachionus koreanus via Multixenobiotic Resistance (MXR) Disruption

Among the various materials found inside microplastic pollution, nanosized microplastics are of particular concern due to difficulties in quantification and detection; moreover, they are predicted to be abundant in aquatic environments with stronger toxicity than microsized microplastics. Here, we demonstrated a stronger accumulation of nanosized microbeads in the marine rotifer Brachionus koreanus compared to microsized ones, which was associated with oxidative stress-induced damages on lipid membranes. In addition, multixenobiotic resistance conferred by P-glycoproteins and multidrug resistance proteins, as a first line of membrane defense, was inhibited by nanoplastic pre-exposure, leading to enhanced toxicity of 2,2',4,4'-tetrabromodiphenyl ether and triclosan in B. koreanus. Our study provides a molecular mechanistic insight into the toxicity of nanosized microplastics toward aquatic invertebrates and further implies the significance of synergetic effects of microplastics with other environmental persistent organic pollutants.

Reverse taxonomy applied to the Brachionus calyciflorus cryptic species complex: Morphometric analysis confirms species delimitations revealed by molecular phylogenetic analysis and allows the (re)description of four species

The discovery and exploration of cryptic species have been profoundly expedited thanks to developments in molecular biology and phylogenetics. In this study, we apply a reverse taxonomy approach to the Brachionus calyciflorus species complex, a commonly studied freshwater monogonont rotifer. By combining phylogenetic, morphometric and morphological analyses, we confirm the existence of four cryptic species that have been recently suggested by a molecular study. Based on these results and according to an exhaustive review of the taxonomic literature, we name each of these four species and provide their taxonomic description alongside a diagnostic key.

Adverse effects of the insecticides chlordecone and fipronil on population growth and expression of the entire cytochrome P450 (CYP) genes in the freshwater rotifer Brachionus calyciflorus and the marine rotifer Brachionus plicatilis

Chlordecone and fipronil are used as an insecticide and have been widely detected in the aquatic environments. However, their toxicity is still poorly investigated in aquatic invertebrates. In this study, we examined effects of chlordecone and fipronil on population growth and transcriptional regulation of the entire cytochrome P450 (CYP) genes in the freshwater rotifer Brachionus calyciflorus and the marine rotifer B. plicatilis. In B. calyciflorus, a 24 h-no observed effect concentration (NOEC-24 h) and a 24 h-median lethal concentration (LC50-24 h) of chlordecone were determined as 100 μg/L and 193.8 μg/L, respectively, while NOEC-24 h and LC50-24 h of fipronil were determined as 1000 μg/L and 2033.0 μg/L, respectively. In B. plicatilis, NOEC-24 h and LC50-24 h of chlordecone were 100 μg/L and 291.0 μg/L, respectively, while NOEC-24 h and LC50-24 h of fipronil were determined as 1000 μg/L and 5735.0 μg/L, respectively. Moreover, retardation in the population growth were observed in response to chlordecone and fipronil in both rotifer species, suggesting that chlordecone and fipronil have a potential adverse effects on life cycle parameters of two rotifer species. Additionally, modulation in the expressions of the entire CYP genes were demonstrated in response to chlordecone and fipronil at 24 h period. These results provide the better understanding on how chlordecone and fipronil can affect in population growth of two rotifers and CYP gene expressions in chlordecone- and fipronil-exposed rotifers.

Genome-wide identification of 99 autophagy-related (Atg) genes in the monogonont rotifer Brachionus spp. and transcriptional modulation in response to cadmium

Autophagy originated from the common ancestor of all life forms, and its function is highly conserved from yeast to humans. Autophagy plays a key role in various fundamental biological processes including defense, and has developed through serial interactions of multiple gene sets referred to as autophagy-related (Atg) genes. Despite their significance in metazoan life and evolution, few studies have been conducted to identify these genes in aquatic invertebrates. In this study, we identified whole Atg genes in four Brachionus rotifer spp., namely B. calyciflorus, B. koreanus, B. plicatilis, and B. rotundiformis, through searches of their entire genomes; and we annotated them according to the yeast nomenclature. Twenty-four genes orthologous to yeast genes were present in all of the Brachionus spp. while three additional gene duplicates were identified in the genome of B. koreanus, indicating that these genes had diversified during the speciation. Also, their transcriptional responses to cadmium exposure indicated regulation by cadmium-induced oxidative-stress-related signaling pathways. This study provides valuable information on 99 conserved Atg genes involved in autophagosome formation in Brachionus spp., with transcriptional modulation in response to cadmium, in the context of the role of autophagy in the damage response.

Effects of environmental stressors on lipid metabolism in aquatic invertebrates

Lipid metabolism is crucial for the survival and propagation of the species, since lipids are an essential cellular component across animal taxa for maintaining homeostasis in the presence of environmental stressors. This review aims to summarize information on the lipid metabolism under environmental stressors in aquatic invertebrates. Fatty acid synthesis from glucose via de novo lipogenesis (DNL) pathway is mostly well-conserved across animal taxa. The structure of free fatty acid (FFA) from both dietary and DNL pathway could be transformed by elongase and desaturase. In addition, FFA can be stored in lipid droplet as triacylglycerol, upon attachment to glycerol. However, due to the limited information on both gene and lipid composition, in-depth studies on the structural modification of FFA and their storage conformation are required. Despite previously validated evidences on the disturbance of the normal life cycle and lipid homeostasis by the environmental stressors (e.g., obesogens, salinity, temperature, pCO₂, and nutrients) in the aquatic invertebrates, the mechanism behind these effects are still poorly understood. To overcome this limitation, omics approaches such as transcriptomic and proteomic analyses have been used, but there are still gaps in our knowledge on aquatic invertebrates as well as the lipidome. This paper provides a deeper understanding of lipid metabolism in aquatic invertebrates.