Comparative mitochondrial genomics and phylogenetics for species of the snakehead genus Channa Scopoli, 1777 (Perciformes: Channidae)

The family Channidae, members of which are commonly known as snakehead fish, includes 53 Channa species and three Parachanna species. In this study, we characterized mitochondrial genomes (mitogenomes) of five Channa species (C. andrao, C. bleheri, C. ornatipinnis, C. pulchra, and C. stewartii) for the first time. We compared the mitogenomes with the mitogenomes of 11 other Channidae fish. The newly sequenced mitogenomes were 16,714 - 16,895 bp in length and contained 37 typical genes [13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs) and 22 transfer RNA genes (tRNAs)]. Positive AT-skews and negative GC-skews were found in the mitogenomes of Channidae. Most PCGs started with the conventional start codon, ATN; however, the sequence of the stop codon was variable. There was no essential difference in relative synonymous codon usage (RSCU) among the Channidae mitogenomes. The fastest-evolving gene atp8 and slowest-evolving gene cox1 were identified using Ka/Ks and pairwise relative genetic distance (p-distance). The displacement loop (D-loop) regions showed great variability, which affected the size of Channa mitogenomes. One origin of replication on the light strand (O_L) region was found between trnN and trnC in the mitogenomes of Channidae. Phylogenetic analysis revealed three new sister pairs (C. andrao + C. bleheri, C. ornatipinnis + C. pulchra, and C. stewartii + C. gachua). Phylogenetic relationships established between the five Channa species based on mitogenomes were also supported by their morphological characteristics and geographical distribution. The novel information we obtained about these mitogenomes will contribute to elucidating the complex relationships among Channa species.

Piscivore stocking significantly suppresses small fish but does not facilitate a clear-water state in subtropical shallow mesocosms: A biomanipulation experiment

Biomanipulation by piscivore stocking has been widely used to combat eutrophication in north temperate lakes, but its applicability in warm lakes has not yet been well elucidated. Here, we used experimental mesocosms to test the effects of a native benthi-piscivore (snakehead, Channa argus Cantor) on water clarity under subtropical conditions where small omni-benthivorous fish like crucian carp (Carassius carassius L.) prevail. Our results showed that, despite of a great reduction of crucian carp biomass, snakehead stocking did not create a strong trophic cascade as neither (herbivorous) zooplankton biomass nor their grazing pressure, indicated by biomass ratio of (herbivorous) zooplankton to phytoplankton, changed significantly. Moreover, snakehead stocking significantly increased water non-algal turbidity as well as nutrient and chlorophyll-a concentrations, suggesting that these benthi-piscivores also disturbed sediments like crucian carp did. Our study showed that biomanipulation by stocking of snakehead does not facilitate clear-water state in warm shallow lakes, even on the short-term.

Presence of two RIG-I-like receptors, MDA5 and LGP2, and their dsRNA binding capacity in a perciform fish, the snakehead Channa argus

Fish retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) are critical RNA sensors in cytoplasm and are involved in antiviral innate immunity. However, some species of fish lack RIG-I gene, and the function of RLR members in RIG-I-absent fish is poorly understood. In the present study, MDA5, LGP2 and MAVS genes were identified in commercially important snakehead Channa argus. But, RIG-I gene was not found in this fish, and a systematic analysis of RLRs in available genome database of fish indicated the absence of RIG-I in the Acanthomorphata, Clupeiformes and Polypteriformes, suggesting that loss events of RIG-I gene may have occurred independently three times in the evolutionary history of fish. The MDA5, LGP2 and MAVS in snakehead have conserved protein domains and genomic location based on sequence, phylogenetic and syntenic analyses. These genes are constitutively expressed in healthy fish and can be induced by polyinosinic and polycytidylic acid (poly(I:C)) stimulation in vitro. It is further revealed that the snakehead MDA5 and LGP2 have binding capacity with dsRNA, such as poly(I:C), and MDA5 can interact with MAVS, implying the antiviral function of MDA5 in the RIG-I-absent fish.

Molecular characterization and functional analysis of IL-18 in snakehead (Channa argus) during Aeromonas schubertii and Nocardia seriolae infections

As a proinflammatory cytokine of the interleukin-1 (IL-1) family, IL-18 plays important roles in host protection against bacterial, viral, and fungal infection. We cloned the open reading frame of snakehead (Channa argus) IL-18 (shIL-18) and found that it contained 609 base pairs and encoded 202 amino acid residues. The shIL-18 included a conserved IL-1-like family signature and two potential IL-1β-converting enzyme cutting sites; one was conserved in all analyzed IL-18s, but the other was unique to shIL-18. Unlike other IL-18s, shIL-18 also contained a predicted signal peptide. In this study, shIL-18 was constitutively expressed in all tested tissues, and its expression was induced by Aeromonas schubertii and Nocardia seriolae in the head kidney and spleen in vivo and by lipoteichoic acid, lipopolysaccharides, and polyinosinic-polycytidylic acid in head kidney leukocytes in vitro. Moreover, recombinant shIL-18 upregulated the expression of interferon-γ, IL-1β, and tumor necrosis factor-α1 and -α2 and promoted the proliferation of leukocytes. Taken together, these results showed that IL-18 played crucial roles in host defense against bacterial infection in fish, as it does in mammals.

Two types of TNF-α and their receptors in snakehead (Channa argus): Functions in antibacterial innate immunity

Tumor necrosis factor-α (TNF-α) is a pluripotent mediator of pro-inflammatory and antimicrobial defense mechanisms and a regulator of lymphoid organ development. Although two types of TNF-α have been identified in several teleost species, their functions in pathogen infection remain largely unexplored, especially in pathogen clearance. Herein, we cloned and characterized two types of TNF-α, termed shTNF-α1 and shTNF-α2, and their receptors, shTNFR1 and shTNFR2, from snakehead (Channa argus). These genes were constitutively expressed in all tested tissues, and were induced by Aeromonas schubertii and Nocardia seriolae in head kidney and spleen in vivo, and by lipoteichoic acid (LTA), lipopolysaccharides (LPS), and Polyinosinic-polycytidylic acid [Poly (I:C)] in head kidney leukocytes (HKLs) in vitro. Moreover, recombinant shTNF-α1 and shTNF-α2 upregulated the expression of endogenous shTNF-α1, shTNF-α2, shTNFR1, and shTNFR2, and enhanced intracellular bactericidal activity, with shTNF-α1 having a greater effect than shTNF-α2. These findings suggest important roles of fish TNFα1, TNFα2, and their receptors in bacterial infection and pathogen clearance, and provide a new insight into their function in antibacterial innate immunity.

Bacteria-induced IL-1β and its receptors in snakehead (Channa argus): Evidence for their involvement in antibacterial innate immunity

As a central pro-inflammatory cytokine, interleukin-1β (IL-1β) plays critical roles in the inflammatory response, pathogen infection, and immunological challenges in mammals. Although fish IL-1β has been confirmed to participate in inflammatory response to pathogen infection, few studies have been performed to characterize the antibacterial and bactericidal functions of fish IL-1β. In this study, snakehead (Channa argus) IL-1β (shIL-1β) and its receptors, shIL-1R1 and shIL-1R2, were cloned and functionally characterized. ShIL-1β contained the IL-1 family signature domain, and a potential cutting site at Asp⁹⁶ that presented in all vertebrate IL-1β sequences. ShIL-1R1 had three extracellular IG-like domains and one intracellular signal TIR domain, while shIL-1R2 had three extracellular IG-like domain but lacked the intracellular signal TIR domain. ShIL-1β, shIL-1R1, and shIL-1R2 were constitutively expressed in all tested tissues, and their expressions could be induced by Aeromonas schubertii and Nocardia seriolae in the head kidney and spleen in vivo, and by LTA, LPS, and Poly (I:C) in head kidney leukocytes (HKLs) in vitro. Moreover, recombinant shIL-1β upregulated the expression of endogenous shIL-1β, shIL-R1, and shIL-R2 in snakehead HKLs, and enhanced intracellular bactericidal activity. Taken together, this study found that, like IL-1β and its receptors in mammals, shIL-1β and its receptors play crucial roles in antibacterial innate immunity. This provides new insight into the evolution of IL-1β function in vertebrates.

Constructing High-Density Genetic Maps and Developing Sexing Markers in Northern Snakehead (Channa argus)

High-density genetic maps are essential for mapping QTL, improving genome assembly, comparative genomics, and studying sex chromosome evolution. The northern snakehead (Channa argus) is an economically important foodfish species with significant sexual dimorphism, where the males grow much faster and bigger than the females. However, to date, the sex determination pattern is still not clear, limiting identification of sex chromosomes, even sex determination genes and development of monosex populations that are valuable for both sex evolution of vertebrates and aquaculture practices. Here, a sex-averaged map and two sex-specific genetic maps were constructed with 2974, 2323, and 2338 SNPs, respectively. Little difference was observed in the pattern of sex-specific recombination between female- and male-specific genetic maps. Genome scan identified a major locus for sex determination at LG16. Females and males are, respectively, homogametic and heterogametic, suggesting an XY sex determination system for this species. By resequencing genomes, InDels in the sex-associated QTL region were discovered and used for developing sex-specific PCR assays for fast sexing of snakehead. These high-density genetic maps provide useful resources for future genomic studies in snakehead and its related species. The PCR assays for sexing are of importance in developing all male populations for aquaculture.

Effect of dietary phospholipid levels on growth, lipid metabolism, and antioxidative status of juvenile hybrid snakehead (Channa argus×Channa maculata)

The study was conducted to evaluate the effect of dietary phospholipids (PLs) on growth, lipid metabolism, and antioxidative status of hybrid snakehead (Channa argus × Channa maculata). Five isonitrogenous and isolipidic diets with graded levels of PLs (8.5, 19.3, 30.7, 41.5, and 50.8 g kg^-1) were fed to triplicate groups of juveniles (initial body weight 12.6 ± 0.23 g) for 8 weeks. Results showed that dietary PL supplementation significantly improved growth of juveniles. The final body weight (FBW) and specific growth rate (SGR) significantly increased with dietary PLs increasing from 8.5 to 41.5 g kg^-1 (P < 0.05). Fish fed with the diet containing 8.5 g kg^-1 PLs showed higher feed conversion ratio (FCR) compared to the other treatments (P < 0.05). Survival rate (SR) was not affected by dietary PL levels (P > 0.05). Liver lipid contents, serum triglyceride (TG), and low-density lipoprotein cholesterol (LDL-C) contents significantly decreased with the increasing levels of dietary PLs (P < 0.05). However, serum total cholesterol (TC) and high-density lipoprotein cholesterol (HDL-C) contents and HDL-C/TC and HDL-C/LDL-C value significantly increased with increasing dietary PL levels (P < 0.05). The catalase (CAT), superoxide dismutase (SOD), and carnitine palmitoyl transferase I (CPT-1) activities in the liver significantly increased with incremental dietary PL level (P < 0.05), while the liver malondialdehyde (MDA) contents and fatty acid synthase (FAS) activity significantly reduced (P < 0.05). No significant difference was observed in the glutathione peroxidase (GPx) activity among dietary treatments (P > 0.05).These results confirmed that dietary PL supplementation has beneficial effects on growth performance and antioxidant capacity of juvenile hybrid snakehead. Dietary PLs might reduce lipid deposition in the liver of juvenile hybrid snakehead.

Growth, Diet Composition and Reproductive Biology of the Invasive Freshwater Fish Chevron snakehead Channa striata on a Subtropical Island

Kuan-chung Li, Bao-sen Shieh, Yuh-wen Chiu, Da-ji Huang, and Shih-hsiung Liang (2016) The Chevron snakehead (Channa striata) has been invading Taiwan for over 30 years, and it is currently widely distributed across diverse aquatic habitats within the island. Due to its strong environmental adaptability and carnivorous diet, C. striata has caused great negative impacts to the biodiversity of native fishes and aquatic organisms in Taiwan. To effectively restrain its spatial distribution and population, the objective of this study was to investigate the growing conditions, diet composition, and reproductive biology of C. striata in the field. In total, 294 individuals were collected from wetlands, irrigation canals, streams, and reservoirs in southern Taiwan from September 2008 to December 2010. Among 272 sex-identified individuals, more females (164) were collected than males (108). The morphological differences between the sexes could not be distinguished by the 10 body measurements recorded. Diverse food items, including snails, odonates, fishes, amphibians, and reptiles, were identified in the stomachs of 35 individuals. The minimum body length of sexually mature C. striata females exhibited at a standard length of 24.5 cm (total length 28 cm). The appearance of mature oocytes were mainly observed from July to November in 2009 and from April to October in 2010. Greater absolute fecundity (oocyte/individual) was estimated in Taiwan for C. striata than in its original distribution range possibly due to less water level fluctuation in the sampling habitats of Taiwan. The relative fecundity (oocyte/g) for C. striata was considered lower but within the documented range in Taiwan when compared with its original habitat in Malaysia. To effectively manage C. striata in Taiwan, regionally eradiating young and adult individuals, especially during the reproductive season and educating people to stop releasing it in the wild are possible ways to restrain and control the further spread of this exotic fish in Taiwan.