The American lobster genome reveals insights on longevity, neural, and immune adaptations

Ocean warming and acidification alter calcification and innate immune system gene expression in juvenile American lobsters, Homarus americanus

The Gulf of Maine, home to American lobster, Homarus americanus, is experiencing rapid ocean warming (OW) and acidification (OA) due to climate change. While some studies have investigated the effects of either ocean acidification (OA) or warming (OW) on lobsters, few explore the interaction of these stressors, particularly on gene expression. We evaluated the effects of OA and OW on early benthic juvenile lobster transcriptomics using RNA sequencing and RT-qPCR through two distinct aquarium experiments. Lobsters were reared under OW/OA conditions aligned with values predicted for 2100: decrease in pH by 0.3-0.4 units; mean sea surface warming of 2.89 °C. RNA was isolated from carapace hypodermal tissue in both experiments. The multi-stressor treatment in the RNAseq experiment had the greatest differential expression. Genes of interest pertaining to calcification and cuticle development were primarily downregulated under high temperature but upregulated under acidified and multi-stressor conditions. In the RT-qPCR experiment, crustin alone was significantly downregulated and only under the most extreme multi-stressor treatment. This gene along with the prophenoloxidase activating enzyme had expression that trended toward downregulation across all treatments, suggesting a possible correlation to immune suppression. Expression profiles for crustin and the calcification gene, carbonic anhydrase differed across treatments based on molt cycle timing, indicating that stressor impacts may vary depending on the molt cycle phase. Elevated temperature had a greater effect on the expression of calcification and cuticle development genes, though the direction of expression reversed with multiple stressors. These results indicate the impacts of OW and OA on early benthic juvenile lobsters are complex, possibly synergistic, vary with molt cycle, and potentially interfere with normal cuticle development, which may increase susceptibility to injury or disease.

Chromosome-level genome assembly of scalloped spiny lobster Panulirus homarus homarus

Lobsters, aquatic organisms of significant economic value, hold an important position in the global aquaculture and fisheries industries. However, due to overfishing and ecological change, the populations of certain lobster species have declined dramatically, prompting conservation efforts in various countries. However, limited genomics research has restricted our capacity to conserve and exploit lobster germplasm resources. Here, we present a chromosome-level reference genome for Panulirus homarus homarus constructed using PacBio long-read sequencing and Hi-C data. The genome assembly size was 2.61 Gb, with a contig N50 of 5.43 Mb, and a scaffold N50 of 36.69 Mb. The assembled sequences were anchored to 73 chromosomes, covering 96.05% of the total genome. A total of 25,580 protein-coding genes were predicted, and 99.98% of the genes were functionally annotated using various protein databases. The high-quality genome assembly provides a valuable resource for studying the biology and evolutionary history of P. h. homarus, and could facilitate sustainable resource management, aquaculture, and conservation of the species.

Roles of a Y-Linked iDmrt1 Paralogue and Insulin-like Androgenic Gland Hormone in Sexual Development in the Tropical Rock Lobster, Panulirus ornatus

Understanding the mechanisms of sexual development would pave the way for producing mono-sex populations to aid the aquaculture industry. This study investigates the functions of the Y-linked iDmrt1 paralogue (Po-iDMY) and insulin-like androgenic gland hormone (Po-IAG) in the process of sexual development in the tropical rock lobster, Panulirus ornatus (TRL). Previously, we identified that Po-iDMY, a male-specific heterogametic (Y-linked) paralogue of the autosomal Po-iDmrt1 found in TRL, is a second sex-linked iDmrt gene identified in invertebrates. Using 5' and 3' rapid amplification of cDNA ends and data from a draft male genome (with an assembly genome size of approximately 2.446 Gbp and 87% BUSCO completeness), we obtained the full-length Po-iDMY gene (encoding a protein of 312 amino acids). A 411 bp male-specific sequence located at the 3' untranslated region of Po-iDMY mRNA was used as a sex marker, which was reported for the first time in our draft genome. However, Po-iDMY is not a master sex-determining factor since it was not expressed across developmental stages of embryos, juveniles and adults. Instead, we silenced Po-IAG at an early juvenile stage, generating two potential neo-females, implying that sexual manipulation could be a promising technique in TRL.

Chromosome-scale assembly of Artemia tibetiana genome, first aquatic invertebrate genome from Tibet Plateau

Genomic-level studies on the adaptive evolution of animals in the Qinghai-Tibet Plateau have been rapidly increasing. However, most studies are concentrated on vertebrates, and there are few reports on invertebrates. Here, we report the chromosome-level genome assembly for the brine shrimp Artemia tibetiana from Kyêbxang Co, a high-altitude (4620 m above sea level) salt lake on the plateau, based on the combination of Illumina, Nanopore long-reads and Hi-C sequencing data. The assembled genome is 1.69 Gb, and 94.83% of the assembled sequences are anchored to 21 pseudo-chromosomes. Approximately 75% of the genome was identified as repetitive sequences, which is higher than most crustaceans documented so far. A total of 17,988 protein-coding genes were identified, among them 14,388 were functionally annotated. This genomic resource provides the foundation for whole-genome level investigation on the genetic adaptation of Artemia to the harsh conditions in the Qinghai-Tibet Plateau.

Decoding Neuropeptide Complexity: Advancing Neurobiological Insights from Invertebrates to Vertebrates through Evolutionary Perspectives

Neuropeptides are vital signaling molecules involved in neural communication, hormonal regulation, and stress response across diverse taxa. Despite their critical roles, neuropeptide research remains challenging due to their low abundance, complex post-translational modifications (PTMs), and dynamic expression patterns. Mass spectrometry (MS)-based neuropeptidomics has revolutionized peptide identification and quantification, enabling the high-throughput characterization of neuropeptides and their PTMs. However, the complexity of vertebrate neural networks poses significant challenges for functional studies. Invertebrate models, such as Cancer borealis, Drosophila melanogaster, and Caenorhabditis elegans, offer simplified neural circuits, well-characterized systems, and experimental tools for elucidating the functional roles of neuropeptides. These models have revealed conserved neuropeptide families, including allatostatins, RFamides, and tachykinin-related peptides, whose vertebrate homologues regulate analogous physiological functions. Recent advancements in MS techniques, including ion mobility spectrometry and MALDI MS imaging, have further enhanced the spatial and temporal resolution of neuropeptide analysis, allowing for insights into peptide signaling systems. Invertebrate neuropeptide research not only expands our understanding of conserved neuropeptide functions but also informs translational applications including the development of peptide-based therapeutics. This review highlights the utility of invertebrate models in neuropeptide discovery, emphasizing their contributions to uncovering fundamental biological principles and their relevance to vertebrate systems.

Molecular and Cellular Function of p63 in Skin Development and Genetic Diseases

The transcription factor p63 is a master regulator of multiple ectodermal derivatives. During epidermal commitment, p63 interacts with several chromatin remodeling complexes to transactivate epidermal-specific genes and repress transcription of simple epithelial and nonepithelial genes. In the postnatal epidermis, p63 is required to control the proliferative potential of progenitor cells, maintain epidermal integrity, and contribute to epidermal differentiation. Autosomal dominant sequence variant in p63 cause a spectrum of syndromic disorders that affect several tissues, including or derived from stratified epithelia. In this review, we describe the recent studies that have provided novel insights into disease pathogenesis and potential therapeutic targets.

Advancing genetic improvement in the omics era: status and priorities for United States aquaculture

BACKGROUND

The innovations of the "Omics Era" have ushered in significant advancements in genetic improvement of agriculturally important animal species through transforming genetics, genomics and breeding strategies. These advancements were often coordinated, in part, by support provided over 30 years through the 1993-2023 National Research Support Project 8 (NRSP8, National Animal Genome Research Program, NAGRP) and affiliate projects focused on enabling genomic discoveries in livestock, poultry, and aquaculture species. These significant and parallel advances demand strategic planning of future research priorities. This paper, as an output from the May 2023 Aquaculture Genomics, Genetics, and Breeding Workshop, provides an updated status of genomic resources for United States aquaculture species, highlighting major achievements and emerging priorities.

MAIN TEXT

Finfish and shellfish genome and omics resources enhance our understanding of genetic architecture and heritability of performance and production traits. The 2023 Workshop identified present aims for aquaculture genomics/omics research to build on this progress: (1) advancing reference genome assembly quality; (2) integrating multi-omics data to enhance analysis of production and performance traits; (3) developing resources for the collection and integration of phenomics data; (4) creating pathways for applying and integrating genomics information across animal industries; and (5) providing training, extension, and outreach to support the application of genome to phenome. Research focuses should emphasize phenomics data collection, artificial intelligence, identifying causative relationships between genotypes and phenotypes, establishing pathways to apply genomic information and tools across aquaculture industries, and an expansion of training programs for the next-generation workforce to facilitate integration of genomic sciences into aquaculture operations to enhance productivity, competitiveness, and sustainability.

CONCLUSION

This collective vision of applying genomics to aquaculture breeding with focus on the highlighted priorities is intended to facilitate the continued advancement of the United States aquaculture genomics, genetics and breeding research community and industries. Critical challenges ahead include the practical application of genomic tools and analytical frameworks beyond academic and research communities that require collaborative partnerships between academia, government, and industry. The scope of this review encompasses the use of omics tools and applications in the study of aquatic animals cultivated for human consumption in aquaculture settings throughout their life-cycle.

The chromosome-level genome provides insights into the adaptive evolution of the visual system in Oratosquilla oratoria

BACKGROUND

The marine crustacean Oratosquilla oratoria is economically significant in seafood and aquaculture industries. However, the lack of high-quality genome assembly has hindered our understanding of O. oratoria, particularly the mechanisms underlying its developed visual system.

RESULTS

We generated a chromosome-level genome assembly for O. oratoria (2.97 Gb, 44 pseudo-chromosomes) using combination sequencing strategies. Our analysis revealed that more than half of the genome was covered by repeat sequences, and LINE elements showed significant expansion. Furthermore, phylogenetic analysis revealed a close relationship of O. oratoria with Dendrobranchiata and Pleocyemata. In addition, the evolutionary rate of O. oratoria was slightly faster than that of Dendrobranchiata and slower than that of Pleocyemata. Interestingly, we observed the significant expansion of middle-wavelength-sensitive (MWS) opsins in the O. oratoria genome by tandem duplication, partially contributing to their unique visual capabilities. Compared with other crustaceans, O. oratoria has evolved a thicker cornea that was possibly driven by visual adaptations and ecological requirements. Employing comparative transcriptome analysis, we identified a tandemly duplicated cuticle protein (CP) cluster that was specifically expanded and expressed in the ocular tissues of O. oratoria, potentially contributing to the thick cornea of O. oratoria.

CONCLUSIONS

Our study established the first chromosome-level genome for Stomatopoda species, providing a valuable genomic resource for studying the molecular mechanisms underlying the developed visual system of O. oratoria.

Chromosome-level reference genome for the Jonah crab, Cancer borealis

The Jonah crab, Cancer borealis, is integral to marine ecosystems and supports a rapidly growing commercial fishery in the northwest Atlantic Ocean. This species also has a long history as a model for neuroscience that has expanded our understanding of central pattern generators, neuromodulation, synaptic plasticity, and the connectivity of neural circuits. Here, we present a highly contiguous reference genome for the Jonah crab that will provide an essential resource to advance fisheries, conservation, and biomedical research. Using a combination of PacBio long-read sequencing and Omni-C scaffolding, we generated a final genome assembly spanning 691 Mb covering 51 chromosome-length scaffolds and 106 additional contigs. Benchmarking Universal Single-Copy Ortholog (BUSCO) analysis indicated a high-quality assembly with a completeness score of 90.8%. Repeat annotation identified 1,649 repeat families making up 48.27% of the Jonah crab genome. Gene model predictions annotated 24,830 protein coding genes with a 92.3% BUSCO score. Gene family evolution analysis revealed the expansion of gene families associated with nervous system function, and targeted analysis revealed an extensive repertoire of neural genes. The Jonah crab genome will not only provide a resource for neuroscience research but will also serve as a foundation to investigate adaptation to stress and population structure to support sustainable fisheries management during this time of rapidly changing environmental conditions in the northwest Atlantic Ocean.

High-resolution chromosome-level genome of Scylla paramamosain provides molecular insights into adaptive evolution in crabs

BACKGROUND

Evolutionary adaptation drives organismal adjustments to environmental pressures, exemplified in the diverse morphological and ecological adaptations seen in Decapoda crustaceans, particularly brachyuran crabs. Crabs thrive in diverse ecosystems, from coral reefs to hydrothermal vents and terrestrial habitats. Despite their ecological importance, the genetic mechanisms underpinning their developmental processes, reproductive strategies, and nutrient acquisition remain poorly understood.

RESULTS

Here, we report a comprehensive genomic analysis of the green mud crab Scylla paramamosain using ultralong sequencing technologies, achieving a high-quality chromosome-level assembly. The refined 1.21 Gb genome, with an impressive contig N50 of 11.45 Mb, offers a valuable genomic resource. The genome exhibits 33,662 protein-coding genes, enriched in various pathways related to development and environmental adaptation. Gene family analysis shows expansion in development-related pathways and contraction in metabolic pathways, indicating niche adaptations. Notably, investigation into Hox gene regulation sheds light on their role in pleopod development, with the Abd-A gene identified as a linchpin. Post-transcriptional regulation involving novel-miR1317 negatively regulates Abd-A levels. Furthermore, the potential role of fru gene in ovarian development and the identification of novel-miR35 as a regulator of Spfru2 add complexity to gene regulatory networks. Comparative functional analysis across Decapoda species reveals neo-functionalization of the elovl6 gene in the synthesis of long-chain polyunsaturated fatty acids (LC-PUFA), suggesting its importance in environmental adaptation.

CONCLUSIONS

Our findings shed light on various aspects of crab biology, including genome sequencing, assembly, and annotation, as well as gene family expansion, contraction, and regulatory mechanisms governing crucial developmental processes such as metamorphosis, reproductive strategies, and fatty acid metabolism.

Chromosome level genome assembly of giant freshwater prawn (Macrobrachium rosenbergii)

The giant freshwater prawn (Macrobrachium rosenbergii) has many advantages in aquaculture, such as fast growth rate, short breeding cycle and good nutrition, which makes it a freshwater shrimp with high economic value. Herein, high-quality chromosome-level genome of both female and male prawns were obtained by combining Illumina paired-end sequencing, PacBio single molecule sequencing technique and High-through chromosome conformation capture (Hi-C) technologies. In ZZ male prawn, a final contig assembly of 3118.58 Mb with a N50 length of 956,237 bp was obtained. In WW female prawn, a final contig assembly of 3333.31 Mb with a N50 length of 1,143,555 bp was obtained. The assembled genome sequences from prawns were anchored to 59 chromosomes. Moreover, the sex chromosomes including W chromosome and Z chromosome were generated in prawn with the length of 36.23 Mb and 27.33 Mb, respectively. The sequence similarity of Z chromosome and W chromosome reached to 74.90%. The high-quality genome resource will be useful for further molecular breeding and functional genomic research of giant freshwater prawns.

Ago4-piRNA complex is a key component of genomic immune system against transposon expression in Penaeus monodon

Argonaute proteins are key constituents of small RNA-guided regulatory pathways. In crustaceans, members of the AGO subfamily of Argonaute proteins that play vital roles in immune defense are well studied, while proteins of the PIWI subfamily are less established. PmAgo4 of the black tiger shrimp, Penaeus monodon, though phylogenetically clustered with the AGO subfamily, has distinctive roles of the PIWI subfamily in safeguarding the genome from transposon invasion and controlling germ cell development. This study explored a molecular mechanism by which PmAgo4 regulates transposon expression in the shrimp germline. PmAgo4-associated small RNAs were co-immunoprecipitated from shrimp testis lysate using a PmAgo4-specific polyclonal antibody. RNA-seq revealed a majority of 26-27 nt long small RNAs in the PmAgo4-IP fraction suggesting that PmAgo4 is predominantly associated with piRNAs. Mapping of these piRNAs on nucleotide sequences of two gypsy and a mariner-like transposons of P. monodon suggested that most piRNAs were originated from the antisense strand of transposons. Suppression of PmAgo4 expression by a specific dsRNA elevated the expression levels of the three transposons while decreasing the levels of transposon-related piRNAs. Taken together, these results imply that PmAgo4 exerts its suppressive function on transposons by controlling the biogenesis of transposon-related piRNAs and thus, provides a defense mechanism against transposon invasion in shrimp germline cells.

Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins

Krill are vital as food for many marine animals but also impacted by global warming. To learn how they and other zooplankton may adapt to a warmer world we studied local adaptation in the widespread Northern krill (Meganyctiphanes norvegica). We assemble and characterize its large genome and compare genome-scale variation among 74 specimens from the colder Atlantic Ocean and warmer Mediterranean Sea. The 19 Gb genome likely evolved through proliferation of retrotransposons, now targeted for inactivation by extensive DNA methylation, and contains many duplicated genes associated with molting and vision. Analysis of 760 million SNPs indicates extensive homogenizing gene-flow among populations. Nevertheless, we detect signatures of adaptive divergence across hundreds of genes, implicated in photoreception, circadian regulation, reproduction and thermal tolerance, indicating polygenic adaptation to light and temperature. The top gene candidate for ecological adaptation was nrf-6, a lipid transporter with a Mediterranean variant that may contribute to early spring reproduction. Such variation could become increasingly important for fitness in Atlantic stocks. Our study underscores the widespread but uneven distribution of adaptive variation, necessitating characterization of genetic variation among natural zooplankton populations to understand their adaptive potential, predict risks and support ocean conservation in the face of climate change.

Rearing condition influences gene expression in postlarval American lobster (Homarus americanus)

The American lobster (Homarus americanus) is an economically important species in the western Atlantic and its climate-driven range shift northward along the east coast of the United States is well documented. The thermal tolerance of lab-reared postlarvae of this species has been extensively investigated to better understand settlement and recruitment dynamics. However, there have been few studies focused on wild-caught postlarvae, and even fewer that have analyzed lab-rearing conditions in context of diet. In this study, we investigated gene transcriptional changes in postlarvae caught in the wild, as well as postlarvae reared in the laboratory on a brine shrimp diet or a wild-sourced zooplankton diet. We found between wild-caught and brine shrimp-reared larvae 3,682 differentially expressed genes, and between wild and zooplankton-reared postlarvae 3,939 differentially expressed genes. Between the two lab-reared groups fed different diets 2,603 genes were differentially expressed. We also exposed individuals in all rearing groups to chronic temperature treatments of 8°C and 26°C and found that both temperature extremes elicit 68-95% fewer transcriptional changes in wild postlarvae compared to either lab-reared group. In wild postlarvae, we identified differential expression of transcripts within the FoxO signaling pathway, a signaling pathway with a central role in cellular physiology, as potential molecular markers for cold tolerance in the American lobster. These findings contextualize the current literature on lab-reared postlarvae as containing conservative estimates for in situ organisms and can be used to inform population distribution modeling efforts. They also provide evidence for the need to adjust lab-rearing techniques or source wild larval crustaceans to augment studies of larval biology.

Neuropeptidomics of the American Lobster Homarus americanus

The American lobster, Homarus americanus, is not only of considerable economic importance but has also emerged as a premier model organism in neuroscience research. Neuropeptides, an important class of cell-to-cell signaling molecules, play crucial roles in a wide array of physiological and psychological processes. Leveraging the recently sequenced high-quality draft genome of the American lobster, our study sought to profile the neuropeptidome of this model organism. Employing advanced mass spectrometry techniques, we identified 24 neuropeptide precursors and 101 unique mature neuropeptides in Homarus americanus. Intriguingly, 67 of these neuropeptides were discovered for the first time. Our findings provide a comprehensive overview of the peptidomic attributes of the lobster's nervous system and highlight the tissue-specific distribution of these neuropeptides. Collectively, this research not only enriches our understanding of the neuronal complexities of the American lobster but also lays a foundation for future investigations into the functional roles that these peptides play in crustacean species. The mass spectrometry data have been deposited in the PRIDE repository with the identifier PXD047230.

Genomic signatures of exceptional longevity and negligible aging in the long-lived red sea urchin

The red sea urchin (Mesocentrotus franciscanus) is one of the Earth's longest-living animals, reported to live more than 100 years with indeterminate growth, life-long reproduction, and no increase in mortality rate with age. To understand the genetic underpinnings of longevity and negligible aging, we constructed a chromosome-level assembly of the red sea urchin genome and compared it to that of short-lived sea urchin species. Genome-wide syntenic alignments identified chromosome rearrangements that distinguish short- and long-lived species. Expanded gene families in long-lived species play a role in innate immunity, sensory nervous system, and genome stability. An integrated network of genes under positive selection in the red sea urchin was involved in genomic regulation, mRNA fidelity, protein homeostasis, and mitochondrial function. Our results implicated known longevity genes in sea urchin longevity but also revealed distinct molecular signatures that may promote long-term maintenance of tissue homeostasis, disease resistance, and negligible aging.

Evaluating conserved domains and motifs of decapod gonadotropin-releasing hormone G protein-coupled receptor superfamily

G protein-coupled receptors (GPCRs) are an ancient family of signal transducers that are both abundant and consequential in metazoan endocrinology. The evolutionary history and function of the GPCRs of the decapod superfamilies of gonadotropin-releasing hormone (GnRH) are yet to be fully elucidated. As part of which, the use of traditional phylogenetics and the recycling of a diminutive set of mis-annotated databases has proven insufficient. To address this, we have collated and revised eight existing and three novel GPCR repertoires for GnRH of decapod species. We developed a novel bioinformatic workflow that included clustering analysis to capture likely GnRH receptor-like proteins, followed by phylogenetic analysis of the seven transmembrane-spanning domains. A high degree of conservation of the sequences and topology of the domains and motifs allowed the identification of species-specific variation (up to ~70%, especially in the extracellular loops) that is thought to be influential to ligand-binding and function. Given the key functional role of the DRY motif across GPCRs, the classification of receptors based on the variation of this motif can be universally applied to resolve cryptic GPCR families, as was achieved in this work. Our results contribute to the resolution of the evolutionary history of invertebrate GnRH receptors and inform the design of bioassays in their deorphanization and functional annotation.

CrustyBase v.2.0: new features and enhanced utilities to support open science

BACKGROUND

Transcriptomes present a rich, multi-dimensional subset of genomics data. They provide broad insights into genetic sequence, and more significantly gene expression, across biological samples. This technology is frequently employed for describing the genetic response to experimental conditions and has created vast libraries of datasets which shed light on gene function across different tissues, diseases, diets and developmental stages in many species. However, public accessibility of these data is impeded by a lack of suitable software interfaces and databases with which to locate and analyse them. BODY: Here we present an update on the status of CrustyBase.org, an online resource for analysing and sharing crustacean transcriptome datasets. Since its release in October 2020, the resource has provided many thousands of transcriptome sequences and expression profiles to its users and received 19 new dataset imports from researchers across the globe. In this article we discuss user analytics which point towards the utilization of this resource. The architecture of the application has proven robust with over 99.5% uptime and effective reporting of bugs through both user engagement and the error logging mechanism. We also introduce several new features that have been developed as part of a new release of CrustyBase.org. Two significant features are described in detail, which allow users to navigate through transcripts directly by submission of transcript identifiers, and then more broadly by searching for encoded protein domains by keyword. The latter is a novel and experimental feature, and grants users the ability to curate gene families from any dataset hosted on CrustyBase in a matter of minutes. We present case studies to demonstrate the utility of these features.

CONCLUSION

Community engagement with this resource has been very positive, and we hope that improvements to the service will further enable the research of users of the platform. Web-based platforms such as CrustyBase have many potential applications across life science domains, including the health sector, which are yet to be realised. This leads to a wider discussion around the role of web-based resources in facilitating an open and collaborative research community.

MarFERReT, an open-source, version-controlled reference library of marine microbial eukaryote functional genes

Metatranscriptomics generates large volumes of sequence data about transcribed genes in natural environments. Taxonomic annotation of these datasets depends on availability of curated reference sequences. For marine microbial eukaryotes, current reference libraries are limited by gaps in sequenced organism diversity and barriers to updating libraries with new sequence data, resulting in taxonomic annotation of about half of eukaryotic environmental transcripts. Here, we introduce Marine Functional EukaRyotic Reference Taxa (MarFERReT), a marine microbial eukaryotic sequence library designed for use with taxonomic annotation of eukaryotic metatranscriptomes. We gathered 902 publicly accessible marine eukaryote genomes and transcriptomes and assessed their sequence quality and cross-contamination issues, selecting 800 validated entries for inclusion in MarFERReT. Version 1.1 of MarFERReT contains reference sequences from 800 marine eukaryotic genomes and transcriptomes, covering 453 species- and strain-level taxa, totaling nearly 28 million protein sequences with associated NCBI and PR2 Taxonomy identifiers and Pfam functional annotations. The MarFERReT project repository hosts containerized build scripts, documentation on installation and use case examples, and information on new versions of MarFERReT.

Monosex Populations of the Giant Freshwater Prawn Macrobrachium rosenbergii-From a Pre-Molecular Start to the Next Generation Era

Sexual manipulation in the giant freshwater prawn Macrobrachium rosenbergii has proven successful in generating monosex (both all-male and all-female) populations for aquaculture using a crustacean-specific endocrine gland, the androgenic gland (AG), which serves as a key masculinizing factor by producing and secreting an insulin-like AG hormone (IAG). Here, we provide a summary of the advancements from the discovery of the AG and IAG in decapods through to the development of monosex populations in M. rosenbergii. We discuss the broader sexual development pathway, which is highly divergent across decapods, and provide our future perspective on the utility of novel genetic and genomic tools in promoting refined approaches towards monosex biotechnology. Finally, the future potential benefits of deploying monosex prawn populations for environmental management are discussed.

Diversity of neuropeptidergic modulation in decapod crustacean cardiac and feeding systems

All nervous systems are multiply modulated by polypeptides. However, a bulk of transmitter and modulation research has historically focused on small molecule transmitters released at synaptic sites. The stomatogastric nervous system (controls digestive movements of the foregut) and cardiac nervous system of decapod crustaceans have long been used to understand the processes that underlie neuromodulation. The circuits governing the rhythmic output from these nervous systems are comprised of a relatively small number of identified neurons, and the details of these nervous systems are well-defined. Here we discuss recent research highlighting advances in our understanding of peptidergic modulation in these systems. In particular, we focus on our ability to identify specific signaling peptide sequences and relate their expression patterns to their physiological effects, as well as on the multiple sites within a pattern generator-effector system at which modulation takes place. Recent efforts have enabled us to understand how co-modulation by two or more peptides can generate surprising effects on circuit physiology and that modulation at different receptor sites can produce supra-additive effects. Finally, we examine the protective role modulation plays in making circuits robust to perturbations, in this case, changes in temperature.

Marine Invertebrate Antimicrobial Peptides and Their Potential as Novel Peptide Antibiotics

Marine invertebrates constantly interact with a wide range of microorganisms in their aquatic environment and possess an effective defense system that has enabled their existence for millions of years. Their lack of acquired immunity sets marine invertebrates apart from other marine animals. Invertebrates could rely on their innate immunity, providing the first line of defense, survival, and thriving. The innate immune system of marine invertebrates includes various biologically active compounds, and specifically, antimicrobial peptides. Nowadays, there is a revive of interest in these peptides due to the urgent need to discover novel drugs against antibiotic-resistant bacterial strains, a pressing global concern in modern healthcare. Modern technologies offer extensive possibilities for the development of innovative drugs based on these compounds, which can act against bacteria, fungi, protozoa, and viruses. This review focuses on structural peculiarities, biological functions, gene expression, biosynthesis, mechanisms of antimicrobial action, regulatory activities, and prospects for the therapeutic use of antimicrobial peptides derived from marine invertebrates.

Abundance and Diversification of Repetitive Elements in Decapoda Genomes

Repetitive elements are a major component of DNA sequences due to their ability to propagate through the genome. Characterization of Metazoan repetitive profiles is improving; however, current pipelines fail to identify a significant proportion of divergent repeats in non-model organisms. The Decapoda order, for which repeat content analyses are largely lacking, is characterized by extremely variable genome sizes that suggest an important presence of repetitive elements. Here, we developed a new standardized pipeline to annotate repetitive elements in non-model organisms, which we applied to twenty Decapoda and six other Crustacea genomes. Using this new tool, we identified 10% more repetitive elements than standard pipelines. Repetitive elements were more abundant in Decapoda species than in other Crustacea, with a very large number of highly repeated satellite DNA families. Moreover, we demonstrated a high correlation between assembly size and transposable elements and different repeat dynamics between Dendrobranchiata and Reptantia. The patterns of repetitive elements largely reflect the phylogenetic relationships of Decapoda and the distinct evolutionary trajectories within Crustacea. In summary, our results highlight the impact of repetitive elements on genome evolution in Decapoda and the value of our novel annotation pipeline, which will provide a baseline for future comparative analyses.

Evo-devo perspectives on cancer

The integration of evolutionary and developmental approaches into the field of evolutionary developmental biology has opened new areas of inquiry- from understanding the evolution of development and its underlying genetic and molecular mechanisms to addressing the role of development in evolution. For the last several decades, the terms 'evolution' and 'development' have been increasingly linked to cancer, in many different frameworks and contexts. This mini-review, as part of a special issue on Evolutionary Developmental Biology, discusses the main areas in cancer research that have been addressed through the lenses of both evolutionary and developmental biology, though not always fully or explicitly integrated in an evo-devo framework. First, it briefly introduces the current views on carcinogenesis that invoke evolutionary and/or developmental perspectives. Then, it discusses the main mechanisms proposed to have specifically evolved to suppress cancer during the evolution of multicellularity. Lastly, it considers whether the evolution of multicellularity and development was shaped by the threat of cancer (a cancer-evo-devo perspective), and/or whether the evolution of developmental programs and life history traits can shape cancer resistance/risk in various lineages (an evo-devo-cancer perspective). A proper evolutionary developmental framework for cancer, both as a disease and in terms of its natural history (in the context of the evolution of multicellularity and development as well as life history traits), could bridge the currently disparate evolutionary and developmental perspectives and uncover aspects that will provide new insights for cancer prevention and treatment.

Animal models of male reproductive ageing to study testosterone production and spermatogenesis

Ageing is the time-dependent gradual decline of the functional characteristics in an organism. It has been shown that it results in the loss of reproductive health and fertility. The age-dependent decline of fertility is a potential issue as the parenthood age is increasing in Western countries, mostly due to socioeconomic factors. In comparison to women, for whom the consequences of ageing are well documented and general awareness of the population is extensively raised, the effects of ageing for male fertility and the consequences of advanced paternal age for the offspring have not been widely studied. Studies with humans are welcome but it is hard to implement relevant experimental approaches to unveil the molecular mechanisms by which ageing affects male reproductive potential. Animal models have thus been extensively used. These models are advantageous due to their reduced costs, general easy maintenance in laboratory facilities, rigorous manipulation tools, short lifespan, known genetic backgrounds, and reduced ethical constraints. Herein, we discuss animal models for the study of male reproductive ageing. The most well-known and studied reproductive ageing models are rodents and non-human primates. The data collected from these models, particularly studies on testicular ageing, steroidogenesis, and genetic and epigenetic changes in spermatogenesis are detailed. Notably, some species challenge the currently accepted ageing theories and the concept of senescence itself, which renders them interesting animal models for the study of male reproductive ageing.

Crustacean shellfish allergens: influence of food processing and their detection strategies

Despite the increasing popularity of crustacean shellfish among consumers due to their rich nutrients, they can induce a serious allergic response, sometimes even life-threatening. In the past decades, a variety of crustacean allergens have been identified to facilitate the diagnosis and management of crustacean allergies. Although food processing techniques can ease the risk of crustacean shellfish allergy, no available processing methods to tackle crustacean allergies thoroughly. Strict dietary avoidance of crustacean shellfish and its component is the best option for the protection of sensitized individuals, which should rely on the compliance of food labeling and, as such, on their verification by sensitive, reliable, and accurate detection techniques. In this present review, the physiochemical properties, structure aspects, and immunological characteristics of the major crustacean allergens have been described and discussed. Subsequently, the current research progresses on how various processing techniques cause the alterations and modifications in crustacean allergens to produce hypoallergenic crustacean food products were summarized and discussed. Particularly, various analytical methodologies employed in crustacean shellfish allergen detection, and the effect of food processing and matrix on these techniques, are also herein emphasized for the appropriate selection of analytical detection tools to safeguard consumers safety.

Landscape genomics of the American lobster (Homarus americanus)

In marine species experiencing intense fishing pressures, knowledge of genetic structure and local adaptation represent a critical information to assist sustainable management. In this study, we performed a landscape genomics analysis in the American lobster to investigate the issues pertaining to the consequences of making use of putative adaptive loci to reliably infer population structure and thus more rigorously delineating biological management units in marine exploited species. Toward this end, we genotyped 14,893 single nucleotide polymorphism (SNPs) in 4190 lobsters sampled across 96 sampling sites distributed along 1000 km in the northwest Atlantic in both Canada and the USA. As typical for most marine species, we observed a weak, albeit highly significant genetic structure. We also found that adaptive genetic variation allows detecting fine-scale population structure not resolved by neutral genetic variation alone. Using the recent genome assembly of the American lobster, we were able to map and annotate several SNPs located in functional genes potentially implicated in adaptive processes such as thermal stress response, salinity tolerance and growth metabolism pathways. Taken together, our study indicates that weak population structure in high gene flow systems can be resolved at various spatial scales, and that putatively adaptive genetic variation can substantially enhance the delineation of biological management units of marine exploited species.

Comparative transcriptomic analysis revealed dynamic changes of distinct classes of genes during development of the Manila clam (Ruditapes philippinarum)

Background

The Manila clam Ruditapesphilippinarum is one of the most economically important marine shellfish. However, the molecular mechanisms of early development in Manila clams are largely unknown. In this study, we collected samples from 13 stages of early development in Manila clam and compared the mRNA expression pattern between samples by RNA-seq techniques.

Results

We applied RNA-seq technology to 13 embryonic and larval stages of the Manila clam to identify critical genes and pathways involved in their development and biological characteristics. Important genes associated with different morphologies during the early fertilized egg, cell division, cell differentiation, hatching, and metamorphosis stages were identified. We detected the highest number of differentially expressed genes in the comparison of the pediveliger and single pipe juvenile stages, which is a time when biological characteristics greatly change during metamorphosis. Gene Ontology (GO) enrichment analysis showed that expression levels of microtubule protein-related molecules and Rho genes were upregulated and that GO terms such as ribosome, translation, and organelle were enriched in the early development stages of the Manila clam. Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the foxo, wnt, and transforming growth factor-beta pathways were significantly enriched during early development. These results provide insights into the molecular mechanisms at work during different periods of early development of Manila clams.

Conclusion

These transcriptomic data provide clues to the molecular mechanisms underlying the development of Manila clam larvae. These results will help to improve Manila clam reproduction and development.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08813-0.

"Omics" data unveil early molecular response underlying limb regeneration in the Chinese mitten crab, Eriocheir sinensis

Limb regeneration is a fascinating and medically interesting trait that has been well preserved in arthropod lineages, particularly in crustaceans. However, the molecular mechanisms underlying arthropod limb regeneration remain largely elusive. The Chinese mitten crab Eriocheir sinensis shows strong regenerative capacity, a trait that has likely allowed it to become a worldwide invasive species. Here, we report a chromosome-level genome of E. sinensis as well as large-scale transcriptome data during the limb regeneration process. Our results reveal that arthropod-specific genes involved in signal transduction, immune response, histone methylation, and cuticle development all play fundamental roles during the regeneration process. Particularly, Innexin2-mediated signal transduction likely facilitates the early stage of the regeneration process, while an effective crustacean-specific prophenoloxidase system (ProPo-AS) plays crucial roles in the initial immune response. Collectively, our findings uncover novel genetic pathways pertaining to arthropod limb regeneration and provide valuable resources for studies on regeneration from a comparative perspective.

Characterization of hemocytes and hematopoietic cells of a freshwater crayfish based on single-cell transcriptome analysis

Crustaceans constitute a species-rich and ecologically important animal group, and their circulating blood cells (hemocytes) are of critical importance in immunity as key players in pathogen recognition, phagocytosis, melanization, and antimicrobial defense. To gain a better understanding of the immune responses to different pathogens, it is crucial that we identify different hemocyte subpopulations with different functions and gain a better understanding of how these cells are formed. Here, we performed single-cell RNA sequencing of isolated hematopoietic tissue (HPT) cells and hemocytes from the crayfish Pacifastacus leniusculus to identify hitherto undescribed hemocyte types in the circulation and show that the circulating cells are more diversified than previously recognized. In addition, we discovered cell populations in the HPT with clear precursor characteristics as well as cells involved in iron homeostasis, representing a previously undiscovered cell type. These findings may improve our understanding of hematopoietic stem cell regulation in crustaceans and other animals.

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Single-cell RNA sequencing of hematopoietic cell types reveals new cell types

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One cell type contains iron homeostasis-associated transcripts

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Hemocytes and hematopoietic cells differ in their transcript profiles

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Prophenoloxidase is only expressed in hemocytes

The salmon louse genome may be much larger than sequencing suggests

The genome size of organisms impacts their evolution and biology and is often assumed to be characteristic of a species. Here we present the first published estimates of genome size of the ecologically and economically important ectoparasite, Lepeophtheirus salmonis (Copepoda, Caligidae). Four independent L. salmonis genome assemblies of the North Atlantic subspecies Lepeophtheirus salmonis salmonis, including two chromosome level assemblies, yield assemblies ranging from 665 to 790 Mbps. These genome assemblies are congruent in their findings, and appear very complete with Benchmarking Universal Single-Copy Orthologs analyses finding > 92% of expected genes and transcriptome datasets routinely mapping > 90% of reads. However, two cytometric techniques, flow cytometry and Feulgen image analysis densitometry, yield measurements of 1.3-1.6 Gb in the haploid genome. Interestingly, earlier cytometric measurements reported genome sizes of 939 and 567 Mbps in L. salmonis salmonis samples from Bay of Fundy and Norway, respectively. Available data thus suggest that the genome sizes of salmon lice are variable. Current understanding of eukaryotic genome dynamics suggests that the most likely explanation for such variability involves repetitive DNA, which for L. salmonis makes up ≈ 60% of the genome assemblies.

Studying phenotypic variation and DNA methylation across development, ecology and evolution in the clonal marbled crayfish: a paradigm for investigating epigenotype-phenotype relationships in macro-invertebrates

Animals can produce different phenotypes from the same genome during development, environmental adaptation and evolution, which is mediated by epigenetic mechanisms including DNA methylation. The obligatory parthenogenetic marbled crayfish, Procambarus virginalis, whose genome and methylome are fully established, proved very suitable to study this issue in detail. Comparison between developmental stages and DNA methylation revealed low expression of Dnmt methylation and Tet demethylation enzymes from the spawned oocyte to the 256 cell embryo and considerably increased expression thereafter. The global 5-methylcytosine level was 2.78% at mid-embryonic development and decreased slightly to 2.41% in 2-year-old adults. Genetically identical clutch-mates raised in the same uniform laboratory setting showed broad variation in morphological, behavioural and life history traits and differences in DNA methylation. The invasion of diverse habitats in tropical to cold-temperate biomes in the last 20 years by the marbled crayfish was associated with the expression of significantly different phenotypic traits and DNA methylation patterns, despite extremely low genetic variation on the whole genome scale, suggesting the establishment of epigenetic ecotypes. The evolution of marbled crayfish from its parent species Procambarus fallax by autotriploidy a few decades ago was accompanied by a significant increase in body size, fertility and life span, a 20% reduction of global DNA methylation and alteration of methylation in hundreds of genes, suggesting that epigenetic mechanisms were involved in speciation and fitness enhancement. The combined analysis of phenotypic traits and DNA methylation across multiple biological contexts in the laboratory and field in marbled crayfish may serve as a blueprint for uncovering the role of epigenetic mechanisms in shaping of phenotypes in macro-invertebrates.

The NGS Magic Pudding: A Nanopore-Led Long-Read Genome Assembly for the Commercial Australian Freshwater Crayfish, Cherax destructor

Cherax destructor, the yabby, is an iconic Australian freshwater crayfish species, which, similar to other major invertebrate groups, is grossly under-represented in genomic databases. The yabby is also the principal commercial freshwater crustacean species in Australia subject to explotation via inland fisheries and aquaculture. To address the genomics knowledge gap for this species and explore cost effective and efficient methods for genome assembly, we generated 106.8 gb of Nanopore reads and performed a long-read only assembly of the Cherax destructor genome. On a mini-server configured with an ultra-fast swap space, the de novo assembly took 131 h (∼5.5 days). Genome polishing with 126.3 gb of PCR-Free Illumina reads generated an assembled genome size of 3.3 gb (74.6% BUSCO completeness) with a contig N50 of 80,900 bp, making it the most contiguous for freshwater crayfish genome assemblies. We found an unusually large number of cellulase genes within the yabby genome which is relevant to understanding the nutritional biology, commercial feed development, and ecological role of this species and crayfish more generally. These resources will be useful for genomic research on freshwater crayfish and our methods for rapid and super-efficient genome assembly will have wide application.

Cytology, function and dynamics of stem and progenitor cells in decapod crustaceans

Stem cells play key roles in development, tissue homeostasis, regeneration, ageing and diseases. Comprehensive reviews on stem cells are available for the determinately growing mammals and insects and some lower invertebrates like hydra but are rare for larger, indeterminately growing invertebrates that can live for many decades. This paper reviews the cytology, function and dynamics of stem and progenitor cells in the decapod crustaceans, a species-rich and ecologically and economically important animal group that includes mainly indeterminate growers but also some determinate growers. Further advantages of decapods for stem cell research are almost 1000-fold differences in body size and longevity, the regeneration of damaged appendages and the virtual absence of age-related diseases and tumours in the indeterminately growing species. The available data demonstrate that the Decapoda possess a remarkable variety of structurally and functionally different stem cells in embryos and larvae, and in the epidermis, musculature, haematopoietic tissue, heart, brain, hepatopancreas, olfactory sense organs and gonads of adults. Some of these seem to be rather continuously active over a lifetime but others are cyclically activated and silenced in periods of days, weeks and years, depending on the specific organ and function. Stem cell proliferation is triggered by signals related to development, moulting, feeding, reproduction, injury, infection, environmental enrichment and social status. Some regulatory pathways have already been identified, including the evolutionarily conserved GATA-binding and runt-domain transcription factors, the widespread neurotransmitter serotonin, the arthropod-specific hormone 20-hydroxyecdysone and the novel astakine growth factors. Knowledge of stem cells in decapods primarily refines our picture on the development, growth and maintenance of tissues and organs in this animal group. Cultured decapod stem cells have good potential for toxicity testing and virus research with practical relevance for aquaculture. Knowledge of stem cells in decapods also broadens our understanding of the evolution of stem cells and regeneration in the animal kingdom. The stem cells of long-lived, indeterminately growing decapods may hold the key to understanding how stem and progenitor cells function into old age without adverse side effects, possibly evoking new ideas for the development of anti-ageing and anti-cancer treatments in humans.

Evolution of glutamatergic signaling and synapses

Glutamate (Glu) is the primary excitatory transmitter in the mammalian brain. But, we know little about the evolutionary history of this adaptation, including the selection of l-glutamate as a signaling molecule in the first place. Here, we used comparative metabolomics and genomic data to reconstruct the genealogy of glutamatergic signaling. The origin of Glu-mediated communications might be traced to primordial nitrogen and carbon metabolic pathways. The versatile chemistry of L-Glu placed this molecule at the crossroad of cellular biochemistry as one of the most abundant metabolites. From there, innovations multiplied. Many stress factors or injuries could increase extracellular glutamate concentration, which led to the development of modular molecular systems for its rapid sensing in bacteria and archaea. More than 20 evolutionarily distinct families of ionotropic glutamate receptors (iGluRs) have been identified in eukaryotes. The domain compositions of iGluRs correlate with the origins of multicellularity in eukaryotes. Although L-Glu was recruited as a neuro-muscular transmitter in the early-branching metazoans, it was predominantly a non-neuronal messenger, with a possibility that glutamatergic synapses evolved more than once. Furthermore, the molecular secretory complexity of glutamatergic synapses in invertebrates (e.g., Aplysia) can exceed their vertebrate counterparts. Comparative genomics also revealed 15+ subfamilies of iGluRs across Metazoa. However, most of this ancestral diversity had been lost in the vertebrate lineage, preserving AMPA, Kainate, Delta, and NMDA receptors. The widespread expansion of glutamate synapses in the cortical areas might be associated with the enhanced metabolic demands of the complex brain and compartmentalization of Glu signaling within modular neuronal ensembles.