Qifan Zeng

• PhD
• Professor at Ocean University of China

Abstract Background Drug-resistant fish pathogens can cause significant economic loss to fish farmers. Since 2012, florfenicol has become an approved drug for treating both septicemia and columnaris diseases in freshwater fish. Due to the limited drug options available for aquaculture, the impact of the therapeutical florfenicol treatment on the mi...

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...

It is of vital importance to understand the population structure, dissect the genetic bases of performance traits, and make proper strategies for selection in breeding programs. However, there is no single webserver covering the specific needs in aquaculture. We present Aquaculture Molecular Breeding Platform (AMBP), the first web server for geneti...

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...

Background The genetic basis underlying spawning abilities in the Pacific white shrimp, Penaeus vannamei, remains largely unexplored. To investigate genetic variations potentially related to reproductive performance, a systematic bioinformatic analysis was conducted to identify structural variations (SVs) with different polymorphic spectra in P. va...

Unlabelled: Genomic selection (GS) applied to the breeding of aquatic animals has been of great interest in recent years due to its higher accuracy and faster genetic progress than pedigree-based methods. The genetic analysis of complex traits in GS does not escape the current excitement around artificial intelligence, including a renewed interest...

The shrimp farming sector has faced significant hurdles due to acute hepatopancreatic necrosis disease (AHPND). In this study, an attempt was made to combine the enzymatic recombinase amplification (ERA) assay and CRISPR-Cas12a (ERA-Cas12a) for the rapid detection of AHPND. A set of crRNA and ssDNA with high sensitivity and good specificity was scr...

Sexual dimorphism is a common feature in all crustaceans. However, little information is available on the relationship between sex and disease resistance in Litopenaeus vannamei. This study aimed to evaluate the differences in innate immunity characteristics between male and female L. vannamei under stimulation with Vibrio parahaemolyticus causing...

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...

The dwarf surf clam, Mulinia lateralis, is considered as a model species for bivalves because of its rapid growth and short generation time. Recently, successful breeding of this species for multiple generations in our laboratory revealed its acquisition of adaptive advantages during artificial breeding. In this study, 310 individuals from five dif...

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...

The leopard coral grouper (Plectropomus leopardus) is a species of significant economic importance. Although artificial cultivation of P. leopardus has thrived in recent decades, the advancement of selective breeding has been hindered by the lack of comprehensive population genomic data. In this study, we identified over 8.73 million single nucleot...

Background Mytilidae, also known as marine mussels, are widely distributed in the oceans worldwide. Members of Mytilidae show a tremendous range of ecological adaptions, from the species distributed in freshwater to those that inhabit in deep-sea. Mitochondria play an important role in energy metabolism, which might contribute to the adaptation of...

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...

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...

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...

The increasing sea temperature caused by global warming has resulted in severe mortalities in maricultural scallops. Therefore, improving thermal tolerance has become an active research area in the scallop farming industry. Bay scallop (Argopecten irradians irradians) was introduced into China in 1982 and has developed into a vast aquaculture indus...

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...

Spiroplasma eriocheiris (S. eriocheiris) infection has caused heavy economic losses in Macrobrachium nipponense (M. nipponense) aquaculture industry. However, the interplay between immune responses of M. nipponense and S. eriocheiris infection has not yet been fully elucidated. Herein, full-length transcriptome profiling of M. nipponense hemocytes...

The bay scallop (Argopecten irradians irradians) is one of the most important shellfish species in China. Since their introduction into China, only mass selection has been used in bay scallop breeding. With its gradual expansion and shortage of mate selection, population homozygosity increased, and fitness decreased. To investigate the effects of i...

The oriental river prawn Macrobrachium nipponense is a commercially important freshwater shrimp that is widely farmed in China. Aeromonas veronii is a conditional pathogen of farmed shrimp, which has caused huge economic losses to the industry. Therefore, there is urgency to study the host-pathogen interactions between M. nipponense and A. veronii...

Aquatic environmental pollutants have various impacts on aquaculture. Specifically, sulfide has been established as being toxic to aquatic animals including the oriental river prawn Macrobrachium nipponense. In response, the hepatopancreas has been broadly studied, as it plays a pivotal role in arthropod nutrient digestion and absorption, energy su...

Spiroplasma eriocheiris (S. eriocheiris) infection causes a significant economic loss in Penaeus vannamei (P. vannamei) culture industry. However, the response of P. vannamei hemocytes to S. eriocheiris infection has not been extensively studied. In this study, we conducted full-length transcriptome and long non-coding RNA (lncRNA) analyses of P. v...

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...

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...

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

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...

Ammonia-N is a major physiological challenge for prawns in culture. The alpha-2-macroglobulin (α2-macroglobulin, α2M) gene is a multifunctional protein with a significant role in the innate immunity. In this study, the full-length cDNA of α2M (Mnα2M) from M. nipponense was amplified and the 4805 bp cDNA contains a 4422 bp open reading frame (ORF)....

Mulinia lateralis (Say, 1822) is a species of the bivalve family Mactridae and represents a promising model species for molluscan research. In this study, the complete mitochondrial genome (mitogenome) of M. lateralis was sequenced and assembled for the first time. The 21,668 bp mitogenome contained 13 protein-coding genes, 2 rRNAs, 22 tRNA genes,...

Background The Chinese razor clam, Sinonovacula constricta , is one of the commercially important marine bivalves with deep-burrowing lifestyle and remarkable adaptability of broad-range salinity. Despite its economic impact and representative of the less-understood deep-burrowing bivalve lifestyle, there are few genomic resources for exploring its...

The oriental river prawn Macrobrachium nipponense is a highly adaptable, tolerant, and fecund freshwater prawn that inhabits a wide range of aquatic environments. The hepatopancreas of crustaceans is not only a site for secretion of digestive enzymes, and also plays important roles in several metabolic processes, such as lipid and carbohydrate meta...

Background Sex determination mechanisms in teleost fish broadly differ from mammals and birds, with sex chromosomes that are far less differentiated and recombination often occurring along the length of the X and Y chromosomes, posing major challenges for the identification of specific sex determination genes. Here, we take an innovative approach o...

Background Walking catfish (Clarias batrachus) is a freshwater fish capable of air-breathing and locomotion on land. It usually inhabits various low-oxygen habitats, burrows inside the mudflat, and sometimes “walks” to search for suitable environments during summer. It has evolved accessory air-breathing organs for respiring air and corresponding m...

Selective breeding is a common and effective approach for genetic improvement of aquaculture stocks with parental selection as the key factor. Genomic selection (GS) has been proposed as a promising tool to facilitate selective breeding. Here, we evaluated the predictability of four GS methods in Zhikong scallop (Chlamys farreri) through real datas...

Targeted genotyping of transcriptome-scale genetic markers is highly attractive for genetic, ecological, and evolutionary studies, but achieving this goal in a cost-effective manner remains a major challenge, especially for laboratories working on nonmodel organisms. Here, we develop a high-throughput, sequencing-based GoldenGate approach (called H...

In selective breeding, a central parameter in summarizing the proportion of variance due to genetics for the purpose of predicting gains from selection is realized heritability (h²). We applied the genome-wide complex trait analysis (GCTA) method to genome-wide SNP data obtained by 2b-RAD reduced-representation genotyping and phenotypic data for fo...

Channel catfish is the leading aquaculture species in the US, and one of the reasons for its application in aquaculture is its relatively high tolerance against hypoxia. However, hypoxia can still cause huge economic losses to the catfish industry. Studies on hypoxia tolerance, therefore, are important for aquaculture. Fish swimbladder has been con...

Significance Barbels are important sensory organs for food seeking of teleosts, reptiles, and amphibians, but the molecular basis of barbel development is unknown. Here, we exploited the barbel-less bottlenose catfish as a natural model to determine the genomic basis for barbel development. Through a series of comparative analyses using genome and...

Microbial communities that are present in aquaculture production systems play significant roles in degrading organic matter, controlling diseases, and formation of antibiotic resistance. It is important to understand the diversity and abundance of microbial communities and their genetic adaptations associated with environmental physical and chemica...

Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commerci...

The swimbladder is an internal gas-filled organ in teleosts. Its major function is to regulate buoyancy. Swimbladder exhibits great variations in size, shape, number of compartments or chambers among teleosts. However, the genomic control of swimbladder variations is unknown. Channel catfish (Ictalurus punctatus), blue catfish (Ictalurus furcatus),...

Chinese mitten crab (Eriocheir sinensis) is one of the most commercially important aquaculture species in China. The androgenic gland (AG) of crustaceans plays pivotal roles in the regulation of male differentiation and in maintaining the male sexual characteristics. In order to reveal related mechanisms in AG, we compared transcriptomes of AG betw...

Rhamnose-binding lectins (RBLs) are crucial elements associated with innate immune responses to infections and have been characterized from a variety of teleost fishes. Given the importance of RBL in teleost fishes, we sought to study the diversity and expression profiles of RBLs in an important cultured fish, Nile tilapia (Oreochromis niloticus) f...

Hypoxic condition is common in aquaculture, leading to major economic losses. Genetic analysis of hypoxia tolerance, therefore, is not only scientifically significant, but also economically important. Catfish is generally regarded as being highly tolerant to low dissolved oxygen, but variations exist among various populations, strains, and species....

In the version of this article that was originally published [1] there was an error with the author name "Karim Khalil" as it was incorrectly put as "Karim Kahlil". The original article was corrected.

DExD/H-box RNA helicases are motor proteins participating in nearly all aspects of cellular processes, especially in RNA metabolism. In this study, a total of 54 DExD/H-box RNA helicase genes including 37 DDX (DEAD-box) and 17 DHX (DEAH-box) genes were characterized in channel catfish (Ictalurus punctatus), and annotated through phylogenetic and sy...

Chemokines are a superfamily of structurally related chemotactic cytokines exerting significant roles in regulating cell migration and activation. Based on the arrangement of the first four cysteine residues, they are classified into CC, CXC, C and CX3C subfamilies. In this study, a complete set of 64 CC chemokine ligand (CCL) genes was systematica...

RNA-Seq is a technology to sequence transcriptomes using next-generation sequencing technologies. It has been widely used for analyses such as gene expression profiling and identification of differentially expressed genes (DEG). This chapter focuses on the design of RNA-Seq experiments and on the bioinformatics issues related to the assembly of RNA...

Single-nucleotide variations/polymorphisms (SNPs) are well-recognized markers for genetic studies due to their amenability to be genotyped with high automation and high abundance in the genome. SNP arrays have been applied to diverse genetic studies and breeding programs, such as genome-wide association studies (GWAS), linkage mapping and quantitat...

The advancement of next-generation sequencing (NGS) and computational abilities on data analysis has made single-nucleotide polymorphisms (SNPs) the most commonly used markers in a wide range of genetic analyses. This chapter introduces specific statistical models to separate true variations from artifacts, and details protocols (including command...

This chapter focuses on the identification of differentially expressed genes (DEGs) and the bioinformatics analysis of co-expressed genes. It presents demonstration of DEG identification using CLC Genomics Workbench and Trinity EdgeR. The chapter also presents demonstration of using the weighted gene co-expression network analysis (WGCNA) package f...

Single nucleotide polymorphisms (SNPs) are capable of providing the highest level of genome coverage for genomic and genetic analysis because of their abundance and relatively even distribution in the genome. Such a capacity, however, cannot be achieved without an efficient genotyping platform such as SNP arrays. In this work, we developed a high-d...

Chemokines are a superfamily of structurally related chemotactic cytokines exerting significant roles in regulating cell migration and activation. They are defined by the presence of four conserved cysteine residues and are divided into four subfamilies depending on the arrangement of the first two conserved cysteines residues: CXC, CC, C and CX3C....

Apolipoproteins are protein component of plasma lipoproteins. They exert crucial roles in lipoprotein metabolism and serve as enzyme cofactors, receptor ligands, and lipid transfer carriers in mammals. In teleosts, apolipoproteins are also involved in diverse processes including embryonic and ontogenic development, liver and digestive system organo...

Channel catfish (Ictalurus punctatus) has been recognized as a dominant freshwater aquaculture species in the United States. It is also a suitable model for studying the mechanisms of sex determination and differentiation as its sexual plasticity and exhibition of both genetic and environmental sex determination. The testicular differentiation in m...

Catfish represent 12% of teleost or 6.3% of all vertebrate species, and are of enormous economic value. Here we report a high-quality reference genome sequence of channel catfish (Ictalurus punctatus), the major aquaculture species in the US. The reference genome sequence was validated by genetic mapping of 54,000 SNPs, and annotated with 26,661 pr...

Interspecific hybrids provide a rich source for the analysis of allele-specific expression (ASE). In this work, we analyzed ASE in F1 hybrid catfish using RNA-Seq datasets. While the vast majority of genes were expressed with both alleles, 7-8 % SNPs exhibited significant differences in allele ratios of expression. Of the 66,251 and 177,841 SNPs id...

Bcl-2 proteins are of vital importance in regulation of apoptosis, and are involved in a number of biological processes such as carcinogenesis and immune responses. Bcl-2 genes have been well studied in mammals, while they are not well investigated in teleost fish including channel catfish, the major aquaculture species in the United States. In thi...

Septins are an evolutionarily conserved family of GTP-binding proteins. They are involved in diverse processes including cytokinesis, apoptosis, infection, neurodegeneration and neoplasia. In this study, through thorough data mining of existed channel catfish genomic resources, we identified a complete set of 15 septin genes. Septins were classifie...