Complete mitochondrial genome of the snakehead (Channa gachua) and its phylogeny.
ABSTRACT: In present study, the mitochondrial genome (mitogenome) of Channa gachua was determined and the phylogenetic relationship of Channidae fish was reconsidered. The mitogenome of the C. gachua is 16547?bp in length, containing 13 protein coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosome RNA genes (rRNAs), a control region (D-loop) and an origin region of replication on the light-strand (OL). The overall nucleotide composition is 28.32% A, 26.58% T, 29.41% C, 15.69% G, with 54.90% AT, respectively. Phylogenetic analyses revealed that C. gachua belongs to the genus Channa and shares a close relationship with C. marulius and C. striata.
Project description:We sequenced and characterized the complete mitochondrial genome of golden yellow snakehead fish, <i>Channa argus.</i> The mitogenomes contained the typical complement of 13 protein-coding genes, 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a non-coding control region. They share the same gene arrangement pattern that was identical with most vertebrates. The entire mitochondrial DNA molecule of golden yellow snakehead fish was 16,558?bp long. All information reported in this article will be a useful source of sequence information for general molecular and evolutionary studies of the family Channidae.
Project description:Seven polymorphic microsatellite loci were isolated and characterized for the snakehead murrel, Channa striata (Channidae), a valuable tropical freshwater fish species. Among 25 specimens collected from Kedah state in Malaysia, the number of alleles per locus ranged from 2 to 7. Observed and expected heterozygosities ranged from 0.120 to 0.880 and 0.117 to 0.698, respectively. A single locus (CS1-C07) was significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction. These novel markers would be useful for population genetic studies of the C. striata.
Project description:The Northern snakehead (Channa argus), a member of the Channidae family of the Perciformes, is an economically important freshwater fish native to East Asia. In North America, it has become notorious as an intentionally released invasive species. Its ability to breathe air with gills and migrate short distances over land makes it a good model for bimodal breath research. Therefore, recent research has focused on the identification of relevant candidate genes. Here, we performed whole genome sequencing of C. argus to construct its draft genome, aiming to offer useful information for further functional studies and identification of target genes related to its unusual facultative air breathing. Findings: We assembled the C. argus genome with a total of 140.3 Gb of raw reads, which were sequenced using the Illumina HiSeq2000 platform. The final draft genome assembly was approximately 615.3 Mb, with a contig N50 of 81.4 kb and scaffold N50 of 4.5 Mb. The identified repeat sequences account for 18.9% of the whole genome. The 19?877 protein-coding genes were predicted from the genome assembly, with an average of 10.5 exons per gene. Conclusion: We generated a high-quality draft genome of C. argus, which will provide a valuable genetic resource for further biomedical investigations of this economically important teleost fish.
Project description:Background:The introduction of northern snakehead (Channa argus; Anabantiformes: Channidae) and their subsequent expansion is one of many problematic biological invasions in the United States. This harmful aquatic invasive species has become established in various parts of the eastern United States, including the Potomac River basin, and has recently become established in the Mississippi River basin in Arkansas. Effective management of C. argus and prevention of its further spread depends upon knowledge of current population structure in the United States. Methods:Novel methods for invasive species using whole genomic scans provide unprecedented levels of data, which are able to investigate fine scale differences between and within populations of organisms. In this study, we utilize 2b-RAD genomic sequencing to recover 1,007 single-nucleotide polymorphism (SNP) loci from genomic DNA extracted from 165 C. argus individuals: 147 individuals sampled along the East Coast of the United States and 18 individuals sampled throughout Arkansas. Results:Analysis of those SNP loci help to resolve existing population structure and recover five genetically distinct populations of C. argus in the United States. Additionally, information from the SNP loci enable us to begin to calculate the long-term effective population size ranges of this harmful aquatic invasive species. We estimate long-term Ne to be 1,840,000-18,400,000 for the Upper Hudson River basin, 4,537,500-45,375,000 for the Lower Hudson River basin, 3,422,500-34,225,000 for the Potomac River basin, 2,715,000-7,150,000 for Philadelphia, and 2,580,000-25,800,000 for Arkansas populations. Discussion and Conclusions:This work provides evidence for the presence of more genetic populations than previously estimated and estimates population size, showing the invasive potential of C. argus in the United States. The valuable information gained from this study will allow effective management of the existing populations to avoid expansion and possibly enable future eradication efforts.
Project description:Cutaneous microbiota play an important role in protecting fish against pathogens. Aphanomyces infection causes epizootic ulcerative syndrome (EUS) in fish, and by perturbing the integrity of the cutaneous microbiota, increases the potential for infection by pathogenic bacteria. However, whether the composition of the cutaneous microbiota is altered in fish with EUS, and if so, which species are changed and how this might influence infected fish, is still largely unclear. Considering the importance of cutaneous microbiota in maintaining host health, we hypothesized that Aphanomyces infection significantly enhances the presence of certain bacterial pathogens in the cutaneous microbiota and causes cutaneous dysbacteriosis. To test this hypothesis, we compared the cutaneous microbiota compositions of hybrid snakehead (Channa maculata? × Channa argus?) with and without Aphanomyces infection using Illumina Miseq sequencing of the 16S rRNA gene. Our results showed that the cutaneous microbiota of hybrid snakehead were significantly altered subsequent to EUS infection and that the numbers of potentially pathogenic bacteria classified into the genera Anaerosinus, Anaerovorax, Dorea, and Clostridium were significantly enhanced in the cutaneous microbiota of hybrid snakehead with EUS, whereas bacteria classified into the genera Arthrobacter, Dysgonomonas, Anoxybacillus, Bacillus, Solibacillus, Carnobacterium, Lactococcus, Streptococcus, Achromobacter, Polynucleobacter, Vogesella, and Pseudomonas were significantly reduced. These results imply that treatment for EUS should not only take into consideration the control of Aphanomyces reproduction but should also focus on regulating the cutaneous microbiota of infected fish.
Project description:Here we have characterized the complete mitochondrial genome of Indonesian snakehead, <i>Channa micropeltes</i>, and described its organization in this paper. The complete mitochondrial genome, 16,567?bp, is composed of 32.54% A, 14.05% G, 25.82% T and 27.59% C. It includes 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a 921-bp D-loop control region. Phylogenetic analysis with five more fish species demonstrated that the Indonesian snakehead is most closely related to the Great snakehead (<i>Channa marulius</i>). Our mitochondrial genomic data will also be valuable for the study on the mitochondrial evolution of fishes.
Project description:The complete mitochondrial genome of <i>Channa striata</i> was determined using NGS technologies. It had a double-stranded DNA molecule with the length of 16,531?bp and was made up 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and one control region. The gene content and arrangement were typical for teleost mtDNA. The molecular data here we presented could play a useful role to study the evolutionary relationships and population genetics of <i>Channa striata</i>.
Project description:As an unclassified species, white-type <i>Channa argus</i> has existed for many years. In the present study, the relationships and genetic diversity in two colour morphs of northern snakehead were determined by the analysis of mitochondrial 12S rRNA gene, as well as other Channa species. The results of sequence analysis showed that the average genetic distance was 0.046 with the interspecies genetic distance ranging from 0.000 to 0.130; and the average interspecies genetic distance was estimated as 0.003 (range: 0.000-0.006). For the two colour morphs of <i>Channa argus</i>, the mean pair-wise genetic distance between them was also estimated as 0.003. Moreover, molecular phylogenetic tree was constructed using MEGA6.0, which showed that all the haploids gathered together as a branch and crossed each other. These results indicated that the white and biocolour-type <i>Channa argus</i> belonged to the same species, rather than subspecies at the molecular level, and the white-type <i>Channa argus</i> should be regard as an albino of biocolour type.
Project description:Northern snakehead, <i>Channa argus</i>, is a commercially important food fish species in China. In the present study, the complete mitochondrial genome of <i>C.argus</i> from the Baima Hu Lake was characterized. It is 16,558 bp in length, consist of 22 tRNA genes, 13 PCD genes, 2 rRNA genes, and 1 D-loop region. The overall base composition of the <i>C. argus</i> mitogenome is 27.26% A, 24.21% T, 31.58% C and 16.95% G, exhibits a similar AT bias (51.47%) feature to other vertebrate mitogenomes. The phylogenetic analysis showed that <i>C. argus</i> clustered in genus <i>Channa</i>. The present resultes provide useful information to population genetics and conservation biology studies of <i>Channa</i> fishes.
Project description:We sequenced the complete genome of the highly virulent Aeromonas schubertii strain WL1483, which was isolated from diseased snakehead fish (Channa argus) in China. The full genome sequence of A. schubertii WL1483 is 4,400,034 bp, which encodes 4,376 proteins and contains 195 predicted RNA genes.