Scallop genome provides insights into evolution of bilaterian karyotype and development

Haplotype-resolved genomes provide insights into the origins and functional significance of genome diversity in bivalves

Bivalves are famed for exhibiting vast genetic diversity of poorly understood origins and functional significance. Through comparative genomics, we demonstrate that high genetic diversity in these invertebrates is not directly linked to genome size. Using oysters as a representative clade, we show that despite genome size reduction during evolution, these bivalves maintain remarkable genetic variability. By constructing a haplotype-resolved genome for Crassostrea sikamea, we identify widespread haplotype divergent sequences (HDSs), representing genomic regions unique to each haplotype. We show that HDSs are driven by transposable elements, playing a key role in creating and maintaining genetic diversity during oyster evolution. Comparisons of haplotype-resolved genomes across four bivalve orders uncover diverse HDS origins, highlighting a role in genetic innovation and expression regulation across broad timescales. Further analyses show that, in oysters, haplotype polymorphisms drive gene expression variation, which is likely to promote phenotypic plasticity and adaptation. These findings advance our understanding of the relationships among genome structure, diversity, and adaptability in a highly successful invertebrate group.

A functional role for myostatin in muscle hyperplasia and hypertrophy revealed by comparative transcriptomics in Yesso scallop Patinopecten yessoensis

Elucidating the molecular regulatory mechanisms underlying muscle growth and development is of profound significance in aquaculture. Yesso scallop is a cold-water bivalve of considerable economic importance, having its primary edible component of adductor muscle. In this study, comparative transcriptomics and histological analysis at different sampling times after Myostatin (MSTN) interference were performed to identify the potential candidate genes potentially involved in muscle growth and development. The comparative transcriptomics revealed that growth factors and cytokines, extracellular matrix proteins and ubiquitin-proteasome system are potentially involved in muscle hypertrophy and hyperplasia. After MSTN interference, striated adductor muscle displays significant muscle hypertrophy (51.77 % increase on day 7 and 59.83 % increase on day 21) and muscle hyperplasia (59.36 % increase on day 7 and 61.83 % increase on day 21). WGCNA identifies the key darkolivegreen module, which may play crucial roles in muscle hyperplasia and hypertrophy within the striated muscle of the scallop. Five key transcription factors (zf-CCCH, zf-C2H2, PPP1R10, LRRFIP2, and Gon4) are identified by analyzing the co-expression patterns of core genes within the module. These findings will aid in understanding the regulatory mechanisms of muscle growth in scallops and provide a basis for genetic improvement in shellfish aquaculture.

Whole Genome Duplication in the Genomics Era: The Hidden Gems in Invertebrates?

Whole genome duplication (WGD) events generate potent new genomic resources for rewiring existing genetic regulatory networks. Studying WGDs in vertebrates is of considerable importance to understand vertebrate evolution. Recent studies have shown that different invertebrate lineages, including lophotrochozoans/spiralians and ecdysozoans, have also undergone WGDs. Here we summarize recent developments and argue that more studies of WGD events in different invertebrate lineages are required to better understand the molecular evolution of metazoans.

Evolutionary History of Bilaterian FoxP Genes: Complex Ancestral Functions and Evolutionary Changes Spanning 2R-WGD in the Vertebrate Lineage

Human and fly FoxP homologs are well-known for their roles in the development of cognitive abilities. These findings have led to the hypothesis that the ancestral function of FoxP was in the development of cognitive neural circuits. However, complex brains in human and fly evolved independently, and the similar cognitive function of FoxP in human and fly may thus be interpreted as a result of convergent evolution. In addition, the 4 gnathostome FoxP paralogs also possess diverse developmental functions unrelated to neurodevelopment, which might have been overlooked in comparative studies of invertebrate FoxP homologs. To resolve these uncertainties, we set out to improve the phylogenetic reconstruction of vertebrate FoxP homologs and broaden the taxonomic sampling of gene expression profiling to include an invertebrate chordate, ambulacrarian deuterostomes, and a spiralian protostome. Using phylogenetic analysis combined with synteny mapping, we elaborated the hypothesis that the 4 FoxP paralogs arose through the 2R-WGD events shared by all gnathostome species. Based on this evolutionary scenario, we examined the FoxP expression pattern in amphioxus development and concluded that FoxP already had complex developmental functions across all germ layers in the chordate ancestor. Moreover, in sea urchin, hemichordate, and catenulid flatworm, FoxP was expressed in the gut prominently, in addition to the anterior neurogenic ectoderm. This surprising similarity shared among these distantly related species implies that FoxP may have a significant function in gut development in addition to the neural development function in the last common ancestor of bilaterians.

Genome of Kumamoto Oyster Crassostrea sikamea Provides Insights Into Bivalve Evolution and Environmental Adaptation

The Kumamoto oyster, Crassostrea sikamea, is a marine bivalve naturally distributed along the coasts of southern China and southern Japan, with a hatchery population that has been under domestication in the United States since its introduction from Japan in the 1940s. To understand its evolutionary history and environmental adaptation, we produced a chromosome-level genome assembly of C. sikamea and conducted whole-genome resequencing of 141 individuals from the US hatchery population and six wild populations from China and Japan. The assembled genome of C. sikamea has a size of 616 Mb covering all 10 chromosomes with a contig N50 of 4.21 Mb and a scaffold N50 of 62.25 Mb. Phylogenetic analysis indicated that C. sikamea diverged from the Crassostrea angulata and Crassostrea gigas clade about 9.9 million years ago. Synteny analysis revealed significant chromosomal rearrangements during bivalve evolution leading to oysters, but remarkable conservation of all 10 oyster chromosomes over ~180 million years, a surprising disparity in chromosomal evolution. Phylogenetic analysis produced three distinct clusters for the US, Japanese, and Chinese populations, with the US population closer to the Japanese population, confirming its origin. No differentiation was detected among the five Chinese populations, indicating strong gene flow. Between the US and Japan populations, 402 genes exhibited selection signals, including three myosin heavy chain genes that were also differentiated in domesticated lines of the eastern oyster, suggesting changes in these genes may be important for domestic production. Among the 768 genes showing selection signals between natural populations of Japan and China, genes related to stress response are most enriched, suggesting responding to environmental stress is critical for local adaptation. These findings provide insights into bivalve evolution and environmental adaptation, as well as useful resources for comparative genomics and genetic improvement of cultured Kumamoto oyster stocks.

Identification, molecular characterization and expression patterns of Cathepsin L in Yesso scallop (Patinopecten yessoensis) shell-infested by Polydora

Patinopecten yessoensis (Yesso scallop), one of the most important aquaculture molluscs in China, has recently suffered severe Polydora disease, causing economic losses. Cathepsin L (CatL), a cysteine protease, has important functions in immune responses in vertebrates and invertebrates. However, little is known regarding the structure and function of CatL in scallops. In this study, a CatL gene named PyCatL was first identified in the genome of P. yessoensis. Gene structure analysis of PyCatL revealed it had 8 exons and 7 introns and a full length of 7916 bp. The gene sequence was analysed, and typically conserved functional domains (signal peptide, inhibitor I29 domain, and peptidase C1 domain) and motifs (ERWNIN, GNYD and GCXGG) of CatL were all predicted in PyCatL, confirming the sequence as belonging to a CatL gene. Phylogenetic analysis showed the evolutionary status of CatL was consistent with the species taxonomy. PyCatL was expressed ubiquitously in all the tested tissues in this study, suggesting its involvement in a wide range of physiological processes. After Polydora infestation, PyCatL exhibited significant upregulation in various mantle regions at both mRNA and protein levels, contrasting with a notable decrease in gene expression in hemocytes. Additionally, the enzyme activity of PyCatL showed a significant increase in the mantle of diseased P. yessoensis. The results suggested a role for mantle tissue in response to Polydora infestation by upregulating expression of PyCatL. The study offers novel insights into the function of CatL in innate immunity in scallops.

Molluscan systematics: historical perspectives and the way ahead

Mollusca, the second-most diverse animal phylum, is estimated to have over 100,000 living species with great genetic and phenotypic diversity, a rich fossil record, and a considerable evolutionary significance. Early work on molluscan systematics was grounded in morphological and anatomical studies. With the transition from oligo gene Sanger sequencing to cutting-edge genomic sequencing technologies, molecular data has been increasingly utilised, providing abundant information for reconstructing the molluscan phylogenetic tree. However, relationships among and within most major lineages of Mollusca have long been contentious, often due to limited genetic markers, insufficient taxon sampling and phylogenetic conflict. Fortunately, remarkable progress in molluscan systematics has been made in recent years, which has shed light on how major molluscan groups have evolved. In this review of molluscan systematics, we first synthesise the current understanding of the molluscan Tree of Life at higher taxonomic levels. We then discuss how micromolluscs, which have adult individuals with a body size smaller than 5 mm, offer unique insights into Mollusca's vast diversity and deep phylogeny. Despite recent advancements, our knowledge of molluscan systematics and phylogeny still needs refinement. Further advancements in molluscan systematics will arise from integrating comprehensive data sets, including genome-scale data, exceptional fossils, and digital morphological data (including internal structures). Enhanced access to these data sets, combined with increased collaboration among morphologists, palaeontologists, evolutionary developmental biologists, and molecular phylogeneticists, will significantly advance this field.

Ascorbic acid transporter MmSLC23A2 functions to inhibit apoptosis via ROS scavenging in hard clam (Mercenaria mercenaria) under acute hypo-salinity stress

Solute carrier family 23 (SLC23) mediates cellular uptake of ascorbic acid, a crucial antioxidant protecting organisms against oxidative stress. Despite advances in understanding SLC23 in mammals, its physiological roles in bivalves remain poorly understood. Notably, euryhaline bivalves exhibit a significant expansion and positive selection of SLC23, highlighting the need for deeper investigation. Here, we identified 25 MmSLC23 in the hard clam genome. These genes predominantly cluster on chromosomes 3 and 14, with tandem duplications driving their expansion. All MmSLC23 localize to the plasma membrane, containing 9-14 transmembrane domains. Syntenic conservation of SLC23 was limited across order Venerida, with most expanded members being lineage-specific paralogs. Transcriptome analysis and fluorescence in situ hybridization revealed that MmSLC23 exhibited divergent expression patterns under acute and chronic salinity stress. Notably, RNA interference of MmSLC23A2 led to a significant reduction in intracellular ascorbic acid levels. Under acute hypo-salinity stress, increased ROS levels and elevated apoptosis rate were observed in MmSLC23A2 knockdown clams, as assessed by flow cytometry and transmission electron microscopy. These findings underscore the crucial role of SLC23 in mitigating oxidative damage and preventing premature apoptosis under acute salinity stress, offering new insights into the molecular mechanisms underlying the remarkable salinity adaptability of euryhaline bivalves.

Gene co-expression network analysis reveals key regulatory and responsive genes regulating the intensity of carotenoid coloration in scallop muscle

Carotenoids are biologically active pigments widely distributed in nature, playing crucial roles in the growth, development, immunity, and coloration of animals. As important nutrients, carotenoids are also considered important parameters for evaluating the economic value of farmed animals, including aquatic organisms. However, for marine animals that accumulate a large amount of specific carotenoids, the molecular mechanism underlying the bioavailability of carotenoids remains insufficiently explored, particularly with regard to the regulation of carotenoid pigmentation intensity. This study investigated the carotenoid coloration mechanism in the adductor muscle of "Haida golden scallop", a variety of Yesso scallop (Patinopecten yessoensis), with high carotenoid content and varying coloration intensity in adductor muscle. Through transcriptomic analysis and weighted gene co-expression network analysis (WGCNA), three carotenoid accumulation-associated modules (MEgreenyellow module, MEgreen, and MEsalmon) were identified. Two PARP9/14/15 genes, previously identified as crucial regulators of carotenoid accumulation at the genomic level, were identified as the hub genes of MEgreenyellow module, which exhibited a significant positive correlation with the concentrations of both pectenolone and pectenoxanthin. Specifically, PARP9/14/15-1 showed strong connectivity with genes involved in carotenoid absorption and transport, such as LRP1, SRB-like 1, ABCA3, and StARD; while PARP9/14/15-2 was associated with NPC1L1, a gene critical for carotenoid absorption. It is proposed that PARP9/14/15s may modulate the accumulation of pectenolone and pectenoxanthin in the adductor muscle of "Haida golden scallop" by regulating the expression of these carotenoid-related genes. Furthermore, genes within the other two carotenoid accumulation-associated modules were significantly enriched in pathways related to immune response (MEgreen) and DNA damage repair (MEsalmon), suggesting that these pathways may be in response to carotenoid accumulation levels. This study provides valuable insights into the molecular mechanisms underlying carotenoid accumulation and pigmentation intensity in bivalves, offering theoretical guidance for the breeding of carotenoid-rich aquaculture strains.

High-throughput neutralization measurements correlate strongly with evolutionary success of human influenza strains

Human influenza viruses rapidly acquire mutations in their hemagglutinin (HA) protein that erode neutralization by antibodies from prior exposures. Here, we use a sequencing-based assay to measure neutralization titers for 78 recent H3N2 HA strains against a large set of children and adult sera, measuring ~10,000 total titers. There is substantial person-to-person heterogeneity in the titers against different viral strains, both within and across age cohorts. The growth rates of H3N2 strains in the human population in 2023 are highly correlated with the fraction of sera with low titers against each strain. Notably, strain growth rates are less correlated with neutralization titers against pools of human sera, demonstrating the importance of population heterogeneity in shaping viral evolution. Overall, these results suggest that high-throughput neutralization measurements of human sera against many different viral strains can help explain the evolution of human influenza.

Chromosome-level genome assembly of the clam, Xishi tongue Coelomactra antiquata

Xishi tongue (Coelomactra antiquata), a commercially valuable marine bivalve, is distributed along the coastal waters of East Asia. In China, significant morphological and genetic differences have been observed between northern and southern populations. Overfishing and pollution have caused a severe decline in its natural populations, rendering the species endangered. In this study, we constructed the first chromosome-level genome of C. antiquata based on PacBio HiFi and Hi-C sequencing data. The assembled genome was 791.83 Mb in size, with the scaffold N50 of 44.05 Mb, and 99.79% of the sequences (790.13 Mb) were anchored to 19 chromosomes. A total of 24,592 protein-coding genes were predicted in the final assembly, of which 89.88% were functionally annotated. The BUSCO analysis revealed a genome completeness of 97.69%. The high-quality genome serves as a critical resource for advancing research on population genetics and germplasm conservation of this commercial shellfish, thereby facilitating sustainable management and conservation efforts.

A genome-based phylogeny for Mollusca is concordant with fossils and morphology

Extreme morphological disparity within Mollusca has long confounded efforts to reconstruct a stable backbone phylogeny for the phylum. Familiar molluscan groups-gastropods, bivalves, and cephalopods-each represent a diverse radiation with myriad morphological, ecological, and behavioral adaptations. The phylum further encompasses many more unfamiliar experiments in animal body-plan evolution. In this work, we reconstructed the phylogeny for living Mollusca on the basis of metazoan BUSCO (Benchmarking Universal Single-Copy Orthologs) genes extracted from 77 (13 new) genomes, including multiple members of all eight classes with two high-quality genome assemblies for monoplacophorans. Our analyses confirm a phylogeny proposed from morphology and show widespread genomic variation. The flexibility of the molluscan genome likely explains both historic challenges with their genomes and their evolutionary success.

Fusion, fission, and scrambling of the bilaterian genome in Bryozoa

Groups of orthologous genes are commonly found together on the same chromosome over vast evolutionary distances. This extensive physical gene linkage, known as macrosynteny, is seen between bilaterian phyla as divergent as Chordata, Echinodermata, Mollusca, and Nemertea. Here, we report a unique pattern of genome evolution in Bryozoa, an understudied phylum of colonial invertebrates. Using comparative genomics, we reconstruct the chromosomal evolutionary history of five bryozoans. Multiple ancient chromosome fusions followed by gene mixing led to the near-complete loss of bilaterian linkage groups in the ancestor of extant bryozoans. A second wave of rearrangements, including chromosome fission, then occurred independently in two bryozoan classes, further scrambling bryozoan genomes. We also discover at least five derived chromosomal fusion events shared between bryozoans and brachiopods, supporting the traditional but highly debated Lophophorata hypothesis and suggesting macrosynteny to be a potentially powerful source of phylogenetic information. Finally, we show that genome rearrangements led to the dispersion of genes from bryozoan Hox clusters onto multiple chromosomes. Our findings demonstrate that the canonical bilaterian genome structure has been lost across all studied representatives of an entire phylum, and reveal that linkage group fission can occur very frequently in specific lineages.

AMPK-mediated regulation of cardiac energy metabolism: Implications for thermotolerance in Argopecten irradians irradians

AMPK is a key regulator of metabolism in eukaryotes across various pathways related to energy regulation. Although extensive investigations of AMPK have been conducted in mammals and some model organisms, research on AMPK in scallops is comparatively limited. In this study, three AMPK family genes (AiAMPKα, AiAMPKβ and AiAMPKγ) in scallop Argopecten irradians irradians were identified through genome scanning. Structure prediction and phylogenetic analyses of AiAMPKs were performed to determine their structural features and evolutionary relationships. Spatiotemporal expression patterns of AiAMPKs at different developmental stages and in healthy adult tissues were analyzed to elucidate the function of AiAMPKs in bay scallops' growth and development. The spatiotemporally specific expression of AiAMPKs implied their important roles in growth and development of bay scallops. Heat stress experiment was performed to determine the regulations of AiAMPKs in four kinds of thermosensitive tissues. Expression profiles revealed distinct molecular mechanisms of AiAMPKs in different tissues in response to heat stress: significant down-regulations in mobile hemocytes, but dominant up-regulations occurring in stationary gills, mantles and hearts. Functional verification including knock-down of AiAMPKα and inhibition of AiAMPK was separately conducted in the thermotolerant tissue heart at the post-transcription and translation levels. The thermotolerant index Arrhenius break temperature (ABT) showed a significant decrease and the rate-amplitude product (RAP) peaked earlier in the individuals after RNAi targeting AiAMPKα, displaying an earlier transition to anaerobic metabolism under heat stress, indicating an impairing ability of aerobic metabolism. After AiAMPK inhibition, widespread down-regulations of genes in key energy metabolism pathways, RNA polymerase II-mediated transcription, and aminoacyl-tRNA synthesis pathways were obviously observed, revealing the post-translational inhibition of AiAMPK hindered cardiac energy metabolism, basal transcription and translation. Overall, our findings provide evidences for exploring the molecular mechanisms of energy regulation in thermotolerant traits in bay scallops under ongoing global warming.

MolluscDB 2.0: a comprehensive functional and evolutionary genomics database for over 1400 molluscan species

Mollusca represents the second-largest animal phylum but remains less explored genomically. The increase in high-quality genomes and diverse functional genomic data holds great promise for advancing our understanding of molluscan biology and evolution. To address the opportunities and challenges facing the molluscan research community in managing vast multi-omics resources, we developed MolluscDB 2.0 (http://mgbase.qnlm.ac), which integrates extensive functional genomic data and offers user-friendly tools for multilevel integrative and comparative analyses. MolluscDB 2.0 covers 1450 species across all eight molluscan classes and compiles ∼4200 datasets, making it the most comprehensive multi-omics resource for molluscs to date. MolluscDB 2.0 expands the layers of multi-omics data, including genomes, bulk transcriptomes, single-cell transcriptomes, proteomes, epigenomes and metagenomes. MolluscDB 2.0 also more than doubles the number of functional modules and analytical tools, updating 14 original modules and introducing 20 new, specialized modules. Overall, MolluscDB 2.0 provides highly valuable, open-access multi-omics platform for the molluscan research community, expediting scientific discoveries and deepening our understanding of molluscan biology and evolution.

The DnaJ-Hsp70-Hsp90 co-chaperon networks in scallops under toxic Alexandrium dinoflagellates exposure

Heat shock proteins (Hsps) are highly conserved molecular chaperones with essential roles against biotic and abiotic stressors. A large set of co-chaperons comprising J-domain proteins (DnaJs) regulate the ATPase cycle of Hsp70s with Hsp90s, together constituting a dynamic and functionally versatile network for protein folding/unfolding and regulation. Marine bivalves could accumulate and tolerate paralytic shellfish toxins (PSTs), the well-noted neurotoxins generated during harmful algal blooms. Here, 37 CfDnaJ and 35 PyDnaJ genes were systematically characterized in Zhikong scallop (Chlamys farreri) and Yesso scallop (Patinopecten yessoensis), the important aquaculture bivalve species in China. After exposure to different PST-producing dinoflagellates, Alexandrium minutum and Alexandrium catenella, diverse DnaJ regulations were presented in scallop hepatopancreas, accumulating incoming PSTs, and kidneys, transforming PSTs into higher toxic analogs. CfDnaJs' up-regulation in kidneys was similar with that in hepatopancreas, while their down-regulation was stronger in kidneys than in hepatopancreas, with CFA.38965.19.DNAJC30 being continuously down-regulated in both tissues of the two algae exposure. Moreover, PyDnaJs' up-regulation was only found in kidneys after A. catenella exposure, and PYE.10799.6.DNAJB1 was down-regulated in both tissues through the experiment. Together with the expression trends and correlation of DnaJ-Hsp70-Hsp90 genes, the organ-, toxin-, and species-dependent Hsp70B2 expressions were coordinately co-expressed with diverse DnaJ members, suggesting the functional diversity of scallop DnaJs with conserved Hsp70B2s in response to stress by PST-producing algae. Our results confirmed the regulated coordination of DnaJ-Hsp70B2 co-chaperons in scallops, and provided vital insights into the function and adaptation of scallop Hsps in response to PST stress.

Tissue-specific, temporal, and core gene-dependent expression patterns of Hsp70s reveal functional allocation in Chlamys farreri under heat stress

Heat shock proteins 70 KDa (Hsp70s) engage in a broad spectrum of cellular functions in response to various stressors. Marine bivalves face substantial threats from the rising seawater temperature attributed to global warming. In the present study, expression patterns of Hsp70s in Zhikong scallop Chlamys farreri (CfHsp70s) were determined in embryos and larvae at all developmental stages, in healthy adult tissues, and across four various tissues exposed to high temperature for acute and chronic periods through in silico analysis. Spatiotemporal expressions suggested CfHsp70s performed specific functional differentiations in scallop's development and growth. Regulatory expression patterns of CfHsp70s, characterized by predominant down-regulation in the mantle, gill and hemocytes, as well as contrasting up-regulation in the heart, suggest differential functional allocation of CfHsp70s among tissues in response to heat stress. Particularly, a core set of 14 CfHsp70s, especially the nine members of the Hsp70B2s, characterized by gene expansion, intron-less structure, shorter gene length, preference for hydrophilic amino acids, and coordinated expression profiles, was predominantly responsible for the inducible up-regulations observed across all four tissue types. Collectively, the tissue-specific, temporal and core gene-dependent expression patterns of CfHsp70s illustrate the functional allocation and molecular evolution of Hsp70 family members in Zhikong scallops.

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.

Carnosine Synthase (TsATPGD) Alleviates Lipid Peroxidation Under Transcriptional Control by an Nfe2-like Gene in Tridacna Squamosa

As an important mollusk in reef ecosystems, Tridacna squamosa forms pro-survival symbiotic relationships that hinge on an exquisite redox equilibrium between the host and the photosynthetic symbiont, zooxanthellae. The exact regulatory mechanisms thereof remain poorly understood. In this study, a novel Nfe2-like transcription factor in T. squamosa was identified and characterized with respect to its antioxidant and cytoprotective roles. Gene structure and phylogenetic analysis reveal that T. squamosa possesses a single transcription factor TsNfe2l in contrast to mammalian Nfe2l1 (Nrf1) and Nfe2l2 (Nrf2), belonging to protein members of the bZIP-NFE2 subfamily and functionally resembling the mammalian Nfe2l1. A conserved bZIP domain permits its binding to the antioxidant response element (ARE) in vitro and in HEK293T cells. Further analyses such as promoter prediction suggest that TsNfe2l target genes engage mainly in the regulation of multiple enzymes involved in antioxidation and allied pathways. Notably, TsNfe2l transcriptionally upregulates carnosine synthase (TsATPGD), which subsequently produces L-carnosine abundantly to shield cells from oxidative damage. Moreover, the blockage of TsNfe2l nucleic acid binding reduced the expression of TsATPGD and L-carnosine content in the gill, resulting in elevated lipid peroxidation. Collectively, our findings establish novel molecular insight into TsNfe2l as a critical regulator of redox homeostasis in T. squamosa through carnosine synthesis.

A Chromosome-Level Genome Assembly of Chiton Acanthochiton rubrolineatus (Chitonida, Polyplacophora, Mollusca)

(1) Background: Chitons (Mollusca, Polyplacophora) are relatively primitive species in Mollusca that allow the study of biomineralization. Although mitochondrial genomes have been isolated from Polyplacophora, there is no genomic information at the chromosomal level; (2) Methods: Here we report a chromosome-level genome assembly for Acanthochiton rubrolineatus using PacBio (Pacific Biosciences, United States) reads and high-throughput chromosome conformation capture (Hi-C) data; (3) Results: The assembly spans 1.08 Gb with a contig N50 of 3.63 Mb and 99.97% of the genome assigned to eight chromosomes. Among the 32,291 predicted genes, 76.32% had functional predictions. The divergence time of Brachiopoda and Mollusca was ~550.8 Mya (million years ago), and that of A. rubrolineatus and other mollusks was ~548.5 Mya; (4) Conclusions: This study not only offers high-quality reference sequences for the Acanthochiton rubrolineatus genome, but also establishes groundwork for investigating the mechanisms of Polyplacophora biomineralization and its evolutionary history. This research will aid in uncovering the genetic foundations of molluscan adaptations across diverse environments.

Srebp-1 bridges gonad development and lipid accumulation by regulating lipogenesis in noble scallop Chlamys nobilis

In bivalve, development of female gonad is accompanied with accumulating lipids which provided energy resource for non-feeding larvae development. As the major transcriptional regulators of lipid metabolism, Srebps play pivotal role in lipid homeostasis during oogenesis. However, little work was conducted on Srebps function in bivalves. The noble scallop Chlamys nobilis accumulated large amount of lipids in its gonad during oogenesis. Here, we identified a single Srebp gene (named Srebp-1) with a high similarity to human Srebp-1c. Disrupting Srebp-1 with Betulin (inhibiting the maturation of Srebp protein) repressed expression of lipogenic genes and de novo lipogenesis, and resulted in reduction of gonad index and lipid deposition, suggesting a crucial role of Srebp-1 for gonad development and lipid synthesis in female gonad. Additionally, scallops with Srebp-1 disruption released fewer eggs with a reduction in their lipid content and D-larvae formation, revealing an impair of fecundity caused by Srebp-1 disruption. Cold exposure stimulated lipid accumulation which required Srebp-1 to regulate de novo lipogenesis and lipid uptake, providing a crosstalk of Srebp-1 activity and environmental variation on lipid accumulation in noble scallop. Thus, our study identified Srebp-1 as a central regulator coordinating the lipid synthesis and accumulation with gonad development in noble scallop.

Functional allocation of Mitogen-activated protein kinases (MAPKs) unveils thermotolerance in scallop Argopecten irradians irradians

Global warming has significantly impacted agriculture, particularly in animal husbandry and aquaculture industry. Rising ocean temperatures due to global warming are severely affecting shellfish production, necessitating an understanding of how shellfish cope with thermal stress. The mitogen-activated protein kinases (MAPK) signaling pathway plays a crucial role in cell growth, differentiation, adaptation to environmental stress, inflammatory response, and managing high temperature stress. To investigate the function of MAPKs in bay scallops, a comparative genomics and bioinformatics approach identified three MAPK genes: AiERK, Aip38, and AiJNK. Structural and phylogenetic analyses of these proteins were conducted to determine their evolutionary relationships. Spatiotemporal expression patterns were examined at different developmental stages and in various tissues of healthy adult scallops. Additionally, the expression regulation of these genes was studied in selected tissues (hemocyte, gill, heart, mantle) following exposure to high temperatures (32 °C) for different durations (0 h, 6 h, 12 h, 24 h, 3 d, 6 d, 10 d). The spatiotemporal expressions of AiMAPKs were ubiquitous, with significant increases in AiERK expression observed at the umbo larval stage (3.09-fold), while Aip38 and AiJNK were identified as potential maternal effect genes. In adult scallops, different gene expression patterns of AiMAPKs were observed across eight tissues, with high expressions in the foot and gill, and lower expressions in the striated muscle. Following high temperature stress, AiMAPKs expressions in the gill and mantle were mainly up-regulated, while in the hemocyte, they were primarily down-regulated. These findings indicate time- and tissue-dependent expression patterns with functional allocation in response to different thermal durations. This study enhances our understanding of the function and evolution of AiMAPKs genes in shellfish and provides a theoretical basis for elucidating the energy regulation mechanism of bay scallops in response to high temperature stress.

Clam Genome and Transcriptomes Provide Insights into Molecular Basis of Morphological Novelties and Adaptations in Mollusks

Bivalve mollusks, comprising animals enclosed in two shell valves, are well-adapted to benthic life in many intertidal zones. Clams have evolved the buried lifestyle, which depends on their unique soft tissue structure and their wedge-shaped muscular foot and long extendible siphons. However, molecular mechanisms of adaptative phenotype evolution remain largely unknown. In the present study, we obtain the high-quality chromosome-level genome of Manila clam R. philippinarum, an economically important marine bivalve in many coastal areas. The genome is constructed by the Hi-C assisted assembly, which yields 19 chromosomes with a total of 1.17 Gb and BUSCO integrity of 92.23%. The de novo assembled genome has a contig N50 length of 307.7 kb and scaffold N50 of 59.5 Mb. Gene family expansion analysis reveals that a total of 24 single-copy gene families have undergone the significant expansion or contraction, including E3 ubiquitin ligase and dynein heavy chain. The significant expansion of transposable elements has been also identified, including long terminal repeats (LTR) and non-LTR retrotransposons. The comparative transcriptomics among different clam tissues reveals that extracellular matrix (ECM) receptors and neuroactive ligand receptors may play the important roles in tissue structural support and neurotransmission during their infaunal life. These findings of gene family expansion and tissue-specific expression may reflect the unique soft tissue structure of clams, suggesting the evolution of lineage-specific morphological novelties. The high-quality genome and transcriptome data of R. philippinarum will not only facilitate the genetic studies on clams but will also provide valuable information on morphological novelties in mollusks.

Advances in biotechnology and breeding innovations in China's marine aquaculture

Biotechnology is the key driving force behind the sustainable development of aquaculture, as biological innovation would significantly improve the capabilities of aquatic breeding and achieve independent and controllable seeding sources to ensure food safety. In this article, we have analyzed the current status and existing problems of marine aquaculture in China. Based on these data, we have summarized the recent (especially the last 10 years) biotechnological innovation and breeding progress of marine aquaculture in China, including whole genome sequencing, sex-related marker screening, genomic selection, and genome editing, as well as progress of improved marine fish varieties in China. Finally, the perspectives in this field have been discussed, and three future countermeasures have been proposed.

Chromosome-level genome assembly of the sacoglossan sea slug Elysia timida (Risso, 1818)

BACKGROUND

Sequencing and annotating genomes of non-model organisms helps to understand genome architecture, the genetic processes underlying species traits, and how these genes have evolved in closely-related taxa, among many other biological processes. However, many metazoan groups, such as the extremely diverse molluscs, are still underrepresented in the number of sequenced and annotated genomes. Although sequencing techniques have recently improved in quality and quantity, molluscs are still neglected due to difficulties in applying standardized protocols for obtaining genomic data.

RESULTS

In this study, we present the chromosome-level genome assembly and annotation of the sacoglossan sea slug species Elysia timida, known for its ability to store the chloroplasts of its food algae. In particular, by optimizing the long-read and chromosome conformation capture library preparations, the genome assembly was performed using PacBio HiFi and Arima HiC data. The scaffold and contig N50s, at 41.8 Mb and 1.92 Mb, respectively, are approximately 30-fold and fourfold higher compared to other published sacoglossan genome assemblies. Structural annotation resulted in 19,904 protein-coding genes, which are more contiguous and complete compared to publicly available annotations of Sacoglossa with respect to metazoan BUSCOs. We found no evidence for horizontal gene transfer (HGT), i.e. no photosynthetic genes encoded in the sacoglossan nucleus genome. However, we detected genes encoding polyketide synthases in E. timida, indicating that polypropionates are produced. HPLC-MS/MS analysis confirmed the presence of a large number of polypropionates, including known and yet uncharacterised compounds.

CONCLUSIONS

We can show that our methodological approach helps to obtain a high-quality genome assembly even for a "difficult-to-sequence" organism, which may facilitate genome sequencing in molluscs. This will enable a better understanding of complex biological processes in molluscs, such as functional kleptoplasty in Sacoglossa, by significantly improving the quality of genome assemblies and annotations.

Core genes of biomineralization and cis-regulatory long non-coding RNA regulate shell growth in bivalves

INTRODUCTION

Bivalve molluscs are abundant in marine and freshwater systems and contribute essential ecosystem services. They are characterized by an exuberant diversity of biomineralized shells and typically have two symmetric valves (a.k.a shells), but oysters (Ostreidae), some clams (Anomiidae and Chamidae) and scallops (Pectinida) have two asymmetrical valves. Predicting and modelling the likely consequences of ocean acidification on bivalve survival, biodiversity and aquaculture makes understanding shell biomineralization and its regulation a priority.

OBJECTIVES

This study aimed to a) exploit the atypical asymmetric shell growth of some bivalves and through comparative analysis of the genome and transcriptome pinpoint candidate biomineralization-related genes and regulatory long non-coding RNAs (LncRNAs) and b) demonstrate their roles in regulating shell biomineralization/growth.

METHODS

Meta-analysis of genomes, de novo generated mantle transcriptomes or transcriptomes and proteomes from public databases for six asymmetric to symmetric bivalve species was used to identify biomineralization-related genes. Bioinformatics filtering uncovered genes and regulatory modules characteristic of bivalves with asymmetric shells and identified candidate biomineralization-related genes and lncRNAs with a biased expression in asymmetric valves. A shell regrowth model in oyster and gene silencing experiments, were used to characterize candidate gene function.

RESULTS

Shell matrix genes with asymmetric expression in the mantle of the two valves were identified and unique cis-regulatory lncRNA modules characterized in Ostreidae. LncRNAs that regulate the expression of the tissue inhibitor of metalloproteinases gene family (TIMPDR) and of the shell matrix protein domain family (SMPDR) were identified. In vitro and in vivo silencing experiments revealed the candidate genes and lncRNA were associated with divergent shell growth rates and modified the microstructure of calcium carbonate (CaCO3) crystals.

CONCLUSION

LncRNAs are putative regulatory factors of the bivalve biomineralization toolbox. In the Ostreidae family of bivalves biomineralization-related genes are cis-regulated by lncRNA and modify the planar growth rate and spatial orientation of crystals in the shell.

Effects of Vibrio harveyi infection on the biochemistry, histology and transcriptome in the hepatopancreas of ivory shell (Babylonia areolata)

The ivory shell (Babylonia areolata) is one of the most promising high quality marine products. However, ivory shell is susceptible to Vibrio harveyi infection during the culture period. In this study, we investigated the biochemical indicators, histological changes and transcriptomic response in the hepatopancreas of ivory shells from the PBS control group (PC) and infection group (A3) with 1 × 109 CFU/mL V. harveyi after 24 h. Results showed that compared to the PC group, biochemical indicators, including malondialdehyde (MDA), reactive oxygen species (ROS), acid phosphatase (ACP), and Caspase 3 (Casp-3) were significantly increased (p < 0.05) in A3 group after V. harveyi infection for 24 h. Compared with the PC group, the hepatopancreas of A3 group were seriously damaged, the columnar epithelial cells of the tissue were enlarged, the space of digestive cells was increased, and vacuolar cavities appeared. A total of 95,581 unigenes were obtained and 2949 (1787 up-regulated and 1162 down-regulated) differential expressed genes (DEGs) were identified in the A3 group. GO and KEGG enrichment analysis showed that DEGs were mainly enriched in immune system process (GO:0002376), antioxidant activity (GO:0016209), lysosome (ko04142), toll and IMD signaling pathway (ko04624), and etc. These biological functions and pathways are associated with immune and inflammatory responses and apoptosis. 12 DEGs were randomly selected for real-time quantitative PCR (RT-qPCR) validation, and the expression profiles of these DEGs were consistent with the transcriptome data, confirming the accuracy and reliability of the transcriptome results. In summary, V. harveyi infection of ivory shells inducing oxidative stress, leading to severe hepatopancreatic damage, stimulating glutathione production to neutralize excessive ROS, and stimulating antimicrobial peptides production to counteract the deleterious effects of bacterial infection, which in turn modifying the immune and inflammatory response, ultimately resulting in apoptosis. This study provided valuable information to explore the immune regulation mechanism after V. harveyi infection and established molecular basis to support the prevention of V. harveyi infection.

Chromosome-level genome assembly of the bay scallop Argopecten irradians

The bay scallop, Argopecten irradians, is a species of major commercial, cultural, and ecological importance. It is endemic to the eastern coast of the United States, but has also been introduced to China, where it supports a significant aquaculture industry. Here, we provide an annotated chromosome-level reference genome assembly for the bay scallop, assembled using PacBio and Hi-C data. The total genome size is 845.9 Mb, distributed over 1,503 scaffolds with a scaffold N50 of 44.3 Mb. The majority (92.9%) of the assembled genome is contained within the 16 largest scaffolds, corresponding to the 16 chromosomes confirmed by Hi-C analysis. The assembly also includes the complete mitochondrial genome. Approximately 36.2% of the genome consists of repetitive elements. The BUSCO analysis showed a completeness of 96.2%. We identified 33,772 protein-coding genes. This genome assembly will be a valuable resource for future research on evolutionary dynamics, adaptive mechanisms, and will support genome-assisted breeding, contributing to the conservation and management of this iconic species in the face of environmental and pathogenic challenges.

Cell type and cell signaling innovations underlying mammalian pregnancy

How fetal and maternal cell types have co-evolved to enable mammalian placentation poses a unique evolutionary puzzle. Here, we present a multi-species atlas integrating single-cell transcriptomes from six species bracketing therian mammal diversity. We find that invasive trophoblasts share a gene-expression signature across eutherians, and evidence that endocrine decidual cells evolved stepwise from an immunomodulatory cell type retained in Tenrec with affinity to human decidua of menstruation. We recover evolutionary patterns in ligand-receptor signaling: fetal and maternal cells show a pronounced tendency towards disambiguation, but a predicted arms race dynamic between them is limited. We reconstruct cell communication networks of extinct mammalian ancestors, finding strong integration of fetal trophoblast into maternal networks. Together, our results reveal a dynamic history of cell type and signaling evolution.

Synopsis

The fetal-maternal interface is one of the most intense loci of cell-cell signaling in the human body. Invasion of cells from the fetal placenta into the uterus, and the corresponding transformation of maternal tissues called decidualization, first evolved in the stem lineage of eutherian mammals( 1 , 2 ). Single-cell studies of the human fetal-maternal interface have provided new insight into the cell type diversity and cell-cell interactions governing this chimeric organ( 3-5 ). However, the fetal-maternal interface is also one of the most rapidly evolving, and hence most diverse, characters among mammals( 6 ), and an evolutionary analysis is missing. Here, we present and compare single-cell data from the fetal-maternal interface of species bracketing key events in mammal phylogeny: a marsupial (opossum, Monodelphis domestica ), the afrotherian Tenrec ecaudatus, and four Euarchontoglires - guinea pig and mouse (Rodentia) together with recent macaque and human data (primates) ( 4 , 5 , 7 ). We infer cell type homologies, identify a gene-expression signature of eutherian invasive trophoblast conserved over 99 million years, and discover a predecidual cell in the tenrec which suggests stepwise evolution of the decidual stromal cell. We reconstruct ancestral cell signaling networks, revealing the integration of fetal cell types into the interface. Finally, we test two long-standing theoretical predictions, the disambiguation hypothesis( 8 ) and escalation hypothesis( 9 ), at transcriptome-wide scale, finding divergence between fetal and maternal signaling repertoires but arms race dynamics restricted to a small subset of ligand-receptor pairs. In so doing, we trace the co-evolutionary history of cell types and their signaling across mammalian viviparity.

A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence

The planarian Schmidtea mediterranea is being studied as a model species for regeneration, but the assembly of planarian genomes remains challenging. Here, we report a high-quality haplotype-phased, chromosome-scale genome assembly of the sexual S2 strain of S. mediterranea and high-quality chromosome-scale assemblies of its three close relatives, S. polychroa, S. nova, and S. lugubris. Using hybrid gene annotations and optimized ATAC-seq and ChIP-seq protocols for regulatory element annotation, we provide valuable genome resources for the planarian research community and a first comparative perspective on planarian genome evolution. Our analyses reveal substantial divergence in protein-coding sequences and regulatory regions but considerable conservation within promoter and enhancer annotations. We also find frequent retrotransposon-associated chromosomal inversions and interchromosomal translocations within the genus Schmidtea and, remarkably, independent and nearly complete losses of ancestral metazoan synteny in Schmidtea and two other flatworm groups. Overall, our results suggest that platyhelminth genomes can evolve without syntenic constraints.

Annelid Comparative Genomics and the Evolution of Massive Lineage-Specific Genome Rearrangement in Bilaterians

The organization of genomes into chromosomes is critical for processes such as genetic recombination, environmental adaptation, and speciation. All animals with bilateral symmetry inherited a genome structure from their last common ancestor that has been highly conserved in some taxa but seemingly unconstrained in others. However, the evolutionary forces driving these differences and the processes by which they emerge have remained largely uncharacterized. Here, we analyze genome organization across the phylum Annelida using 23 chromosome-level annelid genomes. We find that while many annelid lineages have maintained the conserved bilaterian genome structure, the Clitellata, a group containing leeches and earthworms, possesses completely scrambled genomes. We develop a rearrangement index to quantify the extent of genome structure evolution and show that, compared to the last common ancestor of bilaterians, leeches and earthworms have among the most highly rearranged genomes of any currently sampled species. We further show that bilaterian genomes can be classified into two distinct categories-high and low rearrangement-largely influenced by the presence or absence, respectively, of chromosome fission events. Our findings demonstrate that animal genome structure can be highly variable within a phylum and reveal that genome rearrangement can occur both in a gradual, stepwise fashion, or rapid, all-encompassing changes over short evolutionary timescales.

A chromosome-level genome assembly of the disco clam, Ctenoides ales

The bivalve subclass Pteriomorphia, which includes the economically important scallops, oysters, mussels, and ark clams, exhibits extreme ecological, morphological, and behavioral diversity. Among this diversity are five morphologically distinct eye types, making Pteriomorphia an excellent setting to explore the molecular basis for the evolution of novel traits. Of pteriomorphian bivalves, Limida is the only order lacking genomic resources, greatly limiting the potential phylogenomic analyses related to eyes and phototransduction. Here, we present a limid genome assembly, the disco clam, Ctenoides ales (C. ales), which is characterized by invaginated eyes, exceptionally long tentacles, and a flashing light display. This genome assembly was constructed with PacBio long reads and Dovetail Omni-CTM proximity-ligation sequencing. The final assembly is ∼2.3Gb and over 99% of the total length is contained in 18 pseudomolecule scaffolds. We annotated 41,064 protein coding genes and reported a BUSCO completeness of 91.9% for metazoa_obd10. Additionally, we report a complete and annotated mitochondrial genome, which also had been lacking from Limida. The ∼20Kb mitogenome has 12 protein coding genes, 22 tRNAs, 2 rRNA genes, and a 1,589 bp duplicated sequence containing the origin of replication. The C. ales nuclear genome size is substantially larger than other pteriomorphian genomes, mainly accounted for by transposable element sequences. We inventoried the genome for opsins, the signaling proteins that initiate phototransduction, and found that, unlike its closest eyed-relatives, the scallops, C. ales lacks duplication of the rhabdomeric Gq-protein-coupled opsin that is typically used for invertebrate vision. In fact, C. ales has uncharacteristically few opsins relative to the other pteriomorphian families, all of which have unique expansions of xenopsins, a recently discovered opsin subfamily. This chromosome-level assembly, along with the mitogenome, is a valuable resource for comparative genomics and phylogenetics in bivalves and particularly for the understudied but charismatic limids.

Testing ultraconserved elements (UCEs) for phylogenetic inference across bivalves (Mollusca: Bivalvia)

Bivalves constitute an important resource for fisheries and as cultural objects. Bivalve phylogenetics has had a long tradition using both morphological and molecular characters, and genomic resources are available for a good number of commercially important species. However, relationships among bivalve families have been unstable and major conflicting results exist between mitogenomics and results based on Sanger-based amplicon sequencing or phylotranscriptomics. Here we design and test an ultraconserved elements probe set for the class Bivalvia with the aim to use hundreds of loci without the need to sequence full genomes or transcriptomes, which are expensive and complex to analyze, and to open bivalve phylogenetics to museum specimens. Our probe set successfully captured 1,513 UCEs for a total of 263,800 bp with an average length of 174.59 ± 3.44 per UCE (ranging from 28 to 842 bp). Phylogenetic testing of this UCE probe set across Bivalvia and within the family Donacidae using different data matrices and methods for phylogenetic inference shows promising results at multiple taxonomic levels. In addition, our probe set was able to capture large numbers of UCEs for museum specimens collected before 1900 and from DNAs properly stored, of which many museums and laboratories are well stocked. Overall, this constitutes a novel and useful resource for bivalve phylogenetics.

Myocyte enhancer factor 2 upregulates expression of myostatin promoter in Yesso scallop, Patinopecten yessoensis

Myostatin (MSTN) plays an important role in muscle development in animals, especially for mammals and fishes. However, little information has been reported on the regulation of MSTN in marine invertebrates, such as bivalves. In the present study, we cloned the MSTN promoter sequence of Yesso scallop Patinopecten yessoensis, identifying 4 transcription start sites, eleven TATA boxes and one E-box. Additionally, transcription factor binding sites, including myocyte enhancer factor 2 (MEF2) and POU homeodomain protein, were identified. The interaction between the MSTN promoter and MEF2 was analyzed to reveal the transcriptional activity of different fragment sizes of promoters through the dual-luciferase reporter assays. The highest transcriptional activity was found in recombinant plasmids with the most MEF2 binding sites, indicating that this transcription factor upregulates MSTN in Yesso scallop. This study provides new insight into the regulation of muscle growth and development in this species.

Tracking the hologenome dynamics in aquatic invertebrates by the holo-2bRAD approach

The "hologenome" concept is an increasingly popular way of thinking about microbiome-host for marine organisms. However, it is challenging to track hologenome dynamics because of the large amount of material, with tracking itself usually resulting in damage or death of the research object. Here we show the simple and efficient holo-2bRAD approach for the tracking of hologenome dynamics in marine invertebrates (i.e., scallop and shrimp) from one holo-2bRAD library. The stable performance of our approach was shown with high genotyping accuracy of 99.91% and a high correlation of r > 0.99 for the species-level profiling of microorganisms. To explore the host-microbe association underlying mass mortality events of bivalve larvae, core microbial species changed with the stages were found, and two potentially associated host SNPs were identified. Overall, our research provides a powerful tool with various advantages (e.g., cost-effective, simple, and applicable for challenging samples) in genetic, ecological, and evolutionary studies.

Emerging trends in the study of spiralian larvae

Many animals undergo indirect development, where their embryogenesis produces an intermediate life stage, or larva, that is often free-living and later metamorphoses into an adult. As their adult counterparts, larvae can have unique and diverse morphologies and occupy various ecological niches. Given their broad phylogenetic distribution, larvae have been central to hypotheses about animal evolution. However, the evolution of these intermediate forms and the developmental mechanisms diversifying animal life cycles are still debated. This review focuses on Spiralia, a large and diverse clade of bilaterally symmetrical animals with a fascinating array of larval forms, most notably the archetypical trochophore larva. We explore how classic research and modern advances have improved our understanding of spiralian larvae, their development, and evolution. Specifically, we examine three morphological features of spiralian larvae: the anterior neural system, the ciliary bands, and the posterior hyposphere. The combination of molecular and developmental evidence with modern high-throughput techniques, such as comparative genomics, single-cell transcriptomics, and epigenomics, is a promising strategy that will lead to new testable hypotheses about the mechanisms behind the evolution of larvae and life cycles in Spiralia and animals in general. We predict that the increasing number of available genomes for Spiralia and the optimization of genome-wide and single-cell approaches will unlock the study of many emerging spiralian taxa, transforming our views of the evolution of this animal group and their larvae.

The gastropod Lottia peitaihoensis as a model to study the body patterning of trochophore larvae

The body patterning of trochophore larvae is important for understanding spiralian evolution and the origin of the bilateral body plan. However, considerable variations are observed among spiralian lineages, which have adopted varied strategies to develop trochophore larvae or even omit a trochophore stage. Some spiralians, such as patellogastropod mollusks, are suggested to exhibit ancestral traits by producing equal-cleaving fertilized eggs and possessing "typical" trochophore larvae. In recent years, we developed a potential model system using the patellogastropod Lottia peitaihoensis (= Lottia goshimai). Here, we introduce how the species were selected and establish sources and techniques, including gene knockdown, ectopic gene expression, and genome editing. Investigations on this species reveal essential aspects of trochophore body patterning, including organizer signaling, molecular and cellular processes connecting the various developmental functions of the organizer, the specification and behaviors of the endomesoderm and ectomesoderm, and the characteristic dorsoventral decoupling of Hox expression. These findings enrich the knowledge of trochophore body patterning and have important implications regarding the evolution of spiralians as well as bilateral body plans.

Chromosome-level genome assemblies of 2 hemichordates provide new insights into deuterostome origin and chromosome evolution

Deuterostomes are a monophyletic group of animals that includes Hemichordata, Echinodermata (together called Ambulacraria), and Chordata. The diversity of deuterostome body plans has made it challenging to reconstruct their ancestral condition and to decipher the genetic changes that drove the diversification of deuterostome lineages. Here, we generate chromosome-level genome assemblies of 2 hemichordate species, Ptychodera flava and Schizocardium californicum, and use comparative genomic approaches to infer the chromosomal architecture of the deuterostome common ancestor and delineate lineage-specific chromosomal modifications. We show that hemichordate chromosomes (1N = 23) exhibit remarkable chromosome-scale macrosynteny when compared to other deuterostomes and can be derived from 24 deuterostome ancestral linkage groups (ALGs). These deuterostome ALGs in turn match previously inferred bilaterian ALGs, consistent with a relatively short transition from the last common bilaterian ancestor to the origin of deuterostomes. Based on this deuterostome ALG complement, we deduced chromosomal rearrangement events that occurred in different lineages. For example, a fusion-with-mixing event produced an Ambulacraria-specific ALG that subsequently split into 2 chromosomes in extant hemichordates, while this homologous ALG further fused with another chromosome in sea urchins. Orthologous genes distributed in these rearranged chromosomes are enriched for functions in various developmental processes. We found that the deeply conserved Hox clusters are located in highly rearranged chromosomes and that maintenance of the clusters are likely due to lower densities of transposable elements within the clusters. We also provide evidence that the deuterostome-specific pharyngeal gene cluster was established via the combination of 3 pre-assembled microsyntenic blocks. We suggest that since chromosomal rearrangement events and formation of new gene clusters may change the regulatory controls of developmental genes, these events may have contributed to the evolution of diverse body plans among deuterostomes.

Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach

The forthcoming massive genome data generated by the Earth BioGenome Project will open up a new era of comparative genomics, for which genome synteny analysis provides an important framework. Profiling genome synteny represents an essential step in elucidating genome architecture, regulatory blocks/elements and their evolutionary history. Here we describe PanSyn, ( https://github.com/yhw320/PanSyn ), the most comprehensive and up-to-date genome synteny pipeline, providing step-by-step instructions and application examples to demonstrate its usage. PanSyn inherits both basic and advanced functions from existing popular tools, offering a user-friendly, highly customized approach for genome macrosynteny analysis and integrated pan-evolutionary and regulatory analysis of genome architecture, which are not yet available in public synteny software or tools. The advantages of PanSyn include: (i) advanced microsynteny analysis by functional profiling of microsynteny genes and associated regulatory elements; (ii) comprehensive macrosynteny analysis, including the inference of karyotype evolution from ancestors to extant species; and (iii) functional integration of microsynteny and macrosynteny for pan-evolutionary profiling of genome architecture and regulatory blocks, as well as integration with external functional genomics datasets from three- or four-dimensional genome and ENCODE projects. PanSyn requires basic knowledge of the Linux environment and Perl programming language and the ability to access a computer cluster, especially for large-scale genomic comparisons. Our protocol can be easily implemented by a competent graduate student or postdoc and takes several days to weeks to execute for dozens to hundreds of genomes. PanSyn provides yet the most comprehensive and powerful tool for integrated evolutionary and functional genomics.

Revisiting the evolution of Family B1 GPCRs and ligands: Insights from mollusca

Family B1 G protein-coupled receptors (GPCRs) are one of the most well studied neuropeptide receptor families since they play a central role in many biological processes including endocrine, gastrointestinal, cardiovascular and reproduction in animals. The genes for these receptors emerged from a common ancestral gene in bilaterian genomes and evolved via gene/genome duplications and deletions in vertebrate and invertebrate genomes. Their existence and function have mostly been characterized in vertebrates and few studies exist in invertebrate species. Recently, an increased interest in molluscs, means a series of genomes have become available, and since they are less modified than insect and nematode genomes, they are ideal to explore the origin and evolution of neuropeptide gene families. This review provides an overview of Family B1 GPCRs and their peptide ligands and incorporates new data obtained from Mollusca genomes and taking a comparative approach challenges existing models on their origin and evolution.

Somatostatin Receptor Gene Functions in Growth Regulation in Bivalve Scallop and Clam

Bivalves hold an important role in marine aquaculture and the identification of growth-related genes in bivalves could contribute to a better understanding of the mechanism governing their growth, which may benefit high-yielding bivalve breeding. Somatostatin receptor (SSTR) is a conserved negative regulator of growth in vertebrates. Although SSTR genes have been identified in invertebrates, their involvement in growth regulation remains unclear. Here, we identified seven SSTRs (PySSTRs) in the Yesso scallop, Patinopecten yessoensis, which is an economically important bivalve cultured in East Asia. Among the three PySSTRs (PySSTR-1, -2, and -3) expressed in adult tissues, PySSTR-1 showed significantly lower expression in fast-growing scallops than in slow-growing scallops. Then, the function of this gene in growth regulation was evaluated in dwarf surf clams (Mulinia lateralis), a potential model bivalve cultured in the lab, via RNA interference (RNAi) through feeding the clams Escherichia coli containing plasmids expressing double-stranded RNAs (dsRNAs) targeting MlSSTR-1. Suppressing the expression of MlSSTR-1, the homolog of PySSTR-1 in M. lateralis, resulted in a significant increase in shell length, shell width, shell height, soft tissue weight, and muscle weight by 20%, 22%, 20%, 79%, and 92%, respectively. A transcriptome analysis indicated that the up-regulated genes after MlSSTR-1 expression inhibition were significantly enriched in the fat digestion and absorption pathway and the insulin pathway. In summary, we systemically identified the SSTR genes in P. yessoensis and revealed the growth-inhibitory role of SSTR-1 in bivalves. This study indicates the conserved function of somatostatin signaling in growth regulation, and ingesting dsRNA-expressing bacteria is a useful way to verify gene function in bivalves. SSTR-1 is a candidate target for gene editing in bivalves to promote growth and could be used in the breeding of fast-growing bivalves.

Functional Analysis of β-Carotene Oxygenase 2 (BCO2) Gene in Yesso Scallop (Patinopecten yessoensis)

Carotenoids are essential nutrients for humans and animals, and carotenoid coloration represents an important meat quality parameter for many farmed animals. Increasingly, studies have demonstrated that vertebrate carotenoid cleavage oxygenases (CCOs) are essential enzymes in carotenoid metabolism and are therefore potential candidate genes for improving carotenoid deposition. However, our understanding of carotenoid bioavailability and CCOs functions in invertebrates, particularly marine species, is currently quite limited. We previously identified that a CCO homolog, PyBCO-like 1, was the causal gene for carotenoid coloration in the 'Haida golden scallop', a variety of Yesso scallop (Patinopecten yessoensis) characterized by carotenoid enrichment. Here, we found that another CCO-encoding gene named PyBCO2 (β-carotene oxygenase 2) was widely expressed in P. yessoensis organs/tissues, with the highest expression in striated muscle. Inhibiting BCO2 expression in P. yessoensis through RNA interference led to increased carotenoid (pectenolone and pectenoxanthin) deposition in the striated muscle, and the color of the striated muscle changed from white to light orange. Our results indicate that PyBCO2 might be a candidate gene used for improving carotenoid content in normal Yesso scallops, and also in 'Haida golden scallops'.

The First High-Quality Genome Assembly of Freshwater Pearl Mussel Sinohyriopsis cumingii: New Insights into Pearl Biomineralization

China leads the world in freshwater pearl production, an industry in which the triangle sail mussel (Sinohyriopsis cumingii) plays a pivotal role. In this paper, we report a high-quality chromosome-level genome assembly of S. cumingii with a size of 2.90 Gb-the largest yet reported among bivalves-and 89.92% anchorage onto 19 linkage groups. The assembled genome has 37,696 protein-coding genes and 50.86% repeat elements. A comparative genomic analysis revealed expansions of 752 gene families, mostly associated with biomineralization, and 237 genes under strong positive selection. Notably, the fibrillin gene family exhibited gene family expansion and positive selection simultaneously, and it also exhibited multiple high expressions after mantle implantation by transcriptome analysis. Furthermore, RNA silencing and an in vitro calcium carbonate crystallization assay highlighted the pivotal role played by one fibrillin gene in calcium carbonate deposition and aragonite transformation. This study provides a valuable genomic resource and offers new insights into the mechanism of pearl biomineralization.

Chromosome-level genome assembly of Oncomelania hupensis: the intermediate snail host of Schistosoma japonicum

BACKGROUND

Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China, the Philippines and Indonesia. Oncomelania hupensis (Gastropoda: Pomatiopsidae) is the unique intermediate host of S. japonicum. A complete genome sequence of O. hupensis will enable the fundamental understanding of snail biology as well as its co-evolution with the S. japonicum parasite. Assembling a high-quality reference genome of O. hupehensis will provide data for further research on the snail biology and controlling the spread of S. japonicum.

METHODS

The draft genome was de novo assembly using the long-read sequencing technology (PacBio Sequel II) and corrected with Illumina sequencing data. Then, using Hi-C sequencing data, the genome was assembled at the chromosomal level. CAFE was used to do analysis of contraction and expansion of the gene family and CodeML module in PAML was used for positive selection analysis in protein coding sequences.

RESULTS

A total length of 1.46 Gb high-quality O. hupensis genome with 17 unique full-length chromosomes (2n = 34) of the individual including a contig N50 of 1.35 Mb and a scaffold N50 of 75.08 Mb. Additionally, 95.03% of these contig sequences were anchored in 17 chromosomes. After scanning the assembled genome, a total of 30,604 protein-coding genes were predicted. Among them, 86.67% were functionally annotated. Further phylogenetic analysis revealed that O. hupensis was separated from a common ancestor of Pomacea canaliculata and Bellamya purificata approximately 170 million years ago. Comparing the genome of O. hupensis with its most recent common ancestor, it showed 266 significantly expanded and 58 significantly contracted gene families (P < 0.05). Functional enrichment of the expanded gene families indicated that they were mainly involved with intracellular, DNA-mediated transposition, DNA integration and transposase activity.

CONCLUSIONS

Integrated use of multiple sequencing technologies, we have successfully constructed the genome at the chromosomal-level of O. hupensis. These data will not only provide the compressive genomic information, but also benefit future work on population genetics of this snail as well as evolutional studies between S. japonicum and the snail host.

Chromosome-level genome assembly and annotation of rare and endangered tropical bivalve, Tridacna crocea

Tridacna crocea is an ecologically important marine bivalve inhabiting tropical coral reef waters. High quality and available genomic resources will help us understand the population structure and genetic diversity of giant clams. This study reports a high-quality chromosome-scale T. crocea genome sequence of 1.30 Gb, with a scaffold N50 and contig N50 of 56.38 Mb and 1.29 Mb, respectively, which was assembled by combining PacBio long reads and Hi-C sequencing data. Repetitive sequences cover 71.60% of the total length, and a total of 25,440 protein-coding genes were annotated. A total of 1,963 non-coding RNA (ncRNA) were determined in the T. crocea genome, including 62 micro RNA (miRNA), 58 small nuclear RNA (snRNA), 83 ribosomal RNA (rRNA), and 1,760 transfer RNA (tRNA). Phylogenetic analysis revealed that giant clams diverged from oyster about 505.7 Mya during the evolution of bivalves. The genome assembly presented here provides valuable genomic resources to enhance our understanding of the genetic diversity and population structure of giant clams.

Genome-wide investigation of the DMRT gene family sheds new insight into the regulation of sex differentiation in spotted knifejaw (Oplegnathus punctatus) with fusion chromosomes (Y)

The role of the DMRT family in male sex determination and differentiation is significant, but its regulatory role in spotted knifejaw with Y fusion chromosomes remains unclear. Through genome-wide scanning, transcriptome analysis, qPCR, FISH, and RNA interference (RNAi), we investigated the DMRT family and the dmrt1-based sex regulation network. Seven DMRTs were identified (DMRT1/2 (2a,2b)/6, DMRT4/5, DMRT3), and dmrt gene dispersion among chromosomes is possibly driven by three whole-genome duplications. Transcriptome analysis enriched genes were associated with sex regulation and constructed a network associated with dmrt1. qPCR and FISH results showed the expression dimorphism of sex-related genes in dmrt-related regulatory networks. RNAi experiments indicated a distinct sex regulation mode in spotted knifejaw. Dmrt1 knockdown upregulated male-related genes (sox9a, sox9b, dmrt1, amh, amhr2) and hsd11b2 expression, which is critical for androgen synthesis. Amhr2 is located on the heterozygous chromosome (Y) and is specifically localized in primary spermatocytes, and is extremely upregulated after dmrt1 knockdown which suggested besides the important role of dmrt1 in male differentiation, the amhr2 along with amhr2/amh system, also play important regulatory roles in maintaining high expression of the hsd11b2 and male differentiation. This study aims to further investigate sex regulatory mechanisms in species with fusion chromosomes.

Progress in understanding of relationship between inflammation and tumors

Over the past decade, there has been clear evidence that inflammation plays a key role in tumorigenesis. Tumor extrinsic inflammation is caused by many factors, including bacterial and viral infections, autoimmune diseases, obesity, smoking, excessive alcohol consumption, etc., all of which can increase cancer risk and stimulate malignant progression. Conversely, inflammation inherent in cancer or caused by cancer can be triggered by cancer-initiating mutations and can promote malignant progression through recruitment and activation of inflammatory cells. Both exogenous and endogenous inflammation can lead to immunosuppression, thus providing a preferred opportunity for tumor development. Studies have confirmed that chronic inflammation is involved in various steps of tumorigenesis, including cell transformation, promotion, survival, prolifer-ation, invasion, angiogenesis, and metastasis. Recent research has shed new light on the molecular and cellular circuits between inflammation and cancer. Two pathways have been preliminarily identified: Intrinsic and extrinsic. In the intrinsic pathway, genetic events leading to tumors initiate the expression of inflammatory related programs and guide the construction of the inflammatory microenvironment. In the extrinsic pathway, inflammatory conditions promote the development of cancer. This article reviews the recent progress in the understanding of the relationship between inflammation and tumors.

A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes

BACKGROUND

How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum have long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species.

RESULTS

The final assembled and filtered Berghia genome is comparable to other high-quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes) and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low.

CONCLUSIONS

Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.

Chromosome-level genome assemblies of two littorinid marine snails indicate genetic basis of intertidal adaptation and ancient karyotype evolved from bilaterian ancestors

Living in the intertidal environment, littorinid snails are excellent models for understanding genetic mechanisms underlying adaptation to harsh fluctuating environments. Furthermore, the karyotypes of littorinid snails, with the same chromosome number as the presumed bilaterian ancestor, make them valuable for investigating karyotype evolution from the bilaterian ancestor to mollusks. Here, we generated high-quality, chromosome-scale genome assemblies for 2 littorinid marine snails, Littorina brevicula (927.94 Mb) and Littoraria sinensis (882.51 Mb), with contig N50 of 3.43 Mb and 2.31 Mb, respectively. Comparative genomic analyses identified 92 expanded gene families and 85 positively selected genes as potential candidates possibly associated with intertidal adaptation in the littorinid lineage, which were functionally enriched in stimulus responses, innate immunity, and apoptosis process regulation and might be involved in cellular homeostasis maintenance in stressful intertidal environments. Genome macrosynteny analyses indicated that 4 fissions and 4 fusions led to the evolution from the 17 presumed bilaterian ancestral chromosomes to the 17 littorinid chromosomes, implying that the littorinid snails have a highly conserved karyotype with the bilaterian ancestor. Based on the most parsimonious reconstruction of the common ancestral karyotype of scallops and littorinid snails, 3 chromosomal fissions and 1 chromosomal fusion from the bilaterian ancient linkage groups were shared by the bivalve scallop and gastropoda littorinid snails, indicating that the chromosome-scale ancient gene linkages were generally preserved in the mollusk genomes for over 500 million years. The highly conserved karyotype makes the littorinid snail genomes valuable resources for understanding early bilaterian evolution and biology.