cAMP-Mediated CREM-MITF-TYR Axis Regulates Melanin Synthesis in Pacific Oysters.

Colorful shells in bivalves are mostly caused by the presence of biological pigments, among which melanin is a key component in the formation of shell colours. Cyclic adenosine monophosphate (cAMP) is an important messenger in the regulation of pigmentation in some species. However, the role of cAMP in bivalve melanogenesis has not yet been reported. In this study, we performed in vitro and in vivo experiments to determine the role of cAMP in regulating melanogenesis in Pacific oysters. Besides, the function of cAMP-responsive element modulator (CREM) and the interactions between CREM and melanogenic genes were investigated. Our results showed that a high level of cAMP promotes the expression of melanogenic genes in Pacific oysters. CREM controls the expression of the MITF gene under cAMP regulation. In addition, CREM can regulate melanogenic gene expression, tyrosine metabolism, and melanin synthesis. These results indicate that cAMP plays an important role in the regulation of melanogenesis in Pacific oysters. CREM is a key transcription factor in the oyster melanin synthesis pathway, which plays a crucial role in oyster melanin synthesis through a cAMP-mediated CREM-MITF-TYR axis.

Molecular characterization of transcription factor CREB3L2 and CREB3L3 and their role in melanogenesis in Pacific oysters (Crassostrea gigas).

Colorful shells in mollusks are commonly attributable to the presence of biological pigments. In Pacific oysters, the inheritance patterns of several shell colors have been investigated, but little is known about the molecular mechanisms of melanogenesis and pigmentation. cAMP-response element binding proteins (CREB) are important transcription factors in the cAMP-mediated melanogenesis pathway. In this study, we characterized two CREB genes (CREB3L2 and CREB3L3) from Pacific oysters. Both of them contained a conserved DNA-binding and dimerization domain (a basic-leucine zipper domain). CREB3L2 and CREB3L3 were expressed highly in the mantle tissues and exhibited higher expression levels in the black-shell oyster than in the white. Masson-Fontana melanin staining and immunofluorescence analysis showed that the location of CREB3L2 protein was generally consistent with the distribution of melanin in oyster edge mantle. Dual-luciferase reporter assays revealed that CREB3L2 and CREB3L3 could activate the microphthalmia-associated transcription factor (MITF) promoter and this process was regulated by the level of cAMP. Additionally, we found that cAMP regulated melanogenic gene expression through the CREB-MITF-TYR axis. These results implied that CREB3L2 and CREB3L3 play important roles in melanin synthesis and pigmentation in Pacific oysters.

Pore Structure Evolution and Failure Mechanism of Limestone in the Taiyuan Formation of the Ordos Basin under High Temperature.

The study on the destruction of the limestone microstructure after high-temperature treatment has a significant value in the airtightness and safety of underground high-temperature geotechnical engineering. In order to truly simulate the influence of the underground high-temperature environment on limestone, taking seven groups of limestones of the Taiyuan Formation in the Ordos Basin as examples, we carried out a high-temperature (25-1200 °C) heating experiment of limestone in an argon atmosphere. The pore structure of limestone after the high temperature is studied based on scanning electron microscopy (SEM), mercury intrusion porosimetry (MIP), porosity, and permeability, and the change in the fractal dimension of the limestone pore structure was discussed based on the thermodynamic fractal theory, combined with X-ray diffraction (XRD) and thermogravimetry differential scanning calorimetry (TG-DSC), the variation of mineral composition with temperature is characterized, and the evolution mechanism of the limestone microstructure under high temperature is discussed. The results show that the evaporation of pore water does not destroy the lattice structure of limestone minerals; however, with the increase of temperature, the complete decomposition of dolomite and calcite occurs, along with the tensile fracture of calcite crystals under the effect of swelling stress. Moreover, the new minerals generated by the decomposition products under the effect of temperature severely damage the crystal structure, leading to the rapid increase of porosity and permeability. The comprehensive results show that the decomposition, expansion, and recrystallization of calcite and dolomite minerals after 800 °C led to the development of limestone macropores and fissures, increased the pore throat radius, enhanced the pore connectivity, simplified the pore structure, and sharply increased the permeability; thus, 800 °C can be used as the critical temperature to change the limestone pores and fractures. The research results can provide data support for subsurface high-temperature geotechnical engineering.

Transcriptomic and Physiological Analysis Reveal Melanin Synthesis-Related Genes and Pathways in Pacific Oysters (Crassostrea gigas).

Shell color is one of the shell traits of molluscs, which has been regarded as an economic trait in some bivalves. Pacific oysters (Crassostrea gigas) are important aquaculture shellfish worldwide. In the past decade, several shell color strains of C. gigas were developed through selective breeding, which provides valuable materials for research on the inheritance pattern and regulation mechanisms of shell color. The inheritance patterns of different shell colors in C. gigas have been identified in certain research; however, the regulation mechanism of oyster pigmentation and shell color formation remains unclear. In this study, we performed transcriptomic and physiological analyses using black and white shell oysters to investigate the molecular mechanism of melanin synthesis in C. gigas. Several pigmentation-related pathways, such as cytochrome P450, melanogenesis, tyrosine metabolism, and the cAMP signaling pathway were found. The majority of differentially expressed genes and some signaling molecules from these pathways exhibited a higher level in the black shell oysters than in the white, especially after L-tyrosine feeding, suggesting that those differences may cause a variation of tyrosine metabolism and melanin synthesis. In addition, the in vitro assay using primary cells from mantle tissue showed that L-tyrosine incubation increased cAMP level, gene and protein expression, and melanin content. This study reveals the difference in tyrosine metabolism and melanin synthesis in black and white shell oysters and provides evidence for the potential regulatory mechanism of shell color in oysters.

The role of DNA methylation reprogramming during sex determination and sex reversal in the Pacific oyster Crassostrea gigas.

DNA methylation is instrumental in vertebrate sex reversal. However, the mechanism of DNA methylation regulation regarding sex reversal in invertebrates is unclear. In this study, we used whole genome bisulfite sequencing (WGBS) to map single-base resolution methylation profiles of the Pacific oyster, including female-to-male (FMa-to-FMb) and male-to-female (MFa-to-MFb) sex reversal, as well as sex non-reversed males and females (MMa-to-MMb and FFa-to-FFb). The results showed that global DNA methylation levels increase during female-to-male sex reversals, with a particular increase in the proportion of high methylation levels (mCGs >0.75) and a decrease in the proportion of intermediate methylation levels (0.25 < mCGs <0.75). This increase in DNA methylation was mainly associated with the elevated expression of DNA methylase genes. Genome-wide methylation patterns of females were accurately remodeled to those of males after sex reversal, while the opposite was true for the male-to-female reversal. Those findings directly indicate that alterations in DNA methylation play a significant role in sex reversal in Pacific oysters. Comparative analysis of the DNA methylomes of pre- and post- sex reversal gonadal tissues (FMb-vs-FMa or MFb-vs-MFa) revealed that differentially methylated genes were mainly involved in the biological processes of sex determination or gonadal development. However critical genes such as Dmrt1, Foxl2 and Sox-like, which are involved in the putative sex determination pathway in Pacific oysters, showed almost an absence of methylation modifications, varying greatly from vertebrates. Additionally, comparative analysis of the DNA methylomes of sexual reversal and sex non-reversal (FMa-vs-FFa or MFa-vs-MMa) revealed that heat shock protein genes, such as Hsp68-like and Hsp70B, were important for the occurrence of sex reversal. These findings shed light on the epigenetic mechanisms underlying the maintenance of gonadal plasticity and the reversal of organ architecture in oysters.

Comparative transcriptome elucidates key genes and pathways related to golden phenotype of Crassostrea gigas.

Marine bivalves are economically important and exhibit a remarkable diversity in shell color. The Pacific oyster Crassostrea gigas stands out as an important economic species, with the successful development of four distinct color strains through selective breeding. While previous studies have shed light on the genetic mechanism underlying color segregation, the precise molecular regulatory mechanisms responsible for shell coloration in oysters remains elusive. In this study, we confirmed that the golden phenotype is primarily attributed to pheomelanin by histological and ultrastructural observations. Additionally, we conducted a comparative transcriptome analysis of the black and golden shell color oysters to explore the potential genes and pathways contributing to the golden phenotype in C. gigas. Our results revealed a significant increase in differentially expressed genes in the golden phenotype associated with pathways such as glutathione metabolism, and calcium signaling pathway, suggesting a potential role in the synthesis of pheomelanin. Of particular note, we highlighted the potential role of two-pore channel 2 (TPC2) in modulating tyrosinase activity and melanosomal pH, ultimately determining the shade of pigmentation. Our study in this work provided a preliminary exploration of the mechanism, shedding light on the melanosome microenvironment and shell color.

Enhancing effect of cobalt phthalocyanine dispersion on electrocatalytic reduction of CO2 towards methanol.

This paper focuses on enhancing the performance of electrocatalytic CO2 reduction reaction (CO2RR) by improving the dispersion of cobalt phthalocyanine (CoPc), especially for the methanol formation with multi-walled carbon nanotubes (CNTs) as a support. The promising CNTs-supported CoPc hybrid was prepared based on ball milling technique, and the surface morphology was characterized by means of those methods such as scanning electron microscopy (SEM), Fourier transform infrared spectrometer (FT-IR) and X-ray photoelectron spectra (XPS). Then, the synergistic effect of CNTs and ball milling on CO2RR performance was analyzed by those methods of cyclic voltammetry (CV), linear sweep voltammetry (LSV), electrochemical impedance spectroscopy (EIS), gas chromatography (GC), and proton nuclear magnetic resonance spectroscopy (1HNMR). Subsequently, the reduction mechanism of CO2 on ball-milled CoPc/CNTs was revealed based on the DFT calculations. The results showed that the electrocatalyst CoPc/CNTs hybrid prepared with sonication exhibited a conversion efficiency of CO2 above 60% at -1.0 V vs. RHE, accompanied by the Faradaic efficiencies of nearly 50% for CO and 10% for methanol, respectively. The addition of CNTs as the support improved the utilization efficiency of CoPc and reduced the transfer resistance of species and electrons. Then the ball-milling method further improved the dispersion of CoPc on CNTs, which resulted in the fact that the methanol efficiency was raised by 6% and partial current density was increased by nearly 433%. The better dispersion of CoPc on CNTs adjusted the reduction pathway of CO2 and resulted in the enhancement of methanol selectivity and catalytic activity of CO2. The probable pathway for methanol production was proposed as CO2 → *CO2- → *COOH → *CO → *CHO → *CH2O → *OCH3 → CH3OH. This suggests the significance of the ball-milling method during the preparation of better supported catalysts for CO2RR towards those high-valued products.

Nickel/photoredox-catalyzed enantioselective arylation of α-chloro thioesters.

The first dual nickel/photoredox-catalyzed enantioselective reductive cross-coupling of racemic α-chloro thioesters with aryl iodides has been developed. This strategy avoids the need for organometallic reagents or stoichiometric metal reductants. This reaction could tolerate a wide range of substrate scope with excellent reactivity and high enantioselectivities (up to 91% ee) to access a variety of chiral α-aryl thioesters. The synthetic utility of the corresponding α-aryl thioesters is demonstrated. Furthermore, we explored the mechanism of such an enantioselective radical cross-coupling process.

Multi-omic insights into the formation and evolution of a novel shell microstructure in oysters.

BACKGROUND: Molluscan shell, composed of a diverse range of architectures and microstructures, is a classic model system to study the relationships between molecular evolution and biomineralized structure formation. The shells of oysters differ from those of other molluscs by possessing a novel microstructure, chalky calcite, which facilitates adaptation to the sessile lifestyle. However, the genetic basis and evolutionary origin of this adaptive innovation remain largely unexplored. RESULTS: We report the first whole-genome assembly and shell proteomes of the Iwagaki oyster Crassostrea nippona. Multi-omic integrative analyses revealed that independently expanded and co-opted tyrosinase, peroxidase, TIMP genes may contribute to the chalky layer formation in oysters. Comparisons with other molluscan shell proteomes imply that von Willebrand factor type A and chitin-binding domains are basic members of molluscan biomineralization toolkit. Genome-wide identification and analyses of these two domains in 19 metazoans enabled us to propose that the well-known Pif may share a common origin in the last common ancestor of Bilateria. Furthermore, Pif and LamG3 genes acquire new genetic function for shell mineralization in bivalves and the chalky calcite formation in oysters likely through a combination of gene duplication and domain reorganization. CONCLUSIONS: The spatial expression of SMP genes in the mantle and molecular evolution of Pif are potentially involved in regulation of the chalky calcite deposition, thereby shaping the high plasticity of the oyster shell to adapt to a sessile lifestyle. This study further highlights neo-functionalization as a crucial mechanism for the diversification of shell mineralization and microstructures in molluscs, which may be applied more widely for studies on the evolution of metazoan biomineralization.

Parallel evolution in Crassostrea oysters along the latitudinal gradient is associated with variation in multiple genes involved in adipogenesis.

Parallel diversification provides a proper framework for studying the role of natural selection in evolution. Yet, empirical studies from ecological 'non-model' species of invertebrates are limited at the whole genome level. Here, we presented a chromosome-scale genome assembly for Crassostrea angulata and investigated the parallel genomic evolution in oysters. Specifically, we used population genomics approaches to compare two southern-northern oyster species pairs (C. angulata-C. gigas and southern-northern C. ariakensis) along the coast of China. The estimated divergence time of C. angulata and C. gigas is earlier than that of southern and northern C. ariakensis, which aligns with the overall elevated genome-wide divergence. However, the southern-northern C. ariakensis FST profile represented more extremely divergent "islands". Combined with recent reciprocal hybridization studies, we proposed that they are currently at an early stage of speciation. These two southern-northern oyster species pairs exhibited significant repeatability in patterns of genome-wide differentiation, especially in genomic regions with extremely high and low divergence. This suggested that divergent and purifying selection has contributed to the genomic parallelism between southern and northern latitudes. Top differentiated genomic regions shared in these two oyster species pairs contained candidate genes enriched for functions in energy metabolism, especially adipogenesis, which are closely related to reproductive behaviours. These genes might be good candidates for further investigation in vivo. In conclusion, our results suggest that similar divergent selection and shared genomic features could predictably transform standing genetic variation within one species pair into differences in another.

Phylogenomic resolution of Imparidentia (Mollusca: Bivalvia) diversification through mitochondrial genomes.

Despite significant advances in the phylogenomics of bivalves over the past decade, the higher-level phylogeny of Imparidentia (a superorder of Heterodonta) remains elusive. Here, a total of five new mitochondrial sequences (Chama asperella, Chama limbula, Chama dunkeri, Barnea manilensis and Ctena divergens) was added to provide resolution in nodes that required additional study. Although the monophyly of Lucinida remains less clear, the results revealed the overall backbone of the Imparidentia tree and the monophyly of Imparidentia. Likewise, most relationships among the five major Imparidentia lineages-Lucinida, Cardiida, Adapedonta, Myida and Venerida-were addressed with a well-supported topology. Basal relationships of Imparidentia recovered Lucinidae as the sister group to all remaining imparidentian taxa. Thyasiridae is a sister group to other imparidentian bivalves (except Lucinidae species) which is split into Cardiida, Adapedonta and the divergent clade of Neoheterodontei. Neoheterodontei was comprised of Venerida and Myida, the former of which now also contains Chamidae as the sister group to all the remaining venerid taxa. Moreover, molecular divergence times were inferred by calibrating nine nodes in the Imparidentia tree of life by extinct taxa. The origin of these major clades ranged from Ordovician to Permian with the diversification through the Palaeozoic to Mesozoic. Overall, the results obtained in this study demonstrate a better-resolved Imparidentia phylogeny based on mitochondrial genomes. Supplementary Information: The online version contains supplementary material available at 10.1007/s42995-023-00178-x.

Taxonomic review of Kaloplocamus from the Yellow Sea, China with the description of a new species (Nudibranchia, Doridina, Polyceridae).

Species of Kaloplocamus Bergh, 1880 are enigmatic Nudibranchia sea slugs, and only two valid species are reported in the northwestern Pacific. Kaloplocamusjaponicus (Bergh, 1880) was initially described based on alcohol-fixed specimens. In the latest revision of Kaloplocamus, it was synonymized with Kaloplocamusramosus (Cantraine, 1835). Recently, several nudibranchs were collected from Tianheng, Shandong Province, China, and one of them is identified as an undescribed species described here as Kaloplocamusalbopunctatussp. nov. based on integrated approaches incorporating morphological observations, internal anatomy, and phylogenetic analyses of two mitochondrial (COI, 16S rRNA) genes. The other species is identified as K.japonicus Bergh, 1880 based on the anatomy of the reproductive system. The new species K.albopunctatussp. nov. is similar to K.ramosus in having a bright orange-red color pattern but differs significantly in the structure of appendages and reproductive system. Kaloplocamusjaponicus can be easily distinguished from other Kaloplocamus species by its translucent, white-pink coloration and unique features of the female reproductive organ. Both species are supported as distinct species in all molecular analyses. The phylogenetic analyses propose a new estimate of the relationship between Kaloplocamus and Plocamopherus, and the evolution of bioluminescence within Triophinae is discussed. Our results also suggest cryptic biodiversity within the K.ramosus species complex.

Effects of Dietary Cystine and Tyrosine Supplementation on Melanin Synthesis in the Pacific Oyster (Crassostrea gigas).

Melanogenesis is a multistep process to produce melanin for dark pigmentation in skin coloration. Previous studies in vertebrates demonstrated that cystine and tyrosine amino acids are involved in the melanin synthesis. However, very little is known about the melanogenesis in bivalve. In this study, cystine supplementation for 30 days significantly upregulated the expression of CgB-aat1, CgCbs and CgTyr and pheomelanin content in the Pacific oyster Crassostrea gigas. Transmission electron microscope (TEM) results revealed more melanosomes in the connective tissue and melanin granules were secreted in epithelium of mantle. In contrast, tyrosine supplementation had no clear effect on melanogenesis except the gene expression changes of CgB-aat1 and CgCbs. In addition, prolonged supplementation of cystine or tyrosine for 60 days had a negative impact on melanogenesis. Indeed, after 60 days, expression of most of the melanin synthesis-related genes under study was decreased, and melanin content was significantly reduced, indicating that cystine and tyrosine might inhibit production of eumelanin and pheomelanin, respectively. In addition, in vitro analysis using primary cell culture from mantle tissue indicated that incubation with cystine, tyrosine, or B-AAT1 polypeptide, CBS/TYR recombinant proteins induced the increase of CgB-aat1 and CgCbs expression in a dose-dependent manner, suggesting the presence of a regulatory network in response to cystine and tyrosine amino acids intakes in pheomelanin synthesis-related gene expression. Taken together, these data indicate that cystine-CgB-aat1-CgCbs-CgTyr axis is a potential regulator of the pheomelanin biosynthesis pathway, and thus plays an important role in the mantle pigmentation in C. gigas. This work provides a new clue for selective cultivation of oyster strains with specific shell colors in bivalve breeding.

Impact of a medical supply bulk-buy program on treatment of patients with coronary artery disease in China: A single-center study.

BACKGROUND: The Chinese government recently introduced a program to buy medical supplies in bulk to reduce the patient cost burden. For patients undergoing percutaneous coronary intervention (PCI), little is known about the effect on outcomes of this bulk-buy program. AIMS: This study investigated whether the bulk-buy program to decrease the price of stents used in PCI affected clinical decision-making and outcomes. METHODS: This single-center study enrolled patients undergoing PCI from January 2020-December 2021. Prices decreased for stents on January 1, 2021, and balloons on March 1, 2021. Patients were grouped by surgical year as either before (2020) or after (2021) policy implementation. All clinical data were collected. To examine whether clinical decision-making for PCI was affected by the bulk-buy program, procedure appropriateness was analyzed using the 2017 appropriate use criteria (AUC). To assess outcomes, the rates of major adverse cardiac and cerebrovascular events (MACCE) and complications were compared between groups. RESULTS: Study participants were 601 patients in 2020 (before bulk buying) and 699 patients in 2021 (after bulk buying). Results of analysis by AUC for procedure appropriateness were 74.5% appropriate, 21.6% may be appropriate, and 3.8% rarely appropriate in 2020, with no differences for patients who underwent PCI in 2021. Between-group comparisons showed MACCE rates of 0.5% in 2020 and 0.6% in 2021, whereas complication rates were 5.5% and 5.7%, respectively. No statistically significant differences were found between groups (p > 0.05). CONCLUSION: The bulk-buy program did not impact physician clinical decision-making or surgical outcomes for patients undergoing PCI.

A chromosome-level genome assembly of Ostrea denselamellosa provides initial insights into its evolution.

The oyster Ostrea denselamellosa is a live-bearing species with a sharp decline in the natural population. Despite recent breakthroughs in long-read sequencing, high quality genomic data are very limited in O. denselamellosa. Here, we carried out the first whole genome sequencing at the chromosome-level in O. denselamellosa. Our studies yielded a 636 Mb assembly with scaffold N50 around 71.80 Mb. 608.3 Mb (95.6% of the assembly) were anchored to 10 chromosomes. A total of 26,412 protein-coding genes were predicted, of which 22,636 (85.7%) were functionally annotated. By comparative genomics, we found that long interspersed nuclear element (LINE) and short interspersed nuclear element (SINE) made up a larger proportion in O. denselamellosa genome than in other oysters'. Moreover, gene family analysis showed some initial insight into its evolution. This high-quality genome of O. denselamellosa provides a valuable genomic resource for studies of evolution, adaption and conservation in oysters.

Transcription factor CgPOU3F4-like regulates expression of pheomelanin synthesis related gene CgB-aat1 in the Pacific oyster (Crassostrea gigas).

Previous study has found that b (0, +) -type amino acid transporter 1 (CgB-aat1) plays an essential role on mantle pigmentation in the Pacific oyster Crassostrea gigas. However, the molecular regulation of CgB-aat1 gene expression remains unclear. Herein, three POU domain family members, CgPOU2F1, CgPOU3F4-like and CgPOU4F3-X1 were characterized and they all had POUs and HOX domains, respectively, which were important in transcriptional regulation. CgPOU3F4-like gene expression was the highest in mantle edge. Subsequently, the dual-luciferase reporter result showed that the core regulatory region of CgB-aat1 gene was from -632 to -350 bp of promoter. In transient co-transfection assays, the strongest activity was activated only by CgPOU3F4-like, suggesting CgPOU3F4-like was a valid transcriptional activator of CgB-aat1 gene promoter. And the structural integrity of CgPOU3F4-like was essential for its activation function. In addition, site directed mutagenesis assay was applied to detect three key binding sites between CgPOU3F4-like and core region of CgB-aat1 gene promoter, and this interaction was verified by ChIP test. Furthermore, CgPOU3F4-like knockdown by RNA interference led to obvious decreases in CgB-aat1 and cystathionine beta-synthase (CgCbs) expressions at both mRNA and protein levels. Collectively, these results indicate that CgPOU3F4-like positively regulate CgB-aat1 gene expression and it may be a critical upstream transcriptional regulation factor in pheomelanin synthesis in C. gigas.

Transcriptome Analysis of Reciprocal Hybrids Between Crassostrea gigas and C. angulata Reveals the Potential Mechanisms Underlying Thermo-Resistant Heterosis.

Heterosis, also known as hybrid vigor, is widely used in aquaculture, but the molecular causes for this phenomenon remain obscure. Here, we conducted a transcriptome analysis to unveil the gene expression patterns and molecular bases underlying thermo-resistant heterosis in Crassostrea gigas ♀ × Crassostrea angulata ♂ (GA) and C. angulata ♀ × C. gigas ♂ (AG). About 505 million clean reads were obtained, and 38,210 genes were identified, of which 3779 genes were differentially expressed between the reciprocal hybrids and purebreds. The global gene expression levels were toward the C. gigas genome in the reciprocal hybrids. In GA and AG, 95.69% and 92.00% of the differentially expressed genes (DEGs) exhibited a non-additive expression pattern, respectively. We observed all gene expression modes, including additive, partial dominance, high and low dominance, and under- and over-dominance. Of these, 77.52% and 50.00% of the DEGs exhibited under- or over-dominance in GA and AG, respectively. The over-dominance DEGs common to reciprocal hybrids were significantly enriched in protein folding, protein refolding, and intrinsic apoptotic signaling pathway, while the under-dominance DEGs were significantly enriched in cell cycle. As possible candidate genes for thermo-resistant heterosis, GRP78, major egg antigen, BAG, Hsp70, and Hsp27 were over-dominantly expressed, while MCM6 and ANAPC4 were under-dominantly expressed. This study extends our understanding of the thermo-resistant heterosis in oysters.

Chromosome-level genome assembly of the European flat oyster (Ostrea edulis) provides insights into its evolution and adaptation.

The European flat oyster (Ostrea edulis) is an endangered and economically important marine bivalve species that plays a critical role in the coastal ecosystem. Here, we report a high-quality chromosome-level genome assembly of O. edulis, generated using PacBio HiFi-CCS long reads and annotated with Nanopore full-length transcriptome. The O. edulis genome covers 946.06 Mb (scaffold N50 94.82 Mb) containing 34,495 protein-coding genes and a high proportion of repeat sequences (58.49 %). The reconstructed demographic histories show that O. edulis population might be shaped by breeding habit (embryo brooding) and historical climatic change. Comparative genomic analysis indicates that transposable elements may drive lineage-specific evolution in oysters. Notably, the O. edulis genome has a Hox gene cluster rearrangement that has never been reported in bivalves, making this species valuable for evolutionary studies of molluscan diversification. Moreover, genome expansion of O. edulis is probably central to its adaptation to filter-feeding and sessile lifestyles, as well as embryo brooding and pathogen resistance, in coastal ecosystems. This chromosome-level genome assembly provides new insights into the genome feature of oysters, and presents an important resource for genetic research, evolutionary studies, and biological conservation of O. edulis.

Checklist of the micromolluscs in the intertidal zone of the Yellow Sea and Bohai Sea, China.

Background: The diversity of the sedimentary environment and molluscs is rich in the intertidal zone of the Yellow Sea and Bohai Sea. At present, many of the investigations focus on macromolluscs, while the diversity of micromolluscs is seriously underestimated. New information: In this study, the survey of micromolluscs was carried out in the intertidal zone of the Yellow Sea and Bohai Sea. The collection and preservation of micromolluscs, as well as the preparation methods of morphological characteristic structures by scanning electron microscopy (SEM) were explored. A total of 20 species were described in this survey. These can be assigned to 16 families, four orders (Vetigastropoda (1), Caenogastropoda (10), Heterobranchia (5) and Autobranchia (3)) and two classes (Gastropoda (17), Bivalvia (3)).

Comparing the Efficiency of Single-Locus Species Delimitation Methods within Trochoidea (Gastropoda: Vetigastropoda).

In the context of diminishing global biodiversity, the validity and practicality of species delimitation methods for the identification of many neglected and undescribed biodiverse species have been paid increasing attention. DNA sequence-based species delimitation methods are mainly classified into two categories, namely, distance-based and tree-based methods, and have been widely adopted in many studies. In the present study, we performed three distance-based (ad hoc threshold, ABGD, and ASAP) and four tree-based (sGMYC, mGMYC, PTP, and mPTP) analyses based on Trochoidea COI data and analyzed the discordance between them. Moreover, we also observed the performance of these methods at different taxonomic ranks (the genus, subfamily, and family ranks). The results suggested that the distance-based approach is generally superior to the tree-based approach, with the ASAP method being the most efficient. In terms of phylogenetic methods, the single threshold version performed better than the multiple threshold version of GMYC, and PTP showed higher efficiency than mPTP in delimiting species. Additionally, GMYC was found to be significantly influenced by taxonomic rank, showing poorer efficiency in datasets at the genus level than at higher levels. Finally, our results highlighted that cryptic diversity within Trochoidea (Mollusca: Vetigastropoda) might be underestimated, which provides quantitative evidence for excavating the cryptic lineages of these species.