Endemic to Australia, jade perch ( Scortum barcoo ) is a highly profitable freshwater bass species. It has extraordinarily high levels of omega-3 polyunsaturated fatty acids (PUFAs), which detailed genes involved in are largely unclear. Meanwhile, there were four chromosome-level bass species have been previous sequenced, while the bass ancestor genome karyotypes have not been estimated. Therefore, we sequenced, assembled and annotated a genome of jade perch to characterize the detailed genes for biosynthesis of omega-3 PUFAs and to deduce the bass ancestor genome karyotypes. We constructed a chromosome-level genome assembly with 24 pairs of chromosomes, 657.7 Mb in total length, and the contig and the scaffold N50 of 4.8 Mb and 28.6 Mb respectively. We also identified repetitive elements (accounting for 19.7% of the genome assembly) and predicted 26,905 protein-coding genes. Meanwhile, we performed genome-wide localization and characterization of several important genes encoding some key enzymes in the biosynthesis pathway of PUFAs. These genes may contribute to the high concentration of omega-3 in jade perch. Moreover, we conducted a series of comparative genomic analyses among four representative bass species at a chromosome level, resulting in a series of sequences of a deductive bass ancestor genome.

The dsRNA-activated protein kinase R (PKR) is one of key antiviral effectors induced by interferons (IFNs), and its functions are largely unknown in tilapia, an important commercial fish species suffering from several viral infectious diseases. In the present study, a PKR gene named On-PKR was identified and cloned from Nile tilapia, Oreochromis niloticus. On-PKR gene was constitutively expressed in all tissues examined, with the highest expression level observed in head kidney and liver, and was rapidly induced in all organs/tissues tested following the stimulation of poly(I:C). Importantly, the expression of On-PKR is induced by group I and group II IFNs with distinct induction kinetics in vivo: group I IFN elicits a relative delayed but sustained induction of On-PKR, whereas group II IFN triggers a rapid and transient expression of On-PKR. Moreover, the overexpression of On-PKR has been proven to inhibit the protein translation and virus replication in fish cells. The present study thus contributes to a better understanding of the functions of antiviral effectors in tilapia, and may provide clues for the prevention and therapy of viral diseases in fish.

DEAD-box helicase 41 (DDX41) is a key cytosolic DNA sensor playing critical roles in the regulation of type I IFN responses, and their functions have been well-characterized in mammals. However, little information is available regarding the function of fish DDX41. In this study, a DDX41 gene, named On-DDX41, was identified in Nile tilapia, Oreochromis niloticus. The predicted protein of On-DDX41 contains several structural features known in DDX41, including conserved DEADc and HELICc domains, and a conserved sequence "Asp-Glu-Ala-Asp (D-E-A-D)". On-DDX41 gene was constitutively expressed in all tissues examined, with the highest expression level observed in liver and muscle, and was inducible after poly(I:C) stimulation. Moreover, the overexpression of On-DDX41 can elicit a strong activation of both zebrafish IFN1 and IFN3 promoter in fish cells treated with poly(dA:dT). The present study thus contributes to a better understanding of the functional properties of DDX41 in fish.

Interferon regulatory factor 1 (IRF1) is an important regulator in controlling the transcription of type I interferon genes, and its functions have been well-characterized in mammals, birds and fish. However, little information is available regarding the function of amphibian IRF1. In this study, an IRF1 gene homolog named as Xt-IRF1 was identified in the Western clawed frog (Xenopus tropicalis), an amphibian model specie widely used for comparative immunology research. Xt-IRF1 and IRF1 in other vertebrates possess similar genomic structure and flanking genes, and were grouped together to form a separate clade in phylogenetic tree. In addition, Xt-IRF1 gene was constitutively expressed in all tissues examined, with the highest expression level observed in spleen, and was inducible after poly(I:C) stimulation. Importantly, the expression of Xt-IRF1 was markedly induced by recombinant type I interferon, and Xt-IRF1 induced a strong activation of both IFNβ and ISRE promoters. The present study opens the door to investigate the roles of IRF1 in amphibians, and thus contributes to a better understanding of the functional evolution of IRFs in lower tetrapods.

Type I interferons are a subset of cytokines playing central roles in host antiviral defense, and their effects depend on the interaction with the heterodimeric receptor complex. Surprisingly, two pairs of the receptor subunits, CRFB1 and CRFB5, and CRFB2 and CRFB5, have been identified in fish, but the studies about preferential receptor usage of different fish IFN subtypes are rather limited. In this study, the three receptor chains of type I IFNs named as On-CRFB1, On-CRFB2 and On-CRFB5 were identified in Nile tilapia, Oreochromis niloticus. These three genes were constitutively expressed in all tissues examined, with the highest expression level observed in muscle and liver, and were rapidly induced in liver following the stimulation of poly(I:C). Interestingly, it is possible that all three subtypes of tilapia IFNs are able to signal through two pairs of the receptor subunits, On-CRFB1 and On-CRFB5, and On-CRFB2 and On-CRFB5. More importantly, tilapia group I IFNs (On-IFNd and On-IFNh) preferentially signal through a receptor complex composed of On-CRFB1 and On-CRFB5, and group II IFNs (On-IFNc) preferentially signal through a receptor complex comprised of On-CRFB2 and On-CRFB5. The present study thus provides new insights into the receptor usage of group I and group II IFNs in fish.

Streptococcus agalactiae is a Gram-positive facultative intracellular bacterium that leads to severe economic loss of tilapia worldwide. Previous studies demonstrated that CD40 contributes to host protection against intracellular injection. In this study, CD40 was characterized from Nile tilapia (Oreochromis niloticus), named OnCD40. Sequence analysis showed that open reading frame of OnCD40 was 933 bp, containing a single peptide, a transmembrane domain and four cysteine-rich domains. The qRT-PCR revealed that OnCD40 was expressed in all examined tissues with the most abundant ones in spleen and thymus. After S. agalactiae stimulation, the expression of OnCD40 was significantly induced in most of the detected organs. Moreover, OnCD40-overexpressing fish elicited significant protection against subsequent S. agalactiae challenge; approximately 10000-fold fewer bacteria were detected in spleen of OnCD40-overexpressing fish in comparison with control fish. Thus, CD40 had protecting function in Nile tilapia against intracellular pathogens.

Fish appear to harbour a complex type I IFN repertoire containing subgroups a, b, c, d, e, f, and h, and IFNh is only reported in perciform fishes. However, no multiple copies of IFNh gene has been identified in fish to date. In this study, two IFNh genes named On-IFNh1 and On-IFNh2 were cloned from Nile tilapia, Oreochromis niloticus. The predicted proteins of On-IFNh1 and On-IFNh2 contain several structural features known in type I IFNs, and estimation of divergence time revealed that these two genes may have arisen from a much recent local duplication event. On-IFNh genes were constitutively expressed in all tissues examined, with the highest expression level observed in gill, and were rapidly induced in all organs/tissues tested following the stimulation of poly(I:C). In addition, both recombinant On-IFNh1 and On-IFNh2 trigger a relative delayed but sustained induction of interferon-stimulated genes (ISGs), whereas recombinant On-IFNc elicits a rapid and transient expression of ISGs in vivo. The present study thus contributes to a better understanding of the functional properties of tilapia interferons, and also provides a new insight into the evolution of IFNh in fish.

Interferons are a family of class II α-helical cytokines playing vital roles in antiviral immune response, and little information is available to date regarding the interferon system of tilapia. In this study, a type I IFN gene, named On-IFNc, was identified in Nile tilapia, Oreochromis niloticus. The predicted protein of On-IFNc contains several structural features known in type I IFNs, and On-IFNc was clustered together with the known IFNc in fish into a separated clade in the phylogenetic tree. On-IFNc gene was constitutively expressed in all tissues examined, with the highest expression level observed in liver, and was rapidly induced in all organs/tissues tested following the stimulation of poly(I:C). In addition, recombinant On-IFNc has been proven to markedly induce the expression of the antiviral effectors, Mx and viperin, the signalling components, STAT1, STAT2, and IRF9, and the transcription factors, IRF3 and IRF7, as well as the tyrosine phosphorylation of STAT1 and STAT2 in fish cells. Furthermore, recombinant On-IFNc has been proven to possess antiviral activity against ISKNV. The present study thus contributes to a better understanding of the functional properties of the type I IFN system in tilapia.

Nile tilapia (Oreochromis niloticus) is a pivotal economic fish that has been plagued by Streptococcus infections. Tumor necrosis factor receptor-associated factor 5 (TRAF5) is a crucial adaptor molecule, which can trigger downstream signaling cascades involved in immune pathway. In this study, Nile tilapia TRAF5 coding sequence (named OnTRAF5) was obtained, which contained typical functional domains, such as RING, zinc finger, coiled-coil and MATH domain. Different from other TRAF molecules, OnTRAF5 had shown relatively low identify with its homolog, and it was clustered into other teleost TRAF5 proteins. qRT-PCR was used to analysis the expression level of OnTRAF5 in gill, skin, muscle, head kidney, heart, intestine, thymus, liver, spleen and brain, In healthy Nile tilapia, the expression level of OnTRAF5 in intestine, gill and spleen were significantly higher than other tissues. While under Streptococcus agalactiae infection, the expression level of OnTRAF5 was improved significantly in all detected organs. Additionally, over-expression WT OnTRAF5 activated NF-κB, deletion of RING or zinc finger caused the activity impaired. In conclusion, OnTRAF5 participate in anti-bacteria immune response and is crucial for the signaling transduction.

肽聚糖识别蛋白(Peptidoglycan recognition proteins,PGRPs)是一类高度保守的模式识别受体(Pattern recognition receptors,PRRs)家族,能够识别细菌细胞壁的主要成分肽聚糖,进而激活并调节机体的先天性免疫反应.目前已报道的鱼类PGRP共23种,根据氨基酸序列的不同,PGRPs主要分为3类,分别是短型、中型和长型PGRPs.尽管鱼类PGRPs在大小、结构域布局及亚细胞定位方面有一定差异,但其C端的PGRP结构域是高度保守的.鱼类PGRPs在不同组织中广泛表达,在不同细菌的刺激下,鱼类PGRPs在各免疫组织的表达量均明显改变,推测鱼类PGRPs参与了机体的免疫应答过程.此外,鱼类PGRPs在生理过程、胚胎发育的先天性免疫调节中也扮演了重要角色.目前有关鱼类PGRPs的功能研究主要集中在病原识别能力,酰胺酶活性、杀菌抑菌性和免疫调节机制四个方面,尽管已经取得了一定的进展,然而对其作用机制的研究还不够深入,未来需要进一步深入的研究.针对鱼类PGRPs的结构、表达及功能进行综述,旨在为今后深入研究鱼类PGRPs的功能及应用提供思路.

蜡状芽孢杆菌是能产生孢子的革兰氏阳性菌,广泛分布于水体和土壤中,因能引起食物中毒而广为人知.本研究中,从养殖大菱鲆体表分离到一株溶血性细菌,经形态学鉴定和系统发育学分析,鉴定为蜡状芽孢杆菌.根据分离的时间和地点,这株溶血性的菌株被命名为蜡状芽孢杆菌WH2015.溶血试验证实WH2015菌株能够裂解羊红细胞.对蜡状芽孢杆菌WH2015基因组测序和分析的结果显示其基因组大小为5.8Mb,平均G+C含量为35％,有6 568个基因.与其它蜡状芽孢杆菌株系进行比较基因组分析显示,WH2015菌株基因组几乎拥有所有的核心溶血性基因,提示其溶血机理与其它报导过蜡状芽孢杆菌株系的溶血机理相似.本研究在分离鉴定养殖大菱鲆体表溶血性蜡状芽胞杆菌WH2015的基础上,对其基因组进行了测序和分析并鉴定了其所具有的致病性基因和毒力因子,帮助我们理解由蜡状芽孢杆菌引起的养殖大菱鲆疾病,以及为其防治措施的实施和疾病的治疗提供可靠的理论基础.