Shi Wang

Ocean University of China | OUC · College of Marine Life Science

We describe 2b-RAD, a streamlined restriction site-associated DNA (RAD) genotyping method based on sequencing the uniform fragments produced by type IIB restriction endonucleases. Well-studied accessions of Arabidopsis thaliana were genotyped to validate the method's accuracy and to demonstrate fine-tuning of marker density as needed. The simplicit...

Reconstructing the genomes of bilaterian ancestors is central to our understanding of animal evolution, where knowledge from ancient and/or slow-evolving bilaterian lineages is critical. Here we report a high-quality, chromosome-anchored reference genome for the scallop Patinopecten yessoensis, a bivalve mollusc that has a slow-evolving genome with...

Bivalve molluscs are descendants of an early-Cambrian lineage superbly adapted to benthic filter-feeding. Adaptations in form and behavior are well-recognized, but the underlying molecular mechanisms are largely unknown. Here, we investigate the genome, various transcriptomes and proteomes of the scallop Chlamys farreri, a semi-sessile bivalve with...

The transient larva-bearing biphasic life cycle is the hallmark of many metazoan phyla, but how metazoan larvae originated remains a major enigma in animal evolution. There are two hypotheses for larval origin. The ‘larva-first’ hypothesis suggests that the first metazoans were similar to extant larvae, with later evolution of the adult-added bipha...

Contrary to classic theory prediction, sex-chromosome homomorphy is prevalent in the animal kingdom but it is unclear how ancient homomorphic sex chromosomes avoid chromosome-scale degeneration. Molluscs constitute the second largest, Precambrian-originated animal phylum and have ancient, uncharacterized homomorphic sex chromosomes. Here, we profil...

LncRNAs are long non-coding RNAs that are widely recognized as crucial regulators of gene expression and metabolic control, involved in numerous dormancy-related processes. Aestivation is a common hypometabolism strategy of sea cucumber (Apostichopus japonicus) in response to high-temperature conditions and is typically characterized by the degrada...

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 v...

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 system-atics was grounded in morphological and anatomical studies. With the transition from oligo gene Sanger seque...

Background Anadara granosa, commonly known as the blood clam, exhibits the unusual characteristic of having red blood among invertebrates. There is significant individual variation in blood color intensity among blood clams; individuals with vibrant red blood are deemed healthier and exhibit stronger stress resistance. However, the molecular basis...

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 f...

As a biogenic calcium carbonate, the seashell plays a crucial role in marine environmental studies. In these studies, it is essential to investigate the composition of the seashell. In this study, we used laser-induced breakdown spectroscopy (LIBS) to analyze the elemental composition of cultured scallop-shell (Patinopecten yessoensis), with a spec...

The pharyngeal endoderm, an innovation of deuterostome ancestors, contributes to pharyngeal development by influencing the patterning and differentiation of pharyngeal structures in vertebrates; however, the evolutionary origin of the pharyngeal organs in vertebrates is largely unknown. The endostyle, a distinct pharyngeal organ exclusively present...

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 d...

Zygotic genome activation (ZGA) is a universal process in early embryogenesis of metazoan, when the quiescent zygotic nucleus initiates global transcription. However, the mechanisms related to massive genome activation and allele-specific expression (ASE) remain not well understood. Here, we develop hybrids from two deeply diverged (120 Mya) ascidi...

Target enrichment sequencing techniques are gaining widespread use in the field of genomics, prized for their economic efficiency and swift processing times. However, their success depends on the performance of probes and the evenness of sequencing depth among each probe. To accurately predict probe coverage depth, a model called Deqformer is propo...

Hemoglobin (Hb) has been identified in at least 14 molluscan taxa so far. Research spanning over 130 years on molluscan Hbs focuses on their genes, protein structures, functions, and evolution. Molluscan Hbs are categorized into single-, two-, and multiple-domain chains, including red blood cell, gill, and extracellular Hbs, based on the number of...

Unlabelled: The evolution of a two-chambered heart, with an atrium and a ventricle, has improved heart function in both deuterostomes (vertebrates) and some protostomes (invertebrates). Although studies have examined the unique structure and function of these two chambers, molecular comparisons are few and limited to vertebrates. Here, we focus on...

Biotechnology is crucial for the sustainable development of the aquatic seed industry. Therefore, improving the innovation capability in aquatic breeding and making seed sources independent are significant for ensuring food security in China. This study summarizes the development status and problems of aquatic breeding in China and analyzes the sta...

The pharynx is an endoderm innovation in deuterostome ancestors, the vertebrate descendent structure of which is a pharyngeal developmental organizer involving multi-germ layer and organ derivatives. However, the evolutionary origination of complicated pharynx organs in vertebrates is still largely unknown. Endostyle, a transitional pharyngeal orga...

The element ratio of Mg/Ca is a primary proxy in studying the composition of seashells, and laser-induced breakdown spectroscopy (LIBS) is a practical technique for elemental analysis. In this work, we tried to apply LIBS to investigate the Mg/Ca ratio in cultured seashells of two scallop species ( Chlamys farreri and Patinopecten yessoensis). It w...

The increased frequency of marine heat waves (MHWs) caused by global climate change is predicted to threaten the survival of economic bivalves, therefore having severely adverse effects on local ecological communities and aquaculture production. However, the study of scallops facing MHWs is still scarce, particularly in the scallop Argopecten irrad...

Background Gonadal development is driven by a complex genetic cascade in vertebrates. However, related information remains limited in molluscs owing to the long generation time and the difficulty in maintaining whole life cycle in the lab. The dwarf surfclam Mulinia lateralis is considered an ideal bivalve model due to the short generation time and...

Evolutionary developmental biology (evo-devo) has been among the most fascinating interdisciplinary fields for decades, which aims to elucidate the origin and evolution of diverse developmental processes. The rapid accumulation of omics data provides unprecedented opportunities to answer many interesting but unresolved evo-devo questions. However,...

Soft-bodied slow-moving sea creatures such as sea stars and sea cucumbers lack an adaptive immune system and have instead evolved the ability to make specialized protective chemicals (glycosylated steroids and triterpenes) as part of their innate immune system. This raises the intriguing question of how these biosynthetic pathways have evolved. Sea...

High-throughput single nucleotide polymorphism (SNP) genotyping assays are powerful tools for genetic studies and genomic breeding applications for many species. Though large numbers of SNPs have been identified in sea cucumber (Apostichopus japonicus), but, as yet, no high-throughput genotyping platform is available for this species. In this study...

Genome miniaturization drives key evolutionary innovations of adaptive traits in vertebrates, such as the flight evolution of birds. However, a similar evolutionary process remains poorly understood in invertebrates. Derived from the second-largest animal phylum, scallops are a special group of bivalve molluscs and acquire the evolutionary novelty...

Sulfide are widely accumulated in aquatic environments under anaerobic conditions, which cause health problems of aquatic animals, yet their toxic effects to benthic bivalves is not well understood. We investigated the effects of sulfide on innate immunity of the blood clam Tegillarca granosa. Immunity-related indicators and hemolymph microbiota we...

Secretome is involved in almost all physiological, developmental, and pathological processes, but to date there is still a lack of highly-efficient research strategy to comprehensively study the secretome of invertebrates. Adhesive secretion is a ubiquitous and essential physiological process in aquatic invertebrates with complicated protein compon...

Interferon regulatory factors (IRFs) are a family of transcription factors that control many facets during innate and adaptive immune responses. Vertebrate IRFs play important roles in regulating the expression of interferons (IFNs) and IFN-stimulated genes, while only limited studies were conducted on invertebrate IRFs. In the present study, four...

The COMMD (copper metabolism gene MuRR1 domain) gene family, highly conserved among multicellular eukaryotic organisms, plays important roles in a variety of biological processes, ranging from copper homeostasis, ionic transport, protein trafficking, NF-κB-mediated transcription, and cell proliferation. However, systematic identification, spatiotem...

Nanos are conserved genes involved in germline cell specification and differentiation. However, little is known about the role of different members of Nanos family in germ cell development in mollusks. In the present study, we conducted genome-wide identification of Nanos family in an economically important scallop Patinopecten yessoensis, and dete...

The Pacific white shrimp Litopenaeus vannamei is among the top aquatic species of commercial importance around the world. Over the last four decades, the breeding works of L. vannamei have been carried out intensively and have generated multiple strains with improved production and performance traits. However, signatures of domestication and artifi...

Cilia are organelles located on the surface of eukaryotic cells and play important roles in numerous physiological and developmental processes. Cilia- and flagella-associated proteins (CFAP family) are well known due to their close relation to the assembly and functionalization of both cilia and flagella. In vertebrates, Cfap206 is reported to func...

Many marine organisms are generally poikilotherms, making seawater temperature one of the most important environmental factors affecting gonadal sex differentiation. Mollusca is the second-largest animal phylum with diverse reproductive systems, but studies on the impact of temperature on sex differentiation are limited to a few sequential hermaphr...

Microbiome samples with low microbial biomass or severe DNA degradation remain challenging for amplicon-based or whole-metagenome sequencing approaches. Here, we introduce 2bRAD-M, a highly reduced and cost-effective strategy which only sequences ~ 1% of metagenome and can simultaneously produce species-level bacterial, archaeal, and fungal profile...

Yesso scallop, Mizuhopecten yessoensis, is one of the most important bivalve species in aquaculture industry. Two selective improved varieties (Haida golden scallop and Zhangzidaohong) have been developed by artificial selection in recent years and exhibit good performance on growth and production traits. However, there's still a lack of comprehens...

Targeted genotyping is an extremely powerful approach for the detection of known genetic variations that are biologically or clinically important. However, for non-model organisms, large-scale target genotyping in a cost-effective manner remains a major challenge. To address this issue, we present an ultrahigh-multiplex, in-solution probe array-bas...

The king scallop, Pecten maximus is a well-known, commercially important scallop species and is featured with remarkable tolerance to potent phytotoxins such as domoic acid. A high-quality genome can shed light on its biology and innovative evolution of toxin resistance. A reference genome has recently been generated for P. maximus, however, it is...

The deep-sea limpet Bathyacmaea lactea, inhibited in cold seeps of the South China Sea, belongs to the most primitive gastropod groups, the Patellogastropoda (true limpets). Here, we report the complete mitochondrial genome of B. lactea, which is 18,446 bp in length and contains 13 protein-coding genes, 2 rRNAs, and 22 tRNA genes. The mitochondrial...

C1Q (Complement 1Q) is an important recognition molecule in the immunological complement system, which could also be putatively involved in the stress responses induced by endotoxins or exotoxins, potentially through detoxification processes. Marine bivalves are well adapted to highly complex aquatic environments with various stressors. As filter f...

Bay scallop is an economically important bivalve species in aquaculture industry. Due to its rapid growth rate and short reproduction cycle, bay scallop possesses the highest annual yield in Chinese scallop production and serves as a good model species to study the genetic effects of population differentiation and selective breeding. Via whole geno...

Members of the testis-specific serine/threonine kinases (Tssk) family play critical roles in spermatogenesis in vertebrates. But in mollusks, research on Tssk family is still lagging. In this study, we systematically identified Tssk family based on the genomic and transcriptomic data from a commercially important scallop Argopecten irradians and de...

Simultaneous or functional hermaphrodites possessing both ovary and testis at the same time are good materials for studying sexual development. However, previous research on sex determination and differentiation was mainly conducted in gonochoristic species and studies on simultaneous hermaphrodites are still limited. In this study, we conducted a...

Inhibitors of apoptosis proteins (IAPs) are conserved regulators involved in cell cycle, cell migration, cell death, immunity and inflammation, should be due to the fact that they can assist with the ability to cope with different kinds of extrinsic or intrinsic stresses. Bivalve molluscs are well adapted to highly complex marine environments. As f...

Blood clams differ from their molluscan kins by exhibiting a unique red-blood (RB) phenotype, however the genetic basis and biochemical machinery subserving this evolutionary innovation remain unclear. As a fundamental step toward resolving this mystery, we presented the first chromosome-level genome and comprehensive transcriptomes of the blood cl...

Genomic selection (GS) currently represents the hot research area in aquaculture, but implementing GS in some aquatic animals is still hampered by the lacking of efficient nonlethal DNA sampling approach for genome-wide genotyping. This is particularly challenging for bivalve molluscs as they generally have small body size and are vulnerable to mas...

Zhikong scallop (Chlamys farreri Jones et Preston 1904) is one of the most economically important shellfish in the aquaculture industry of China. Improving thermal tolerance of the scallop by breeding has become a critical task for the sustainable farming industry. The detection of the majority of the current indicators of the thermal tolerance of...

Microbiome samples with low microbial biomass or severe DNA degradation remain challenging for amplicon-based (e.g., 16S/18S-rRNA) or whole-metagenome sequencing (WMS) approaches. Here, we introduce 2bRAD-M, a “reduction” metagenome-sequencing strategy that simultaneously produces species-level bacterial, archaeal, and fungal profiles for low-bioma...

Most marine copiotrophic bacteria can produce extracellular enzymes to degrade biopolymers into bio‐available smaller solutes, while oligotrophic bacteria usually cannot. Bacterial extracellular enzymes and enzymatic products can be a common resource that could be utilized by both copiotrophs and oligotrophs; when present, oligotrophs may outcompet...

Mollusca represents the second largest animal phylum but remains poorly explored from a genomic perspective. While the recent increase in genomic resources holds great promise for a deep understanding of molluscan biology and evolution, access and utilization of these resources still pose a challenge. Here, we present the first comprehensive mollus...

The hydrolysis of sugar-containing compounds by glycoside hydrolases (GHs) plays essential roles in many major biological processes, but to date our systematic understanding of the functional diversity and evolution of GH families remains largely limited to a few well-studied terrestrial animals. Molluscs represent the largest marine phylum in the...

Gonadotropin-releasing hormone (GnRH) controls synthesis of sex steroid hormones through hypothalamic-pituitary-gonadal (HPG) axis in vertebrates. But in mollusks, research on GnRH and steroidogenesis pathways is still limited. In this study, we first identified two gonadotropin receptor like genes (LGR and LGR5L) and four steroidogenesis-related g...

Tunicates occupy the evolutionary position at the boundary of invertebrates and vertebrates. It exhibits adaptation to broad environmental conditions and is distributed globally. Despite hundreds of years of embryogenesis studies, the genetic basis of the invasive habits of ascidians remains largely unknown. The leathery sea squirt, Styela clava, i...

The genus Hiatella is one of most abundant and widespread marine bivalves. To date, its intra-generic phylogeny remains disputed and mitogenome information is therefore much needed. Here, we first report the complete circular mitogenome of Hiatella sp. J that is distributed in the coast of Asia Pacific. The total length of this mitochondrial genome...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Molluscs represent one of ancient and evolutionarily most successful groups of marine invertebrates, with a tremendous diversity of morphology, behavior, and lifestyle. Molluscs are excellent subjects for evo‐devo studies; however, understanding of the evo‐devo of molluscs has been largely hampered by incomplete fossil records and limited molecular...

The bay scallop and Peruvian scallop are economically important species. Interspecific hybrids of these two scallops outperformed both of their parent species in multiple growth traits but exhibited decreased fertility, which provides good models for the study of heterosis and species divergence. Genetic mapping serves as a chromosomal-level framew...