As one of the key components of innate immune system, piscidins are likely to play pivotal role in the first defense line in fish. Piscidins own multiple resistance activity. A novel piscidin 5-like type 4 was excavated from Larimichthys crocea (termed Lc-P5L4) liver transcriptome immuned by Cryptocaryon irritans, and upregulated at 7 days post infection when secondary bacterial infection occurred. In the study, we characterized the antibacterial activity of Lc-P5L4. The liquid growth inhibition assay detected the recombinant Lc-P5L4 (rLc-P5L) had potent antibacterial activity to Photobacterium damselae. Scanning electron microscope (SEM) observed the cell surface of P. damselae collapsed to form pit, and membrane of some bacteria ruptured after co-incubation with rLc-P5L. Further, transmission electron microscope (TEM) was also employed to observe the intracellular microstructural damage, rLc-P5L4 caused cytoplasm contraction, pores formation and contents leakage. After knowing about its antibacterial effects, the preliminary antibacterial mechanism was also explored, western blot analysis showed rLc-P5L4 could bind to P. damselae through targeting to LPS. Agarose gel eletrophoresis analysis further showed rLc-P5L4 could also penetrate into cells and brought about genome DNA degradation. Therefore, rLc-P5L4 was of potential being a candidate to explore new antimicrobial drug or additive agent, especially to P. damselae.

优异种质资源的发掘利用对保障我国优质水产蛋白供给具有关键作用.大黄鱼是我国海水鱼类养殖产量最高的品种,种质资源是大黄鱼养殖产业健康和可持续发展不可或缺的物质基础,系统开展大黄鱼种质资源收集保存、鉴定评价和保护利用具有十分重要的战略意义.本文回顾了大黄鱼种质资源保护和开发利用的历史与现状,从科研、育种技术体系、产业和人才等方面剖析了当前面临的主要问题,围绕大黄鱼种业科技创新和新品种创制主线,提出了针对复杂经济性状(如抗病、抗逆和饲料利用效率等)创制重大新品种的发展方向,为实现大黄鱼良种覆盖率的显著提升,以及大黄鱼产业健康发展提供良种保障.

Abstract Background Kuruma shrimp, a major commercial shrimp species in the world, has two cryptic or sibling species, Marsupenaeus japonicus and Marsupenaeus pulchricaudatus. Codon usage analysis would contribute to our understanding of the genetic and evolutionary characteristics of the two Marsupenaeus species. In this study, we analyzed codon usage and related indices using coding sequences (CDSs) from RNA-seq data. Results Using CodonW 1.4.2 software, we performed the codon bias analysis of transcriptomes obtained from hepatopancreas tissues, which indicated weak codon bias. Almost all parameters had similar correlations for both species. The gene expression level (FPKM) was negatively correlated with A/T3s. We determined 12 and 14 optimal codons for M. japonicus and M. pulchricaudatus, respectively, and all optimal codons have a C/G-ending. The two Marsupenaeus species had different usage frequencies of codon pairs, which contributed to further analysis of transcriptional differences between them. Orthologous genes that underwent positive selection (ω > 1) had a higher correlation coefficient than that of experienced purifying selection (ω < 1). Parity Rule 2 (PR2) and effective number of codons (ENc) plot analysis showed that the codon usage patterns of both species were influenced by both mutations and selection. Moreover, the average observed ENc value was lower than the expected value for both species, suggesting that factors other than GC may play roles in these phenomena. The results of multispecies clustering based on codon preference were consistent with traditional classification. Conclusions This study provides a relatively comprehensive understanding of the correlations among codon usage bias, gene expression, and selection pressures of CDSs for M. japonicus and M. pulchricaudatus. The genetic evolution was driven by mutations and selection pressure. Moreover, the results point out new insights into the specificities and evolutionary characteristics of the two Marsupenaeus species.

The carbohydrate recognition domain (CRD) is the key component of C-type lectins (CTLs) with the capacity to recognize and eliminate invading pathogens. Herein, the recombinant proteins of four CRDs identified from the kuruma shrimp, Marsupenaeus japonicus, were produced and purified by an Escherichia coli expression system and affinity chromatography. Bacterial binding and antibacterial assays showed that the four CRDs displayed various bacterial binding and antibacterial activities against different bacteria. Among the four recombinant CRDs, His-CRD2-3 exhibited the broadest spectrum of bacterial binding and antibacterial activities against gram-negative bacteria (Vibrio parahaemolyticus, V. alginolyticus and V. harveyi) and gram-positive bacteria (Staphylococcus aureus and Micrococcus lysodeikticus). Moreover, the four recombinant CRDs showed different capacities to regulate the expression of several immune effector genes (MjCTL3, MjCTL4, MjCTL, Mjily and Mjsty), among which His-CRD2-3 displayed broader and stronger inductive effects on these immune effector genes. This study indicated that the four CRDs participated in immune defense by binding and killing bacteria and regulating the transcription of other immune effector genes. In addition, our results suggested that His-CRD2-3 might be a promising agent for the prevention and treatment of bacteriosis.

福建省是我国海洋渔业大省,海水养殖产量位居全国第一,海洋捕捞产量位居全国第三,海洋渔业为保障优质动物蛋白供给、提高全民营养健康水平、促进渔业产业兴旺和渔民生活富裕等做出突出贡献,同时,在实现碳中和/减排二氧化碳、净化水质/缓解水域富营养化等生态服务功能方面也发挥着重要作用.该文在广泛调研福建省海洋渔业资源禀赋、发展现状、制度建设等方面的基础上,深入剖析福建省海水养殖、伏季休渔、限额捕捞、增殖渔业等面临的问题和挑战,综合分析了国内外渔业高效管理和实践的成功案例,从发展环境友好型的海水养殖业和发展资源养护型的捕捞业两个方面,提出了适宜福建省海洋渔业绿色发展的实施路径、保障措施和政策建议,以期为福建省海洋渔业绿色发展提供技术支撑.

Stocking density is a biotic factor affecting the production of cultivated animals in aquaculture. Herein, a rearing trial was conducted to investigate the impact of stocking density on the survival, growth performance and physical injury of Marsupenaeus japonicus juveniles in a flowing water aquaculture system. Five stocking densities were examined in this study, that is, 10, 20, 40, 80 and 160 individuals/m(2). Throughout the experiment, ammonia nitrogen and nitrite concentrations ranged from 0.02 +/- 0.006 mg/L to 0.08 +/- 0.035 mg/L and 0.002 +/- 0.001 mg/L to 0.076 +/- 0.021 mg/L respectively. The survival rate, specific growth rate (SGR), weight gain (WG), absolute growth rate (AGR) and coefficient of variation for weight (CV) across the stocking densities ranged from 90.38 +/- 3.20% to 94.33 +/- 4.73%, 1.42 +/- 0.16%/day to 1.53 +/- 0.05%/day, 1.09 +/- 0.19 g to 1.15 +/- 0.16 g, 0.018 +/- 0.003 g/day to 0.019 +/- 0.004 g/day and 16.21 +/- 5.78% to 35.09 +/- 10.68% respectively. Within the investigated densities, the survival rate and the abovementioned growth parameters were not significantly (p > .05) affected by the stocking density, consequently, a higher stocking density resulted in a significantly (p < .05) greater final biomass. The results regarding physical injury showed that the antennal breakage rate displayed a tendency of a positive correlation with the stocking density. Overall, the current study provides basic data for establishing a viable intensive farming system for M. japonicus and a promising indicator for easily assessing the crowding stress status of M. japonicus.

Air exposure stress is a common phenomenon for commercial crustacean species in aquaculture and during waterless transportation. However, the antioxidant responses to air exposure discussed in previous studies may be insufficient to present the complexities involved in this process. The comprehensive immune responses, especially considering the immune genes, cell apoptosis, and epigenetic changes, are still unknown. Accordingly, we investigated the multifaceted responses of Marsupenaeus japonicus to air exposure. The results showed that the expression profiles of the apoptosis genes (e.g., IAP, TXNIP, caspase, and caspase-3) and the hypoxia-related genes (e.g., hsp70, hif-1α, and HcY) were all dramatically induced in the hepatopancreas and gills of M. japonicus. Heart rates, T-AOC (total antioxidant capacity) and lactate contents showed time-dependent changes upon air exposure. Air exposure significantly induced apoptosis in hepatopancreas and gills. Compared with the control group, the apoptosis index (AI) of the 12.5 h experimental group increased significantly (p < 0.05) in the hepatopancreas and gills. Most individuals in the experimental group (EG, 12.5 h) had lower methylation ratios than the control group (CG). Air exposure markedly reduced the full-methylation and total-methylation ratios (31.39% for the CG and 26.46% for the EG). This study provided a comprehensive understanding of the antioxidant responses of M. japonicus considering its physiology, innate immunity, apoptosis, and DNA methylation levels, and provided theoretical guidance for waterless transportation.

Pseudomonas plecoglossicida is a rod-shaped, gram-negative bacterium with flagella. It causes visceral white spot disease and high mortality in Larimichthys crocea during culture, resulting in serious economic loss. Analysis of transcriptome and quantitative real-time polymerase chain reaction (PCR) data showed that dksA gene expression was significantly up-regulated after 48 h of infection with Epinephelus coioides (log 2FC=3.12, P<0.001). RNAi of five shRNAs significantly reduced the expression of dksA in P. plecoglossicida, and the optimal silencing efficiency was 96.23%. Compared with wild-type strains, the symptoms of visceral white spot disease in L. crocea infected with RNAi strains were reduced, with time of death delayed by 48 h and mortality reduced by 25%. The dksA silencing led to a substantial down-regulation in cellular component-, flagellum-, and ribosome assembly-related genes in P. plecoglossicida, and the significant up-regulation of fliC may be a way in which virulence is maintained in P. plecoglossicida. The GO and KEGG results showed that RNAi strain infection in L. crocea led to the down-regulation of inflammatory factor genes in immune-related pathways, which were associated with multiple immune response processes. Results also showed that dksA was a virulence gene in P. plecoglossicida. Compared with the wild-type strains, RNAi strain infection induced a weaker immune response in L. crocea.

The kuruma shrimp (Marsupenaeus japonicus) includes two cryptic species, which are distributed mostly allopatrically but co-occur in the northern South China Sea (from Huilai to Beihai). To obtain a better understanding of the fine-scale genetic structure and parapatric diversification of these two varieties in the northwestern Pacific region, we used a genotyping-by-sequencing (GBS) and comparative transcriptomics approach to establish their phylogenetic relationships. Using the GBS technique, we genotyped 28891 SNPs in 160 individuals in the Northwest Pacific. The results supported two highly diverged evolutionary lineages of kuruma shrimp (var. I and II). The ND and XM populations showed complex genetic patterns, which might be affected by the complex environment of the Taiwan Strait. In addition, the migration rates and inbreeding coefficients of XM and BH were much lower than those of the other populations, which might be related to the land-sea changes and complex ocean currents in the Taiwan Strait and Qiongzhou Strait. Based on the synonymous substitution rates (ds) of 2,491 candidate orthologs, we estimated that the divergence time between the two varieties was 0.26~0.69 Mya. Choice and no-choice interbreeding experiments provided support for the biological species concept, by showing the existence of reproductive isolation or incompatibility. In view of these differences between the two Marsupenaeus species, we believe that it is essential and urgent to establish a genetic database for each and reevaluate their ecological suitable conditions in order to improve species-specific culturing techniques. Moreover, this research can serve as a case study for future research on speciation and hybridization.

C-type lectins (CTLs) are vital molecules in crustacean innate immunity with the capacity to recognize and eliminate invaders, such as viruses and bacteria. Here, two novel CTLs were identified from the kuruma shrimp Marsupenaeus japonicus, and their molecular characteristics and immune function were investigated. Sequence analysis revealed that the two CTLs possessed the typical CTL structure and function features. Tissue distribution analysis showed that the two CTLs were most abundantly expressed in the hepatopancreas and weakly expressed in other examined tissues. The transcription of the two CTLs significantly increased in the hepatopancreas of shrimp challenged with both white spot syndrome virus (WSSV) and Vibrio parahaemolyticus, and MjCTL4 was found to be more sensitive to the two pathogens than MjCTL3, being induced at relatively faster and higher increments. GST pull-down assays showed that the two CTLs could directly interact with several WSSV envelope proteins (VP19, VP24, VP26 and VP28). Moreover, the two CTLs displayed obvious binding and antibacterial ability to V. parahaemolyticus, and MjCTL3 exhibited stronger anti-V. parahaemolyticus activity than MjCTL4. These results suggest that the two novel CTLs might function as pattern recognition receptors (PRRs) and antibacterial molecules in M. japonicus innate immunity, and the two CTLs may be alternative agents for the prevention and treatment of diseases caused by WSSV and V. parahaemolyticus.

Heat shock factors (HSFs) and heat shock proteins (HSPs) are crucial regulators and effectors of the heat shock response (HSR). In this study, the full-length cDNA sequences of MjHSP10 and MjHSF1 were cloned by rapid amplification of cDNA ends (RACE). The deduced MjHSP10 and MjHSF1 amino acid (aa) sequences exhibited conserved structures and the functional features of HSP10 and HSF1, respectively. The tissue distributions and mRNA expression profiles of the two genes in response to heat stress were analyzed by quantitative real-time PCR (qRT-PCR). MjHSP10 and MjHSF1 were ubiquitously expressed in various tissues. Heat stress induced a significant increase in MjHSP10 expression that tend to positively correlate with temperature. Additionally, MjHSF1 transcription was up-regulated less than MjHSP10 transcription under heat stress. MjHSF1 expression in the hepatopancreas was up-regulated under only long-term (48 h) heat stress, and MjHSF1 transcription in the gill increased under only acute (34 °C) heat stress. MjHSF1 knockdown by RNA interference (RNAi) down-regulated MjHSP10 expression. Glutathione-S-transferase (GST) pull-down assays showed an interaction between MjHSP10 and the DNA-binding domain (DBD) of MjHSF1. This study provided new insights into cross talk between HSP10 and HSF1 in Marsupenaeus japonicus.

As invertebrates, shrimp are generally thought to solely rely on their innate immune system to combat invading pathogens. Recently, an increasing number of studies have revealed that the innate immune response of invertebrates exhibits diversity and specificity based on their diverse immune molecules. Herein, a full-length transcriptome analysis of several immune-related tissues (hepatopancreas, gill, hemocytes, stomach and intestine) in the kuruma shrimp (Marsupenaeus japonicus) was conducted to identify immune-related molecules with a focus on transcript variations. In total, 11,222 nonredundant full-length transcripts with an N50 length of 5174 were obtained, and most of these transcripts (94.84%) were successfully annotated. In addition, a total of 147 long noncoding RNAs (lncRNAs) were also predicted. Importantly, transcript variants of several vital immune-related genes were observed, including twenty-five alpha-2-macroglobulins (α2-Ms), ten Toll-like receptors (TLRs), six C-type lectins (CTLs), five M-type lectins (MTLs) and three Down syndrome cell adhesion molecules (Dscams). Furthermore, 509 nonredundant full-length transcripts were predicted to be generated from alternative splicing (AS) events, which contribute to the diversity of immune molecules. Overall, our study provides valuable data on the full-length transcripts of M. japonicus, which will facilitate the exploration of immune molecules in this species. Moreover, numerous transcript variants of immune molecules detected in this study provide clues for further investigating the diversity and specificity of the innate immune response in shrimp.

Marsupenaeus japonicus is one of the most important penaeid shrimp farmed in China. As a typical closed thelycum penaeid shrimp, the morphological changes in the spermatozoa during the journey from the testis to the female thelycum remain unclear in this species. Herein, an ultrastructural comparison of the spermatozoa in the testis (TE), vas deferens (VD), and the spermatophore in the male terminal ampoule (SA) and the female seminal receptacle (SR) of M. japonicus was conducted. The spermatozoa in the VD, SA and SR shared typical morphological characteristics of the spermatozoa of decapod dendrobranchiates, including a spherical main body and a slender spike. However, no spike was observed in the spermatozoa collected from the TE. The spike of the spermatozoa in the SA and SR was longer than that in the VD, whereas no significant difference in spike length was observed between the spermatozoa from the SA and SR. The basic ultrastructure of the spermatozoa in the VD, SA and SR was similar, except for some differences in the nuclear region. The main body of the spermatozoa comprised the cytoplasmic band, nuclear region, several small and large vesicles, and the basal region of the acrosomal structure. The nuclear materials in the spermatozoa from the TE were more electron-dense than those in the VD, SA and SR, while the nuclear region of the spermatozoa was more electron-lucent in the SR than in the VD and SA. These findings preliminarily reveal the ultrastructural changes in M. japonicus spermatozoa during the journey from the testis to the female thelycum and provided a theoretical foundation for developing effective artificial insemination methods in this species.

C-type lectins (CTLs) are immune molecules that are crucial to the invertebrate innate immune system with the primary function of recognizing invading pathogens. In the present study, a novel CTL was cloned from Marsupenaeus japonicus (MjCTL), and its tissue distribution and expression patterns over time in response to white spot syndrome virus (WSSV) and Vibrio parahaemolyticus were further investigated. The open reading frame (ORF) of MjCTL was 513 bp and encoded a polypeptide of 170 amino acids, which contained a signal peptide and a carbohydrate recognition domain (CRD) that are typical for CTLs. MjCTL was primarily expressed in the hepatopancreas and weakly expressed in hemocytes, gill, stomach, intestine, heart, muscle and eyestalk. The expression level of MjCTL in the hepatopancreas was dramatically increased at 48 h post-injection with WSSV at a dosage of 1 × 105 virions. Glutathione-S-transferase (GST) pull-down assays showed that MjCTL could directly bind to several WSSV envelope proteins, including VP19, VP24, VP26 and VP28. Moreover, MjCTL displayed antibacterial activity against V. parahaemolyticus. Our results indicated that MjCTL exhibited multiple functions in innate immune response against pathogens.

采用Piscidin基因串联表达的方案,通过Eco31Ⅰ限制性内切酶定向连接方法合成Pseudosciaena crocea-

Temperature is one of the most important variables that influence aquatic organisms. This study aimed to test physiological and molecular differences in the thermal tolerance of two morphologically similar Marsupenaeus japonicus. The physiological parameter was the upper thermal limit, tested via the critical thermal maximum, and the molecular parameter was the relative messenger RNA expression of heat shock proteins (HSP40, HSP60, HSP70 and HSP90), quantified via real-time polymerase chain reaction. Oxygen consumption of shrimp was measured with a respirometer. M. japonicus variety II showed a higher critical thermal maxima and survival rate and lower oxygen consumption rate than variety I, suggesting that it had higher thermal tolerance and acclimatory plasticity. M. japonicus variety I showed significantly higher production of HSP70 and HSP90, suggesting that these shrimp may have experienced more thermal damage. By comparing the differences in the stress response between two morphologically similar M. japonicus, this study provides useful information for the aquaculture of M. japonicus.

Host-pathogen interactions are highly complex, involving large dynamic changes in gene expression during infection. These interactions are fundamental to understanding anti-infection immunity of hosts, as well as the pathogenesis of pathogens. For bacterial pathogens interacting with animal hosts, time-resolved dual RNA-seq of infected tissue is difficult to perform due to low pathogen load in infected tissue. In this study, an acute infection model of Larimichthys crocea infected by Pseudomonas plecoglossicida was established. The spleens of infected fish exhibited typical symptoms, with a maximum bacterial load at two days post-injection (dpi). Time-resolved dual RNA-seq of infected spleens was successfully applied to study host-pathogen interactions between L. crocea and P. plecoglossicida. The spleens of infected L. crocea were subjected to dual RNA-seq, and transcriptome data were compared with those of noninfected spleens or in vitro cultured bacteria. Results showed that pathogen-host interactions were highly dynamically regulated, with corresponding fluctuations in host and pathogen transcriptomes during infection. The expression levels of many immunogenes involved in cytokine-cytokine receptor, Toll-like receptor signaling, and other immune-related pathways were significantly up-regulated during the infection period. Furthermore, metabolic processes and the use of oxygen in L. crocea were strongly affected by P. plecoglossicida infection. The WGCNA results showed that the metabolic process was strongly related to the entire immune process. For P. plecoglossicida, the expression levels of motility-related genes and flagellum assembly-related genes were significantly up-regulated. The results of this study may help to elucidate the interactions between L. crocea and P. plecoglossicida.

Background: Marsupenaeus japonicus , a major commercial shrimp species in the world, has two cryptic or sibling species, Marsupenaeus japonicus and Marsupenaeus pulchricaudatus . Due to the lack of genomic information, little is known about the correlations among codon usage bias, gene expression, and evolutionary trends in Marsupenaeus orthologs. Results: Using the CodonW 1.4.2 software, we performed the codon bias analysis of two Marsupenaeus species transcriptomes. The average contents of GC and ENc were 51.61% and 52.1 for VI ( M. japonicus ), 51.54% and 52.22 for VII ( M. pulchricaudatus ), respectively. Parity Rule 2 (PR2) plot analysis showed that purines (A and G) were used more frequently than pyrimidines (C and T) in two Marsupenaeus species. The average ENc value was 52.1 and 52.22 for M. japonicus and M. pulchricaudatus , respectively. Overall, orthologous genes that underwent positive selection (ω > 1) had a higher correlation coefficient than that experienced purifying selection (ω < 1). In M. japonicus , the relationships were highly significant positive about Axis 1 and A3, T3 and ENc ( p < 0.01). However, all relationships in M. pulchricaudatus were the opposite. We determined 12 and 14 optimal codons for M. japonicus and M. pulchricaudatus , respectively. Two Marsupenaeus species had 31 different codon pairs. The results of multi-species clustering based on codon preference were consistent with traditional classification. Conclusions: We characterized the codon usage patterns of the two Marsupenaeus species and the evolutionary trends in Marsupenaeus orthologs, which provides new insights into the genetic divergence and the phylogenetic relationships of two Marsupenaeus species.

The interactions between host and pathogen is exceedingly complex, which involves alterations at multiple molecular layers. However, research to simultaneously monitor the alterations of transcriptome and proteome between a bacterial pathogen and aquatic animal host through integrated dual RNA-seq and dual iTRAQ of tissue during infection is currently lacking. The important role of a diguanylate cyclase gene (L321_RS15240) in pathogenicity of Pseudomonas plecoglossicida against Epinephelus coioides was suggested by previous dual RNA-seq of our lab. Then L321_RS15240-RNAi strains of P. plecoglossicida were constructed with pCM130/tac, and the mutant with the best silencing effect was selected for follow-up study. The RNAi of L321_RS15240 resulted in a significant decrease in bacterial virulence of P. plecoglossicida. The E. coioides spleens infected by wild type strain or L321_RS15240-RNAi strain of P. plecoglossicida were subjected to dual RNA-seq and dual iTRAQ, respectively. The results showed that: RNAi of L321_RS15240 led to 1)alterations of host transcriptome associated with complement and coagulation cascades, ribosome, arginine and proline metabolism, and oxidative phosphorylation; 2)high expression of host proteins which related to phagosome and metabolism responses (metabolism of glutathione, amino sugar and nucleotide sugar); 3)the highly differentially expression of host lncRNAs and miRNAs. The differentially expressed proteins and mRNAs of pathogen were different after infection, but the functions of these proteins and mRNAs were mainly related to metabolism and virulence. This study provides a new insight to comprehensively understand the gene functions of pathogens and hosts at multiple molecular layers during in vivo infection.

Kuruma shrimp, a major farmed shrimp species in the world, includes two cryptic or sibling species, Form I (Marsupenaeus japonicus) and Form II (Marsupenaeus pulchricaudatus). Due to the lack of genomic resources, little is known about the molecular mechanisms associated with immune defense and hypoxia tolerance. Here, we sequenced the transcriptomes of two closely related Marsupenaeus species and compared genomic divergence. This study obtained 77049 and 84561 unigenes with N50 values of 1281bp and 1244bp for M. japonicus and M. pulchricaudatus, respectively, and 5036 pairs of putative orthologs were identified between two Marsupenaeus species. Estimation of Ka/Ks ratios indicated that 165 orthologous genes may be under positive selection (Ka/Ks > 0.5), including 49 pairs with a Ka/Ks ratio >1. According to the peak of synonymous rates, the divergence time between M. japonicus and M. pulchricaudatus was about 0.26-0.69 Mya. These positively selected orthologous genes related to the immune process mainly comprised single VWC domain protein, legumain, ras-related C3 botulinum, caspase, C-type lectin and were enriched in functions related to immune (Toll-like receptor and PI3K-Akt signaling) and hypoxia signaling (HIF-1 signaling and VEGF signaling). In this study, dozens of caspase-like unigenes were screened from two Marsupenaeus transcriptomes. Among these, the PjCaspase orthologous gene was subjected to positive selection (Ka/Ks = 1.22), which had different secondary and three-dimensional structure prediction. Based on the single copy caspase gene, eight populations of Marsupenaeus species were divided into two phylogeographic lineages from the East and South China. We characterized the transcriptomes of the two Marsupenaeus species and obtained several key orthologs associated with immune defense and hypoxia tolerance, which provides new insights into the immunity and genetic divergence of the two varieties. Moreover, this study will facilitate further comparative genomic studies of the two varieties.