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Evolutionary innovations in chemical secretion-such as the production of secondary metabolites, pheromones, and toxins-profoundly impact ecological interactions across a broad diversity of life. These secretory innovations may involve a "legacy-plus-innovation" mode of evolution, whereby new biochemical pathways are integrated with conserved secretory processes to create novel products. Among secretory innovations, bioluminescence is important because it evolved convergently many times to influence predator-prey interactions, while often producing courtship signals linked to increased rates of speciation. However, whether or not deeply conserved secretory genes are used in secretory bioluminescence remains unexplored. Here, we show that in the ostracod Vargula tsujii, the evolutionary novel c-luciferase gene is co-expressed with many conserved genes, including those related to toxin production and high-output protein secretion. Our results demonstrate that the legacy-plus-innovation mode of secretory evolution, previously applied to sensory modalities of olfaction, gustation, and nociception, also encompasses light-producing signals generated by bioluminescent secretions. This extension broadens the paradigm of secretory diversification to include not only chemical signals but also bioluminescent light as an important medium of ecological interaction and evolutionary innovation., Competing Interests: Conflict of Interest The authors declare no competing interests., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Sampling groundwater biodiversity is difficult because of limited access and issues with species identification. Environmental DNA (eDNA) provides a viable alternative to traditional sampling approaches, however limited knowledge of the abundance and fate of DNA in groundwater hinders the interpretation of data from these environments. Groundwater environments are dark and have lower oxygen concentrations and microbial activity than surface waters. Consequently, assumptions about DNA fate in surface ecosystems may not apply to groundwaters. Here, we test the longevity and transport of eDNA in groundwater within a static microcosm and a flow-through mesocosm. A variety of invertebrates were placed within a mesocosm and microcosm to enable DNA shedding, and then removed. DNA persisted for up to 5 weeks after their removal in the static experiment and was detected between 9 and 33 days in the flow-through experiment. Sediments and water both proved important for eDNA detection. Crustacean DNA was detected sporadically and unpredictably, whereas non-crustacean DNA was detected more frequently despite their lower densities. We suggest that detecting crustaceans poses a challenge to utilising eDNA approaches for stygofauna monitoring. This is confounded by the scarcity of sequences for stygofauna in reference databases. Further research is needed before eDNA alone can be routinely employed for stygofauna detection., (© 2024. The Author(s).)

Balancing selection is an evolutionary process that maintains genetic polymorphisms at selected loci and strongly reduces the likelihood of allele fixation. When allelic polymorphisms that predate speciation events are maintained independently in the resulting lineages, a pattern of trans-species polymorphisms may occur. Trans-species polymorphisms have been identified for loci related to mating systems and the MHC, but they are generally rare. Trans-species polymorphisms in disease loci are believed to be a consequence of long-term host-parasite coevolution by balancing selection, the so-called Red Queen dynamics. Here we scan the genomes of three crustaceans with a divergence of over 15 million years and identify 11 genes containing identical-by-descent trans-species polymorphisms with the same polymorphisms in all three species. Four of these genes display molecular footprints of balancing selection and have a function related to immunity. Three of them are located in or close to loci involved in resistance to a virulent bacterial pathogen, Pasteuria, with which the Daphnia host is known to coevolve. This provides rare evidence of trans-species polymorphisms for loci known to be functionally relevant in interactions with a widespread and highly specific parasite. These findings support the theory that specific antagonistic coevolution is able to maintain genetic diversity over millions of years., (© 2024. The Author(s).)

Virus infection causes the metabolic disorder of host cells, whereas the metabolic disorder of cells is one of the major causes of tumorigenesis, suggesting that antiviral molecules might possess anti-tumor activities by regulating cell metabolism. As the key regulators of gene expression, long non-coding RNAs (lncRNAs) play vital roles in the regulation of cell metabolism. However, the influence of antiviral lncRNAs on tumorigenesis has not been explored. To address this issue, the antiviral and anti-tumor capacities of shrimp lncRNAs were characterized in this study. The results revealed that shrimp lncRNA06, having antiviral activity in shrimp, could suppress the tumorigenesis of human gastric cancer stem cells (GCSCs) via triggering apoptosis of GCSCs in a cross-species manner. Shrimp lncRNA06 could sponge human miR-17-5p to suppress the stemness of GCSCs via the miR-17-5p-p21 axis. At the same time, shrimp lncRNA06 could bind to ATP synthase subunit beta (ATP5F1B) to enhance the stability of the ATP5F1B protein in GCSCs, thus suppressing the tumorigenesis of GCSCs. The in vivo data demonstrated that shrimp lncRNA06 promoted apoptosis and inhibited the stemness of GCSCs through interactions with ATP5F1B and miR-17-5p, leading to the suppression of the tumorigenesis of GCSCs. Therefore, our findings highlighted that antiviral lncRNAs possessed anti-tumor capacities and that antiviral lncRNAs could be the anti-tumor reservoir for the treatment of human cancers.

Genes from ancient families are sometimes involved in the convergent evolutionary origins of similar traits, even across vast phylogenetic distances. Sulfotransferases are an ancient family of enzymes that transfer sulfate from a donor to a wide variety of substrates, including probable roles in some bioluminescence systems. Here, we demonstrate multiple sulfotransferases, highly expressed in light organs of the bioluminescent ostracod Vargula tsujii , transfer sulfate in vitro to the luciferin substrate, vargulin. We find luciferin sulfotransferases (LSTs) of ostracods are not orthologous to known LSTs of fireflies or sea pansies; animals with distinct and convergently evolved bioluminescence systems compared to ostracods. Therefore, distantly related sulfotransferases were independently recruited at least three times, leading to parallel evolution of luciferin metabolism in three highly diverged organisms. Reuse of homologous genes is surprising in these bioluminescence systems because the other components, including luciferins and luciferases, are completely distinct. Whether convergently evolved traits incorporate ancient genes with similar functions or instead use distinct, often newer, genes may be constrained by how many genetic solutions exist for a particular function. When fewer solutions exist, as in genetic sulfation of small molecules, evolution may be more constrained to use the same genes time and again.

Despite discovery more than 100years ago and documented global occurrence from shallow waters to the deep sea, the life cycle of the enigmatic crustacean y-larvae isincompletely understood and adult forms remain unknown. To date, only 2 of the 17 formally described species, all based on larval stages, have been investigated using an integrative taxonomic approach. This approach provided descriptions of the morphology of the naupliar and cyprid stages, and made use of exuvial voucher material and DNA barcodes. To improve our knowledge about the evolutionary history and ecological importance of y-larvae, we developed a novel protocol that maximises the amount of morpho-ecological and molecular data that can be harvested from single larval specimens. This includes single-specimen DNA barcoding and daily imaging of y-nauplii reared in culture dishes, mounting of the last naupliar exuviae on a slide as a reference voucher, live imaging of the y-cyprid instar that follows, and fixation, DNA extraction, amplification and sequencing of the y-cyprid specimen. Through development and testing of a suite of new primers for both nuclear and mitochondrial protein-coding and ribosomal genes, we showcase how new sequence data can be used to estimate the phylogeny of Facetotecta. We expect that our novel procedure will help to unravel the complex systematics of y-larvae and show how these fascinating larval forms have evolved. Moreover, we posit that our protocols should work on larval specimens from a diverse array of moulting marine invertebrate taxa.

Long noncoding RNA (lncRNA) is a potential regulator of biological processes, including immunity, reproduction, and development. Although several transcriptome studies have focused on responses of viral infections in several organisms, the role of lncRNAs in viral responses in shrimp is still unclear. Therefore, this work aimed to identify putative lncRNAs and study their role in white spot syndrome virus (WSSV) infection in white shrimp. The hepatopancreas transcriptome from WSSV infected shrimp was analyzed in silico to identify putative lncRNAs. Among 221,347 unigenes of the de novo assembled transcriptome, 44,539 putative lncRNAs were identified, 32 of which were differentially expressed between WSSV-infected and control shrimp. Five candidate lncRNAs were validated for their expressions in shrimp tissues and in response to WSSV infection. Lnc164 was chosen for further investigation of its role in WSSV infection. Knockdown of lnc164 prolonged survival of shrimp when challenged with WSSV, suggesting a role in shrimp immunity. In addition, lnc164 was not directly involved in the control of total hemocytes and viral loads in hemolymph of WSSV-infected shrimp. A set of lnc164-regulated genes was obtained by RNA sequencing among which 251 transcripts were differentially expressed between lnc164 knockdown and control shrimp. Six immune-related genes were validated for their expression profiles. Our work sheds light on lncRNA profiles in L. vannamei in response to WSSV infection and paves the way to a functional study of lnc164 in host antiviral response., Competing Interests: Declaration of competing interest None., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

The special rhabdom structure of the mid-band ommatidium in compound eye contributes to the mantis shrimp being the only animal species known to science that can recognize circularly polarized light (CPL). Although the number of mid-band ommatidium of Oratosquilla oratoria is reduced, the mid-band ommatidium still has orthogonal geometric interleaved rhabdom and short oval distal rhabdom, which may mean that the O. oratoria has weakened circular polarized light vision (CPLV). Here we explored the molecular mechanisms of how O. oratoria response to the polarization of light. Based on the specific expression patterns of vision-related functional genes and proteins, we suggest that the order of light response by O. oratoria compound eye was first natural light, then left-circularly polarized light (LCPL), linearly polarized light, right-circularly polarized light (RCPL) and dark. Meanwhile, we found that the expression levels of vision-related functional genes and proteins in O. oratoria compound eye under RCPL were not significantly different from those in DL, which may imply that O. oratoria cannot respond to RCPL. Furthermore, the response of LCPL is likely facilitated by the differential expression of opsin and microvilli - related functional genes and proteins (arrestin and sodium-coupled neutral amino acid transporter). In conclusion, this study systematically illustrated for the first time how O. oratoria compound eye response to the polarization of light at the genetic level, and it can improve the visual ecological theory behind polarized light vision evolution., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier B.V.)

In the species-rich Phylum Arthropoda, the mitochondrial genome is relatively well conserved both in terms of number and order of genes. However, specific clades have a 'typical' gene order that differs from the putative arthropod ancestral arrangement. The aim of this work was to compare the rate of mitochondrial gene rearrangements at inter- and intra-taxonomic levels in the Arthropoda and to postulate the most parsimonious ancestral orders representing the four major arthropod lineages. For this purpose, we performed a comparative genomic analysis of arthropod mitochondrial genomes available in the NCBI database. Using a combination of bioinformatics methods that examined mitochondrial gene rearrangements in 464 species of arthropods from three subphyla (Chelicerata, Myriapoda, and Crustacea [except Hexapoda, previously analyzed]), we observed differences in the rate of rearrangement within major lineages. A higher rate of mitochondrial genome rearrangement was observed in Crustacea and Chelicerata compared to Myriapoda. Likewise, early branching clades exhibit less variability in mitochondrial genome order than late branching clades, within each subphylum. We identified 'hot regions' in the mitochondrial genome of each studied subphylum, and postulated the most likely ancestral gene order in each subphylum and taxonomic order. Our work provides new evidence on the evolutionary dynamics of mitochondrial genome gene order in arthropods and new mitochondrial genome architectures in different taxonomic divisions within each major lineage of arthropods., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)

Ferroptosis, characterized by iron-dependent cell death, has recently emerged as a critical defense mechanism against microbial infections. The present study aims to investigate the involvement of exosomes in the induction of ferroptosis and the inhibition of bacterial infection in crustaceans. Our findings provide compelling evidence for the pivotal role of exosomes in the immune response of crustaceans, wherein they facilitate intracellular iron accumulation and activate the ferroptotic pathways. Using RNA-seq and bioinformatic analysis, we demonstrate that cytochrome P450 (CYP) can effectively trigger ferroptosis. Moreover, by conducting an analysis of exosome cargo proteins, we have identified the participation of six-transmembrane epithelial antigen of prostate 4 in the regulation of hemocyte ferroptotic sensitivity. Subsequent functional investigations unveil that six-transmembrane epithelial antigen of prostate 4 enhances cellular Fe 2+ levels, thereby triggering Fenton reactions and accelerating CYP-mediated lipid peroxidation, ultimately culminating in ferroptotic cell death. Additionally, the Fe 2+ -dependent CYP catalyzes the conversion of arachidonic acid into 20-hydroxyeicosatetraenoic acid, which activates the peroxisome proliferator-activated receptor. Consequently, the downstream target of peroxisome proliferator-activated receptor, cluster of differentiation 36, promotes intracellular fatty acid accumulation, lipid peroxidation, and ferroptosis. These significant findings shed light on the immune defense mechanisms employed by crustaceans and provide potential strategies for combating bacterial infections in this species., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

The light-dark cycle significantly impacts the growth and development of animals. Mantis shrimps (Oratosquilla oratoria) receive light through their complex photoreceptors. To reveal the adaptive expression mechanism of the mantis shrimp induced in a dark environment, we performed comparative transcriptome analysis with O. oratoria cultured in a light environment (Oo-L) as the control group and O. oratoria cultured in a dark environment (Oo-D) as the experimental group. In the screening of differentially expressed genes (DEGs) between the Oo-L and Oo-D groups, a total of 88 DEGs with |log2FC| > 1 and FDR < 0.05 were identified, of which 78 were upregulated and 10 were downregulated. Then, FBP1 and Pepck were downregulated in the gluconeogenesis pathway, and MKNK2 was upregulated in the MAPK classical pathway, which promoted cell proliferation and differentiation, indicating that the activity of mantis shrimp was slowed and the metabolic rate decreases in the dark environment. As a result, the energy was saved for its growth and development. At the same time, we performed gene set enrichment analysis (GSEA) on all DEGs. In the KEGG pathway analysis, each metabolic pathway in the dark environment showed a slowing trend. GO was enriched in biological processes such as eye development, sensory perception and sensory organ development. The study showed that mantis shrimp slowed down metabolism in the dark, while the role of sensory organs prominent. It provides important information for further understanding the energy metabolism and has great significance to study the physiology of mantis shrimp in dark environment., (© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

Concentrations of fipronil (Fip) and several of its derivatives were detected in samples from four rivers and four estuaries in Japan. LC-MS/MS analysis detected Fip and its derivatives, except for fipronil detrifluoromethylsulfinyl, in almost all samples. The total concentrations of the five compounds were approximately two-fold greater in river water (mean: 21.2, 14.1, and 9.95 ng/L in June, July, and September, respectively) compared to those in estuarine water (mean: 10.3, 8.67, and 6.71 ng/L, respectively). Fipronil, fipronil sulfone (Fip-S), and fipronil sulfide (Fip-Sf) represented more than 70 % of all compounds. This is the first report to demonstrate the contamination of estuarine waters of Japan by these compounds. We further investigated the potentially toxic effects of Fip, Fip-S, and Fip-Sf on the exotic mysid, Americamysis bahia (Crustacea: Mysidae). The lowest effective concentrations of Fip-S (10.9 ng/L) and Fip-Sf (19.2 ng/L) on mysid growth and molting was approximately 12.9- and 7.3-fold lower than Fip (140.3 ng/L), suggesting they had higher toxicity. Quantitative reverse transcription polymerase chain reaction analysis revealed that ecdysone receptor and ultraspiracle gene expression were not affected after 96-h of exposure to Fip, Fip-S, and Fip-Sf, suggesting that these genes may not be involved in the molting disruption induced by Fip, Fip-S, and Fip-Sf. Our findings suggest that environmentally relevant concentrations of Fip and its derivatives can disrupt the growth of A. bahia by promoting molting. However, further studies are required to elucidate its molecular mechanism., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier B.V.)

Aquaculture assumes a pivotal role in meeting the escalating global food demand, and shrimp farming, in particular, holds a significant role in the global economy and food security, providing a rich source of nutrients for human consumption. Nonetheless, the industry faces formidable challenges, primarily attributed to disease outbreaks and the diminishing efficacy of conventional disease management approaches, such as antibiotic usage. Consequently, there is an urgent imperative to explore alternative strategies to ensure the sustainability of the industry. In this context, the field of epigenetics emerges as a promising avenue for combating infectious diseases in shrimp aquaculture. Epigenetic modulations entail chemical alterations in DNA and proteins, orchestrating gene expression patterns without modifying the underlying DNA sequence through DNA methylation, histone modifications, and non-coding RNA molecules. Utilizing epigenetic mechanisms presents an opportunity to enhance immune gene expression and bolster disease resistance in shrimp, thereby contributing to disease management strategies and optimizing shrimp health and productivity. Additionally, the concept of epigenetic inheritability in marine animals holds immense potential for the future of the shrimp farming industry. To this end, this comprehensive review thoroughly explores the dynamics of epigenetic modulations in shrimp aquaculture, with a particular emphasis on its pivotal role in disease management. It conveys the significance of harnessing advantageous epigenetic changes to ensure the long-term viability of shrimp farming while deliberating on the potential consequences of these interventions. Overall, this appraisal highlights the promising trajectory of epigenetic applications, propelling the field toward strengthening sustainability in shrimp aquaculture.

Parasitic euglenids have rarely been studied. We found parasitic euglenids in two species of ostracods (Cyprinotus cassidula, Dolerocypris sinensis) and two species of rhabdocoels (Mesostoma lingua, Microdalyellia armigera) in a rice field. These parasites grew and proliferated inside the host body. These parasites had pellicle strips, one emergent flagellum, and a red stigma, but no chloroplasts, and showed euglenoid movement. Inside the living host, they did not have emergent flagella and moved only by euglenoid movement, but when the host died or the parasites were isolated from the host, they extended their flagella and switched to swimming movement. We conclude that the parasites found in the four hosts that we examined are of the same species, considering the morphological characteristics and identities in the nSSU and nLSU rDNA sequences of those parasites. Molecular phylogenetic analysis showed that the parasite formed a clade with the free-living photoautotrophic species of Euglenaformis, with moderate statistical support. Therefore, the parasite is a secondary osmotroph derived from a photoautotrophic ancestor. Based on the results of morphological observation and molecular phylogenetic analysis, we propose a new species of parasitic euglenid, Euglenaformis parasitica sp. nov., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier GmbH. All rights reserved.)

Transcriptomes from nontraditional model organisms often harbor a wealth of unexplored data. Examining these data sets can lead to clarity and novel insights in traditional systems, as well as to discoveries across a multitude of fields. Despite significant advances in DNA sequencing technologies and in their adoption, access to genomic and transcriptomic resources for nontraditional model organisms remains limited. Crustaceans, for example, being among the most numerous, diverse, and widely distributed taxa on the planet, often serve as excellent systems to address ecological, evolutionary, and organismal questions. While they are ubiquitously present across environments, and of economic and food security importance, they remain severely underrepresented in publicly available sequence databases. Here, we present CrusTome, a multispecies, multitissue, transcriptome database of 201 assembled mRNA transcriptomes (189 crustaceans, 30 of which were previously unpublished, and 12 ecdysozoans for phylogenetic context) as an evolving and publicly available resource. This database is suitable for evolutionary, ecological, and functional studies that employ genomic/transcriptomic techniques and data sets. CrusTome is presented in BLAST and DIAMOND formats, providing robust data sets for sequence similarity searches, orthology assignments, phylogenetic inference, etc. and thus allowing for straightforward incorporation into existing custom pipelines for high-throughput analyses. In addition, to illustrate the use and potential of CrusTome, we conducted phylogenetic analyses elucidating the identity and evolution of the cryptochrome/photolyase family of proteins across crustaceans., Competing Interests: Conflicts of interest The author(s) declare no conflict of interest., (© The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America.)

Marine-terrestrial transition represents an important aspect of organismal evolution that requires numerous morphological and genetic innovations and has been hypothesized to be caused by geological changes. We used talitrid crustaceans with marine-coastal-montane extant species at a global scale to investigate the marine origination and terrestrial adaptation. Using genomic data, we demonstrated that marine ancestors repeatedly colonized montane terrestrial habitats during the Oligocene to Miocene. Biological transitions were well correlated with plate collisions or volcanic island formation, and top-down cladogenesis was observed on the basis of a positive relationship between ancestral habitat elevation and divergence time for montane lineages. We detected convergent variations of convoluted gills and convergent evolution of SMC3 associated with montane transitions. Moreover, using CRISPR-Cas9 mutagenesis, we proposed that SMC3 potentially regulates the development of exites, such as talitrid gills. Our results provide a living model for understanding biological innovations and related genetic regulatory mechanisms associated with marine-terrestrial transitions.

Although the diversity, beauty, and intricacy of sexually selected courtship displays command the attention of evolutionists, the longevity of these traits in deep time is poorly understood. Population-based theory suggests sexual selection could either lower or raise extinction risk, resulting in high or low persistence of lineages with sexually selected traits. Furthermore, empirical studies that directly estimate the longevity of sexually selected traits are uncommon. Sexually selected signals-including bioluminescent courtship-originated multiple times during evolution, allowing the empirical study of their longevity after careful phylogenetic and divergence time analyses. Here, we estimate the first transcriptome-based molecular phylogeny and divergence times of Cypridinidae. We report extreme longevity of bioluminescent courtship, a trait important in mate choice and probably under sexual selection. Our relaxed-clock estimates of divergence times coupled with stochastic character mapping show luminous courtship evolved only once in Cypridinidae-in a Sub-Tribe, we name Luxorina-at least 151 millions of years ago from cypridinid ancestors that used bioluminescence only in antipredator displays, defining a Tribe we name Luminini. This time-calibrated molecular phylogeny of cypridinids will serve as a foundation for integrative and comparative studies on the biochemistry, molecular evolution, courtship, diversification, and ecology of cypridinid bioluminescence. The persistence of luminous courtship for hundreds of millions of years suggests that sexual selection did not cause a rapid loss of associated traits, and that rates of speciation within the group exceeded extinction risk, which may contribute to the persistence of a diverse clade of signaling species. [Ancestral state reconstruction; Biodiversity; co-option; divergence time estimates; macroevolution; Ostracoda; phylogenomics; sexual selection.]., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Society of Systematic Biologists.)

The immune deficiency (IMD) pathway is critical for elevating host immunity in both insects and crustaceans. The IMD pathway activation in insects is mediated by peptidoglycan recognition proteins, which do not exist in crustaceans, suggesting a previously unidentified mechanism involved in crustacean IMD pathway activation. In this study, we identified a Marsupenaeus japonicus B class type III scavenger receptor, SRB2, as a receptor for activation of the IMD pathway. SRB2 is up-regulated upon bacterial challenge, while its depletion exacerbates bacterial proliferation and shrimp mortality via abolishing the expression of antimicrobial peptides. The extracellular domain of SRB2 recognizes bacterial lipopolysaccharide (LPS), while its C-terminal intracellular region containing a cryptic RHIM-like motif interacts with IMD, and activates the pathway by promoting nuclear translocation of RELISH. Overexpressing shrimp SRB2 in Drosophila melanogaster S2 cells potentiates LPS-induced IMD pathway activation and diptericin expression. These results unveil a previously unrecognized SRB2-IMD axis responsible for antimicrobial peptide induction and restriction of bacterial infection in crustaceans and provide evidence of biological diversity of IMD signaling in animals. A better understanding of the innate immunity of crustaceans will permit the optimization of prevention and treatment strategies against the arising shrimp diseases.

Crabs can be transported beyond their native range via anthropogenic-mediated means such as aquarium trade, live seafood trade and shipping. Once introduced into new locations, they can establish persisting populations and become invasive, often leading to negative impacts on the recipient environment and native species. Molecular techniques are increasingly being used as complementary tools in biosecurity surveillance and monitoring plans for invasive species. Molecular tools can be particularly useful for early detection, rapid identification and discrimination of closely related species, including when diagnostic morphological characters are absent or challenging, such as early life stages, or when only part of the animal is available. In this study, we developed a species-specific qPCR assay, which targets the cytochrome c oxidase subunit 1 (CO1) region of the Asian paddle crab Charybdis japonica . In Australia, as well as many parts of the world, this species is considered invasive and routine biosecurity surveillance is conducted to reduce the risk of establishment. Through rigorous testing of tissue from target and non-target species we demonstrate that this assay is sensitive enough to detect as little as two copies per reaction and does not cross amplify with other closely related species. Field samples and environmental samples spiked with C. japonica DNA in high and low concentrations indicate that this assay is also a promising tool for detecting trace amounts of C. japonica eDNA in complex substrates, making it a useful complementary tool in marine biosecurity assessments., Competing Interests: Heather Veilleux and Michael Snow are employed by Ecometrix Incorporated and Genotyping Australia respectively. The other authors declare that they have no competing interests., (© 2023 Simpson et al.)

A new species of the alpheid shrimp genus Athanas Leach, 1814 is described based on a holotype from Wakasa Bay, Sea of Japan side of Honshu, Japan, at a depth of 90 m. Athanas exilis n. sp. appears close to A. sydnyensis Anker & Ahyong, 2007, but is distinguished from the latter by some morphological features, including the different shape of the telson, the shorter antennular stylocerite, more strongly produced distal lamella of the antennal scaphocerite, and less developed armature of the merus of the major cheliped. Preliminary genetic analysis using the mitochondrial 16S rRNA gene was performed to compare interspecific genetic divergence within the genus.

Background: As the dominant species of Stomatopoda, Oratosquilla oratoria has not been fully cultivated artificially, and the fishery production mainly depends on marine fishing. Due to the lack of stomatopod genome, the development of molecular breeding of mantis shrimps still lags behind., Methods and Results: A survey analysis was performed to obtain the genome size, GC content and heterozygosity ratio in order to provide a fundation for subsequent whole-genome sequencing. The results showed that the estimated genome size of the O. oratoria was about 2.56 G, and the heterozygosity ratio was 1.81%, indicating that it is a complex genome. Then the sequencing data was preliminarily assembled with k-mer = 51 by SOAPdenovo software to obtain a genome size of 3.01G and GC content of 40.37%. According to ReapeatMasker and RepeatModerler analysis, the percentage of repeats in O. oratoria was 45.23% in the total genome, similar to 44% in Survey analysis. The MISA tool was used to analyze the simple sequence repeat (SSR) characteristics of genome sequences including Oratosquilla oratoria, Macrobrachium nipponense, Fenneropenaeus chinensis, Eriocheir japonica sinensis, Scylla paramamosain and Paralithodes platypus. All crustacean genomes showed similar SSRs characteristics, with the highest proportion of di-nucleotide repeat sequences. And AC/GT and AGG/CCT repeats were the main types of di-nucleotide and tri-nucleotide repeats in O. oratoria., Conclusion: This study provided a reference for the genome assembly and annotation of the O. oratoria, and also provided a theoretical basis for the development of molecular markers of O. oratoria., (© 2023. The Author(s), under exclusive licence to Springer Nature B.V.)

The environmental biotic and abiotic factors form a complicated relationship with the host intestinal microbiota. In our study, we applied different levels of C/N ratio (10, 15, 20) and frequent addition times (once, twice, triple a day) in a factorial experimental design. GC/LC analysis of filtrated biofloc (BF) samples revealed the highest relative fold change for the untargeted bioactive molecules among different treatments, whereas the 16s rRNA analysis revealed the change in the shrimp gut microbiota composition. Based on the available literature on the relationship between the bioactive molecules and the available bacteria in this study, the next bioactive molecules were discussed. Proline was associated with Bacteroidota, Flavobacteriaceae, Gammaproteobacteria, and Flavobacteriales. Plumbagine was associated with Norcardiaceae. Phytosphingosin was associated with Bacteroidota. Phosphocholine compound was associated with Bacteroidota. The monobutyl ether, benzofuran, and piperidone were associated with Micobacteriaceae and Mycobacterium. Generally, C/N 15 and 20 once a day, and C/N 20 triple a day have showed a merit over other treatments in term of low pathogenic and unfavorable bacteria, and high commensal bacterial abundances. The revealed bioactive molecule composition showed the complicity of BF as a source for novel compounds as biosecurity agents in BF system. These molecules could be developed to feed additives upgrading the biosecurity level in aquaculture systems. Other bioactive molecules require future studies to reveal novel molecules in term of aquaculture biosecurity control., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Ghonimy et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Chinese mitten crab (Eriocheir sinensis) is an economically important aquaculture species, and its growth and development are regulated by temperature, but the molecular mechanisms of the responses to temperature remain unclear. Herein, we identified TRPA1 from E. sinensis, a member of the TRP family of heat receptor potential channels, performed RACE cloning and bioinformatics analysis, and investigated the effect of TRPA1 on temperature responses and molting by real-time PCR and RNA interference (RNAi). The open reading frame of Es-TRPA1 is 3660 bp, and the encoded protein has a molecular weight of 136.91 kDa, and is expressed in embryos and juveniles. RNAi-mediated silencing decreased Es-TRPA1 expression in juvenile crabs, molting rate was decreased, mortality was increased, and crabs avoided cold areas (4 °C) much less than control juvenile crabs. The results suggest that Es-TRPA1 is involved in regulating temperature adaptation and molting processes in E. sinensis. The findings lay a foundation for further exploration of temperature regulation mechanisms in E. sinensis and other crustaceans., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022. Published by Elsevier Inc.)

We present the reference genome of the Vernal Pool Fairy Shrimp Branchinecta lynchi. This branchiopod crustacean is endemic to California's freshwater ephemeral ponds. It faces enormous habitat loss and fragmentation as urbanization and agriculture have fundamentally changed the vernal pool landscape over the past 3 centuries. The assembled genome consists of 22 chromosome-length scaffolds that account for 96.85% of the total sequence. One hundred and ninety-five unscaffolded contigs comprise the rest of the genome's 575.6 Mb length. The genome is substantially complete with a BUSCO score of 90.0%. There is no immediately identifiable sex chromosome, typical for this class of organism. This new resource will permit researchers to better understand the adaptive capacity of this imperiled species, as well as answer lingering questions about anostracan physiology, sex determination, and development., (© The American Genetic Association. 2022.)

Ostracod shells are used extensively in paleontology, but we know little about their evolution, especially in ancient lakes. Lake Baikal (LB) is the world's most important stronghold of Candonidae diversity. These crustaceans radiated here rapidly (12-5 Ma) and with an unprecedented morphological diversity. We reconstruct their molecular phylogeny with 46 species and two markers (18S and 16S rRNA), and use it to estimate the evolution of the shell shape and size with landmark-based geometric morphometrics (LBGM). High posterior probabilities support four major clades, which differ in node depth and morphospace clustering. After removing a significant allometry, the first three principal components (PCs) describe about 88% of total variability, suggesting a strong integration. Reconstructed ancestral shapes are similar for all four clades, indicating that diversification happened after colonization. Major evolutionary changes occurred from trapezoidal to elongated shapes. Sister species are separated in morphospace, by centroid size, or both, as well as by vertical and horizontal distributions in LB. Ostracod shell is a strongly integrated structure that exhibits high evolvability, with some extreme shapes, although mostly along the first PC. This is the first study that combines molecular phylogeny and LBGM for ostracods and for any LB group., (© 2023. The Author(s).)

The taxonomic status of the sergestid shrimp, Acetes americanus, has been questioned for several decades. No specific study has been performed thus far to resolve the incongruences. This species has a wide geographical range in the western Atlantic and is represented by two formally accepted subspecies: Acetes americanus carolinae , distributed in North America, and Acetes americanus americanus , present in South America. However, there are regions where the coexistence of both subspecies has been reported, such as Central America. This study aimed to genetically compare specimens of A. a. americanus collected in South America with A. a. carolinae sampled in North America to check for possible differences and the existence of more than one subspecies of A. americanus on the Brazilian coast. Based on the sequences of two informative markers, the cytochrome oxidase I region (COI) and 16S rRNA, phylogenetic reconstruction demonstrated well-defined clades with high support values, reinforcing the idea that A. a. americanus is genetically different from A. a. carolinae . Our hypothesis was corroborated as the specimens collected in Brazil were divided into two distinct lineages: the first composed of A. a. americanus sensu stricto (Brazil 1) and the second by Acetes americanus (Brazil 2). The three groups evidenced in the haplotype network were the same as those observed in the phylogenetic tree. The morphometric character (height/length of the thelycum) was effective in distinguishing A. a. Brazil 1 from A. a. carolinae . However, more detailed and conclusive studies comprising other characteristics to propose and describe a possible new entity are necessary. To the best of our knowledge, for the first time, the results of this study provide some insights into the taxonomic status of the sergestid shrimp A. americanus in the western Atlantic., Competing Interests: The authors declare there are no competing interests., (©2023 Morilhas Simões et al.)

Three species of nannosquillid mantis shrimps, including two new species, Acanthosquilla ryukyuensis n. sp. and Acanthosquilla shoheii n. sp., are described based on specimens collected from the Ryukyu Islands, Japan. The two new species resemble A. derijardi Manning, 1970, but can be distinguished from A. derijardi by the following features: 1) rostral plate anterolateral corner forms almost a right angle; 2) the distal tip of the antennular somite dorsal process reaches or slightly falls short of proximal half of rostral plate; and 3) eighth thoracic somite (= TS8) posterior margin is black medially. Furthermore, A. ryukyuensis n. sp. and A. shoheii n. sp. are easy to identify by the bifurcated lateral tooth of the telson, and by the posterodorsal pattern of the telson, respectively. In this study, molecular analyses based on partial sequences of mitochondrial 12S and 16S ribosomal DNA, cytochrome oxidase subunit I (COI), and the partial nuclear gene of 28S ribosomal DNA recovers these three species of Acanthosquilla and A. multifasciata (Wood-Mason, 1895) (the type species of the genus) in a single clade. The resulting trees also suggest the polyphyly of Nannosquillidae but with low nodal support. Detailed examinations of the morphological and color features and DNA barcoding results allowed us to delineate intraspecific variations and interspecific differences. The number and shape of setae under the dorsal spine of raptorial claw carpus was found to be useful in distinguishing A. shoheii n. sp. from A. derijardi and A. ryukyuensis n. sp., while combinations of the coloration of the rostral plate, posterior margin of TS8 and posterodorsal surface of telson are useful to distinguish the three species.

We reported a new microsporidium Neoflabelliforma dubium n. sp. from the adipose tissue of Diaphanosoma dubium in China. The infected daphnids generally appeared opaque due to the presence of numerous spore aggregates located in the adipose tissue. All developmental stages were in direct contact with the host cell cytoplasm. Multinucleate sporogonial plasmodia developed into uninucleate sporoblasts by rosette-like fashion. Mature spores were pyriform and monokaryotic, measuring 4.02 ± 0.24 (3.63-4.53) µm long and 2.27 ± 0.15 (2.12-2.57) µm wide (N = 40). The polaroplast was bipartite with a tightly packed anterior lamellae and a loosely aligned posterior lamellae. Isofilar polar filament was coiled 9-11 turns and arranged in 2-3 rows. The phylogenetic analysis based on the obtained SSU rDNA sequence indicated that the N. dubium n. sp. clustered with the freshwater oligochaete-infecting N. aurantiae to form an independent monophyletic group, positioned at the base of Clade 4. In addition, we analyzed the genetic diversity in three N . dubium n. sp. isolates based on the rDNA (SSU rDNA, ITS and LSU rDNA) and Rpb1 gene. The genetic variation among the rDNA sequences was not distinct, however, high nucleotide diversity could be observed in Rpb1 gene, and a wide variety of Rpb1 haplotypes were identified within each isolate. Genetic recombination detected in the Rpb1 sequences presumes cryptic sexual process occurring in N . dubium n. sp. Statistical evolutionary analyses further indicated that the purifying selection eliminated mutations in the Rpb1 gene., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Weng, Zhang, Xin, Xue, Zhang, Li and Zhang.)

Estimating stomatopod species diversity using morphology alone has long been difficult; though over 450 species have been described, new species are still being discovered regularly despite the cryptic behaviors of adults. However, the larvae of stomatopods are more easily obtained due to their pelagic habitat, and have been the focus of recent studies of diversity. Studies of morphological diversity describe both conserved and divergent traits in larval stomatopods, but generally cannot be linked to a particular species. Conversely, genetic studies of stomatopod larvae using DNA barcoding can be used to estimate species diversity, but are generally not linked to known species by analyses of morphological characters. Here we combine these two approaches, larval morphology and genetics, to estimate stomatopod species diversity in the Hawaiian Islands. Over 22 operational taxonomic units (OTUs) were identified genetically, corresponding to 20 characterized morphological types. Species from three major superfamilies of stomatopod were identified: Squilloidea (4 OTUs, 3 morphotypes), Gonodactyloidea (9, 8), and Lysiosquilloidea (6, 7). Among these, lysiosquilloids were more diverse based on larval morphotypes and OTUs as compared to previously documented Hawaiian species (3), while squilloids had a lower diversity of species represented by collected larvae as compared to the seven species previously documented. Two OTUs / morphotypes could not be identified to superfamily as their molecular and morphological features did not closely match any available information, suggesting they belong to poorly sampled superfamilies. The pseudosquillid, Pseudosquillana richeri, was discovered for the first time from Hawai'i. This study contributes an updated estimate for Hawaiian stomatopod diversity for a total of 24 documented species, provides references for identification of larval stomatopods across the three major superfamilies, and emphasizes the lack of knowledge of species diversity in more cryptic stomatopod superfamilies, such as Lysiosquilloidea.

In this paper, we report on the scaffold-level assembled genome for the federally endangered, California endemic crustacean Lepidurus packardi (the Vernal Pool Tadpole Shrimp). L. packardi is a key food source for other conserved California species including the California Tiger Salamander Ambystoma californiense. It faces significant habitat loss and fragmentation as vernal pools are threatened by urbanization, agricultural conversion, and climate change. This resource represents the first scaffold-level genome of any Lepidurus species. The assembled genome spans 108.6 Mbps, with 6 chromosome-length scaffolds comprising 71% of total genomic length and 444 total contigs. The BUSCO score for this genome is 97.3%, suggesting a high level of completeness. We produced a predicted gene set for this species trained on the Daphnia magna set of genes and predicted 17,650 genes. These tools can aid researchers in understanding the evolution and adaptive potential of alternative reproductive modes within this species., (© The American Genetic Association. 2022.)

Background: The Japanese mantis shrimp Oratosquilla oratoria has two genetic lineages in its Chinese and Japanese populations, which are considered cryptic species. However, the Korean O. oratoria populations have only been studied morphologically, and their genetic diversity pattern remains unknown., Objective: To examine the genetic diversity of the Korean O. oratoria populations to explore its cryptic diversity and underlying processes., Methods: We sequenced the mitochondrial cytochrome c oxidase I gene of 107 O. oratoria individuals from 8 sampling sites in South Korea. Their genetic diversity and haplotype data were compared to previously reported data from 16 Chinese and 6 Japanese populations., Results: The haplotype network, analysis of molecular variance, F ST values, and Bayesian skyline plot of the Korean O. oratoria populations confirmed that they were divided into two genetic lineages corresponding to the two previously identified cryptic species, which might be correlated to ocean currents and water temperature. In addition, the population genetic analysis indicated that both lineages had high genetic diversity. Although the Geoje region belongs to the southern group, it only contained lineage N, which could be related to the specific environmental characteristics of Geoje or the hybridization of the two lineages of O. oratoria., Conclusion: Korean O. oratoria populations have enough cryptic diversity to be described as cryptic species and are correlated with ocean currents and water temperatures. Lineage N dominance in Geoje might be related to environmental characteristics or hybridization., (© 2022. The Author(s) under exclusive licence to The Genetics Society of Korea.)

In aquaculture, nutrigenomics or "nutritional genomics" is concerned with studying the impacts of nutrients and food ingredients on gene expressions and understanding the interactions that may occur between nutrients and dietary bioactive ingredients with the genome and cellular molecules of the treated aquatic animals at the molecular levels that will, in turn, mediate gene expression. This concept will throw light on or provide important information to recognize better how specific nutrients may influence the overall health status of aquatic organisms. In crustaceans, it is well known that the nutritional requirements vary among different species. Thus, studying the nutrigenomics in different crustacean species is of significant importance. Of interest, recognition of the actual mechanisms that may be associated with the effects of the nutrients on the immune responses of crustaceans will provide clear outstanding protection, build a solid immune system, and also decrease the possibilities of the emergence of infectious diseases in the culture systems. Similarly, the growth, molting, lipid metabolism, antioxidant capacity, and reproduction could be effectively enhanced by using specific nutrients. In the area of crustacean research, nutrigenomics has been rapidly grown for addressing several aspects related to the influences of nutrients on crustacean development. Several researchers have studied the relationships between several functional genes and their expression profile with several physiological functions of crustaceans. They found a close association between the effects of optimal feeding with efficient production, growth, reproduction development, and health status of several crustacean species. Moreover, they illustrated that regulation of the gene expression in individual cells by different nutrients and formulated feeds could improve the growth development and immunity-boosting of several crustacean species. The present review will spotlight on such relationships between the dietary nutrients and expression of genes linked with growth, metabolism, molting, antioxidant, reproduction, and immunity of several crustacean species. The literature included in this review article will provide references and future outlooks for the upcoming research plans. This will contribute positively for maintaining the sustainability of the sector of the crustacean industry., Competing Interests: Declaration of competing interest None., (Copyright © 2022. Published by Elsevier Ltd.)

Background: Next-generation sequencing technology has allowed for the rapid development of microsatellites, neutral polymorphic markers that can be used for the analysis of population structure., Methods and Results: In this study, we performed whole-genome sequencing using the Illumina MiSeq system and de novo assembly to design microsatellite primers for Triops granarius populations in Qatar. The developed microsatellites are suitable for future studies of genetic structuring among geographically isolated freshwater pools. A total of 23 different primer pairs produced typical microsatellite results, with each pair successfully amplified in up to 40 individuals. Only five of the loci produced a significant departure from Hardy-Weinberg equilibrium., Conclusions: Some of the underlying mechanisms regarding the few loci that deviated from HWE may be further investigated to determine the source of deviation. As T. granarius is the most widely distributed species of the family, the development of these molecular markers would be useful for conducting population genetics and biogeographical studies broadly., (© 2022. The Author(s).)

Thamnocephalidae, a family of Anostraca which is widely distributed on all continents of the world except Antarctica, currently consists of six genera and approximately 63 recognized species. The relationships among genera in Thamnocephalidae and the monophyly of Thamnocephalidae, determined using morphological characteristics or gene markers, remain controversial. In order to address the relationships within Thamnocephalidae, we sequenced Branchinella kugenumaensis mitogenomes and conducted a comparative analysis to reveal the divergence across mitogenomes of B. kugenumaensis . Using newly obtained mitogenomes together with available Anostracan genomic sequences, we present the most complete phylogenomic understanding of Anostraca to date. We observed high divergence across mitogenomes of B . kugenumaensis . Meanwhile, phylogenetic analyses based on both amino acids and nucleotides of the protein-coding genes (PCG) provide significant support for a non-monophyletic Thamnocephalidae within Anostraca, with Asian Branchinella more closely related to Streptocephalidae than Australian Branchinella . The phylogenetic relationships within Anostraca were recovered as follows: Branchinectidae + Chirocephalidae as the basal group of Anostraca and halophilic Artemiidae as a sister to the clade Thamnocephalidae + Streptocephalidae. Both Bayesian inference (BI)- and maximum likelihood (ML)-based analyses produced identical topologies.

Body organization within arthropods is enormously diverse, but a fusion of segments into "functional groups" (tagmatization) is found in all species. Within Tetraconata/Pancrustacea, an anterior head, a locomotory thorax region, and a posterior, mostly limbless tagma known as the abdomen is present. The posterior-most tagma in crustaceans is frequently confused with the malacostracan, for example, decapod pleon often misleadingly termed abdomen, however, its evolutionary and developmental origin continues to pose a riddle, especially the completely limbless abdomen of the "entomostracan morphotype" (e.g., fairy shrimps). Since the discovery of Hox genes and their involvement in specifying the morphology or identity of segments, tagmata, or regions along the anteroposterior axis of an organism, only a few studies have focused on model organisms representing the "entomostracan morphotype" and used a variety of dedicated Hox genes and their transcription products to shine light on abdomen formation. The homeotic genes or the molecular processes that determine the identity of the entomostracan abdomen remain unknown to date. This study focuses on the "entomostracan morphotype" representative Derocheilocaris remanei (Mystacocarida). We present a complete overview of development throughout larval stages and investigate homeotic gene expression data using the antibody FP6.87 that binds specifically to epitopes of Ultrabithorax/Abdominal-A proteins. Our results suggest that the abdomen in Mystacocarida is bipartite (abdomen I + abdomen II). We suggest that the limbless abdomen is an evolutionary novelty that evolved several times independently within crustaceans and which might be the result of a progressive reduction of former thoracic segments into abdominal segments., (© 2022 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution published by Wiley Periodicals LLC.)

Shrimps of the family Alvinocarididae, endemic species to deep sea chemosynthetic ecosystems, harbor epibiotic microbes on gills which probably play important roles in the survival of the shrimps. Among them, Alvinocaris longirostris and Shinkaicaris leurokolos occupy different ecological niches within the same hydrothermal vent in Okinawa Trough, and A. longirostris also exists in a methane seep of the South China Sea. In this study, full-length 16S rRNA sequences of the gill associated bacteria of two alvinocaridid species from different chemosynthetically ecological niches were first captured by single-molecule real-time sequencing. Totally, 120,792 optimized circular consensus sequences with ∼1,450 bp in length were obtained and clustered into 578 operational taxonomic units. Alpha diversity analysis showed seep A. longirostris had the highest species richness and evenness (average Chao1 = 213.68, Shannon = 3.39). Beta diversity analysis revealed that all samples were clearly divided into three groups, and microbial community of A. longirostris from seep and vent were more related than the other comparisons. By permutational multivariate analysis of variance, the most significant community compositional variance was detected between seep A. longirostris and vent S. leurokolos ( R 2  = 0.731, P  = 0.001). The taxon tags were further classified into 21 phyla, 40 classes, 89 orders, 124 families and 135 genera. Overall, the microbial communities were dominated by Campylobacteria and Gammaproteobacteria. Alphaproteobacteria, Bacteroidia, Verrucomicrobiae, Bacilli and other minor groups were also detected at lower abundance. Taxonomic groups recovered from the vent S. leurokolos samples were only dominated by Sulfurovaceae (94.06%). In comparison, gill-associated microbiota of vent A. longirostris consisted of more diverse sulfur-oxidizing bacteria, including Sulfurovaceae (69.21%), Thiotrichaceae (6.77%) and a putative novel Gammaproteobacteria group (14.37%), while in seep A. longirostris , Gammaproteobacteria un-group (44.01%) constituted the major component, following the methane-oxidizing bacteria Methylomonadaceae (19.38%), and Sulfurovaceae (18.66%). Therefore, the gill associated bacteria composition and abundance of alvinocaridid shrimps are closely related to the habitat heterogeneity and the selection of microbiota by the host. However, the interaction between these alvinocaridid shrimps and the epibiotic communities requires further study based on metagenome sequencing and fluorescence in situ hybridization., Competing Interests: The authors declare there are no competing interests., (©2022 Hui et al.)

Our current view of the evolutionary history, coding and adaptive capacities of Apicomplexa, protozoan parasites of a wide range of metazoan, is currently strongly biased toward species infecting humans, as data on early diverging apicomplexan lineages infecting invertebrates is extremely limited. Here, we characterized the genome of the marine eugregarine Porospora gigantea, intestinal parasite of Lobsters, remarkable for the macroscopic size of its vegetative feeding forms (trophozoites) and its gliding speed, the fastest so far recorded for Apicomplexa. Two highly syntenic genomes named A and B were assembled. Similar in size (~ 9 Mb) and coding capacity (~ 5300 genes), A and B genomes are 10.8% divergent at the nucleotide level, corresponding to 16-38 My in divergent time. Orthogroup analysis across 25 (proto)Apicomplexa species, including Gregarina niphandrodes, showed that A and B are highly divergent from all other known apicomplexan species, revealing an unexpected breadth of diversity. Phylogenetically these two species branch sisters to Cephaloidophoroidea, and thus expand the known crustacean gregarine superfamily. The genomes were mined for genes encoding proteins necessary for gliding, a key feature of apicomplexans parasites, currently studied through the molecular model called glideosome. Sequence analysis shows that actin-related proteins and regulatory factors are strongly conserved within apicomplexans. In contrast, the predicted protein sequences of core glideosome proteins and adhesion proteins are highly variable among apicomplexan lineages, especially in gregarines. These results confirm the importance of studying gregarines to widen our biological and evolutionary view of apicomplexan species diversity, and to deepen our understanding of the molecular bases of key functions such as gliding, well known to allow access to the intracellular parasitic lifestyle in Apicomplexa., (© 2022. The Author(s).)

Vitellogenin is an essential protein involved in ovary maturation in many animals. Detection of this protein correlated with reproductive capacity may be important if carried out on marine organisms such as the red spiny lobster Palinurus elephas, a crustacean that is an economically important crop from wild fish catches. Moreover, in recent years, vitellogenin has assumed an important role as a possible biomarker of marine environmental pollution, as its expression levels can be influenced by the presence of similar estrogen pollutants and can affect the reproductive sphere of marine organisms such as crustaceans. The P. elephas vitellogenin protein and its coding gene have never been isolated, so there is little information about its presence in this lobster. The aim of the present study was to develop a molecular strategy to create, for the first time, an antibody for the detection and quantization of vitellogenin in P. elephas., Competing Interests: Competing interests The authors declare no competing or financial interests., (© 2022. Published by The Company of Biologists Ltd.)

Foodborne diseases have become a serious havoc, where antimicrobial resistance is throwing significant challenges on daily basis. With the increase of drug-resistant bacteria and food-borne infection associated with Vibrio parahaemolyticus, new and effective strategies were needed to control the emergence of vibriosis. Lytic bacteriophages come up as a promising way to resist the pathogenic population in various applications. In this study, a V. parahaemolyticus specific phage vB&#95;VpS&#95;PG28 was isolated from sewage in the seafood market. Results showed vB&#95;VpS&#95;PG28, is strictly a lytic bacteriophage and has a relatively large burst size of 103 plaque-forming units per infected cell. Comparative genomic and bioinformatic analyses proved that vB&#95;VpS&#95;PG28 is a new bacteriophage that had a homologous relation with Vibrio phages of family Siphoviridae, especially with phage VH2&#95;2019, but transmission electron microscopy of vB&#95;VpS&#95;PG28 morphology characterized its morphology is similar to that of Myoviridae family. In silico analysis indicated that the vB&#95;VpS&#95;PG28 genome consists of 82712 bp (48.08% GC content) encoding 114 putative ORFs without tRNA,and any gene associated with resistance or virulence factors has not been found. The bacteriophage in the present study has shown significant outcomes in order to control bacterial growth under in vitro conditions. Thus, we are suggesting a beneficiary agent against foodborne pathogens. Further, to ensure the safe usage of phage oral toxicity testing is recommended., Competing Interests: The authors have declared that no competing interests exist.

Contamination of vegan products and vegan shrimps with real shrimps and crustaceans must be avoided to comply with vegan claims, even more for preventing strong allergenic reactions. Therefore, the detection of crustaceans must be reliable and sensitive enough for authenticity, traceability, and food safety purposes. A new real-time PCR assay was developed targeting the mitochondrial 16S rRNA gene of crustaceans and was optimised to avoid critical mismatches with primers and probe. By testing several crustacean species and common food ingredients, the method was demonstrated to be specific to crustaceans only. To comply with the limit of non-vegan contamination established at 0.1% (w/w) by the European Vegetarian Union, dedicated cut-off C T values were determined on vegan raw materials and on vegan shrimps spiked with crustacean materials. The method reached a sensitivity ≤ 0.0005% (w/w), which was further confirmed on reference materials containing a similar amount of crustacean.

Beyrichitine ammonoids of NV Nevada reveal a high taxonomic diversity of Anisian (Middle Triassic). This diversity is, however, in contrast to their relatively low morphologic disparity. Depending on the exact definition, morphologic disparity of a data set is a direct consequence of the sum of all ontogenetic changes. In the past, however, the interplay of both morphological processes has only rarely been addressed. Using geometric morphometric methods, this study aims at a quantification of allometric processes and the morphologic disparity of beyrichitine ammonoids. The multivariate statistical analysis revealed that morphologic disparity, intraspecific variation respectively, within and between the studied species seems to be the result of deviations in the ontogenetic allometric growth pattern (i.e. heterochrony). During deposition of the studied stratigraphic sequence, a general progressive pedomorphism (juvenilization) was observed. The intraspecific variability pattern coincides with the total morphologic disparity of the analyzed species, which suggests that intraspecific variability facilitated morphologic disparity. The comparison of ontogenetic allometric patterns and changes in intraspecific variation and morphologic disparity are likely to refine our understanding of the intrinsic factors influencing the speciation of this group., Competing Interests: There are no competing interests.

We describe a new typhlotanaid species, Hamatipeda kohtsukai sp. nov., collected from between 167 and 488 m depth in the Sagami Sea, Japan. This is the first record of Hamatipeda from the northern hemisphere. Hamatipeda kohtsukai resembles Hamatipeda trapezoida from the Subantarctic region in having pereonites 1-3 widest anteriorly (not rectangular), but differs from it in the length ratio of antennal articles 4/5; the number of setae on the dactyli of pereopods 1-3, ischia of pereopods 4-6, and carpi of pereopods 4-6; the shape of the unguis of pereopods 4-6; and the shape of the uropodal endopod. We determined partial sequences for the cytochrome c oxidase subunit I (COI; cox1) and 18S rRNA (18S) genes in H. kohtsukai . A phylogenetic reconstruction based on the 18S sequences recovered a highly supported Typhlotanaidae clade containing H. kohtsukai and Typhlotanais mixtus , with Paranarthrura sp. (Agathotanaidae) as the sister taxon. A key to species of Hamatipeda is presented.

The use of nonclassical model organisms for biological rhythm research has become popular in the last two decades. Here we describe techniques for delivery of dsRNAi molecules to knock down clock gene transcripts in a small intertidal crustacean, Eurydice pulchra, as well as our method for immunodetection of clock proteins in the brain. These methods can be generalized for gene knockdown in any small crustacean or arthropod in which mutagenesis by other methods is neither practical nor possible., (© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Small cryptic invertebrates (the cryptofauna) are extremely abundant, ecologically important, and species rich on coral reefs. Ongoing ocean acidification is likely to have both direct effects on the biology of these organisms, as well as indirect effects through cascading impacts on their habitats and trophic relationships. Naturally acidified habitats have been important model systems for studying these complex interactions because entire communities that are adapted to these environmental conditions can be analyzed. However, few studies have examined the cryptofauna because they are difficult to census quantitatively in topographically complex habitats and are challenging to identify. We addressed these challenges by using Autonomous Reef Monitoring Structures (ARMS) for sampling reef-dwelling invertebrates >2 mm in size and by using DNA barcoding for taxonomic identifications. The study took place in Papua New Guinea at two reef localities, each with three sites at varying distances from carbon dioxide seeps, thereby sampling across a natural gradient in acidification. We observed sharp overall declines in both the abundance (34-56%) and diversity (42-45%) of organisms in ARMS under the lowest pH conditions sampled (7.64-7.75). However, the overall abundance of gastropods increased slightly in lower pH conditions, and crustacean and gastropod families exhibited varying patterns. There was also variability in response between the two localities, despite their close proximity, as one control pH site displayed unusually low diversity and abundances for all invertebrate groups. The data illustrate the complexity of responses of the reef fauna to pH conditions, and the role of additional factors that influence the diversity and abundance of cryptic reef invertebrates., Competing Interests: The authors have declared that no competing interests exist.

Tanaidaceans are small benthic crustaceans that mainly inhabit diverse marine environments, and they comprise one of the most diverse and abundant macrofaunal groups in the deep sea. Tanaidacea is one of the most thread-dependent taxa in the Crustacea, constructing tubes, spun with their silk, for shelter. In this work, we sequenced and assembled the comprehensive transcriptome of 23 tanaidaceans encompassing 14 families and 4 superfamilies of Tanaidacea, and performed silk proteomics of Zeuxo ezoensis to search for its silk genes. As a result, we identified two families of silk proteins that are conserved across the four superfamilies. The long and repetitive nature of these silk genes resembles that of other silk-producing organisms, and the two families of proteins are similar in composition to silkworm and caddisworm fibroins, respectively. Moreover, the amino acid composition of the repetitive motifs of tanaidacean silk tends to be more hydrophilic, and therefore could be a useful resource in studying their unique adaptation of silk use in a marine environment. The availability of comprehensive transcriptome data in these taxa, coupled with proteomic evidence of their silk genes, will facilitate evolutionary and ecological studies., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

This analysis presents five genome assemblies of four Notostraca taxa. Notostraca origin dates to the Permian/Upper Devonian and the extant forms show a striking morphological similarity to fossil taxa. The comparison of sequenced genomes with other Branchiopoda genomes shows that, despite the morphological stasis, Notostraca share a dynamic genome evolution with high turnover for gene families' expansion/contraction and a transposable elements content comparable to other branchiopods. While Notostraca substitutions rate appears similar or lower in comparison to other branchiopods, a subset of genes shows a faster evolutionary pace, highlighting the difficulty of generalizing about genomic stasis versus dynamism. Moreover, we found that the variation of Triops cancriformis transposable elements content appeared linked to reproductive strategies, in line with theoretical expectations. Overall, besides providing new genomic resources for the study of these organisms, which appear relevant for their ecology and evolution, we also confirmed the decoupling of morphological and molecular evolution., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

It is still a challenge to reconstruct the deep phylogenetic relationships within spinicaudatans, and there are several different competing hypotheses regarding the interrelationships among Eocyzicidae, Cyzicidae s. s., Leptestheriidae, and Limnadiidae of the Suborder Spinicaudata. In order to explore the source of the inconsistencies, we focus on the sequence variation and the structure model of two rRNA genes based on extensive taxa sampling. The comparative sequence analysis revealed heterogeneity across species and the existence of conserved motifs in all spinicaudatan species. The level of intraspecific heterogeneity differed among species, which suggested that some species might have undergone a relaxed concerted evolution with respect to the 28S rRNA gene. The Bayesian analyses were performed on nuclear ( 28S rRNA , EF1α ) and mitochondrial ( 16S rRNA , COI ) genes. Further, we investigated compositional heterogeneity between lineages and assessed the potential for phylogenetic noise compared to signal in the combined data set. Reducing the non-phylogenetic signals and application of optimal rRNA model recovered a topology congruent with inference from the transcriptome data, whereby Limnadiidae was placed as a sister group to Leptestheriidae + Eocyzicidae with high support (topology I). Tests of alternative hypotheses provided implicit support for four competing topologies, and topology I was the best.

Only few genes are known from insects that encode multiple neuropeptides, i.e., peptides that activate different receptors. Among those are the capa and pk genes, which differentiated within Hexapoda following gene duplication. In our study, we focus on the early stages of differentiation of these genes. Specifically: (1) What was the expression pattern of the ancestral capa/pk gene, i.e., prior to gene duplication? (2) What is the expression pattern of capa and pk in silverfish, whose ancestors diverged from Pterygota more than 400 mya? Our results suggest the location and projection of CAPA immunoreactive Va cells in abdominal ganglia (trunk ganglia in Remipedia) are a plesiomorphic trait that was already present in the ancestor of Remipedia and Hexapoda. General features of serial homology such as location of cells bodies, contralateral projection of primary neurites, and presumed peripheral peptide release from segmentally arranged neurohemal release sites could be observed in Remipedia and silverfish, but also in all Pterygota studied so far. Differences are mainly in the specific location of these peripheral release sites. This hypothetical basic pattern of capa/pk neurons underwent modifications in the anterior ganglia of the ventral nerve cord already in Remipedia. In silverfish, as in all Pterygota studied so far, pk expression in the CNS is apparently restricted to the gnathal ganglia, whereas capa expression is typical of abdominal Va cells. Thus, differentiation in the expression pattern of capa and pk genes occurred early in the evolution of Hexapoda; likely soon after the appearance of two separate genes., (Copyright © 2021 Elsevier Inc. All rights reserved.)