Complete mitochondrial genome of the Pacific cod, Gadus macrocephalus (Gadiformes, Gadidae).
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ABSTRACT:
SUBMITTER: Song HY
PROVIDER: S-EPMC7800020 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundIgE reactivity to fish allergens in atopic dogs, which are used as models for food allergy, has not been elucidated to date. We investigated IgE reactivity to crude extracts and purified allergens derived from the Pacific cod (Gadus macrocephalus) in atopic dogs to identify the allergenic proteins of cod.ResultsThe levels of specific IgE to crude cod extracts were measured in the sera of 179 atopic dogs, including 27 dogs with cod allergy, using enzyme-linked immunosorbent assay (ELISA). Specific IgE to crude cod extracts were present in 36 (20%) of the 179 atopic dogs and in 12 (44%) of the 27 dogs with cod allergy. The allergens in crude cod extracts were analyzed by ELISA, immunoblotting, and liquid chromatography-tandem mass spectrometry. In allergen component analysis, IgE reactivity to tropomyosin and enolase was observed in the sera of dogs with cod allergy. IgE reactivity to parvalbumin, collagen, and tropomyosin was evaluated using the sera of atopic dogs that tested positive for specific IgE to crude cod extracts. Among the 36 dogs with IgE reactivity to crude cod extracts, 9 (25%), 14 (39%), and 18 (50%) dogs tested positive for specific IgE to parvalbumin, collagen, and tropomyosin, respectively.ConclusionsThe IgE reactivity to cod allergens observed in dogs was similar to that in humans, and this finding further supports the use of atopic dogs with fish allergy as a model for fish allergy in humans.
| S-EPMC7493343 | biostudies-literature
Project description:The discernment of populations as management units is a fundamental prerequisite for sustainable exploitation of species. A lack of clear stock boundaries complicates not only the identification of spatial management units, but also the assessment of mixed fisheries by population assignment and mixed stock analysis. Many marine species, such as Pacific cod, are characterized by isolation by distance, showing significant differentiation but no clear stock boundaries. Here, we used restriction-site-associated DNA (RAD) sequencing to investigate population structure and assess power to genetically assign Pacific cod to putative populations of origin. Samples were collected across the species range in the eastern Pacific Ocean, from the Salish Sea to the Aleutian Islands. A total of 6,425 putative biallelic single nucleotide polymorphisms were identified from 276 individuals. We found a strong isolation-by-distance signal along coastlines that mirrored previous microsatellite results and pronounced genetic differentiation between coastal samples and those from the inland waters of the Salish Sea, with no evidence for hybridization between these two populations. Individual assignment success based on two methods was high overall (?84%) but decreased from south to north. Assignment to geographic location of origin also was successful, with average distance between capture and assignment location of 220 km. Outlier analyses identified more loci potentially under selection along the coast than between Salish Sea and coastal samples, suggesting more diverse adaptation to latitudinal environmental factors than inshore vs. offshore environments. Our results confirm previous observations of sharp genetic differentiation of the Salish Sea population and isolation by distance along the coast, but also highlight the feasibility of using modern genomic techniques to inform stock boundaries and fisheries management in a low FST marine species.
| S-EPMC6100185 | biostudies-literature
Project description:BackgroundEpidermal pseudotumours from Hippoglossoides dubius and Acanthogobius flavimanus in Japan and gill lesions in Limanda limanda from the UK have been shown to be caused by phylogenetically related protozoan parasites, known collectively as X-cells. However, the phylogenetic position of the X-cell group is not well supported within any of the existing protozoan phyla and they are currently thought to be members of the Alveolata.Ultrastructural features of X-cells in fish pseudotumours are somewhat limited and no typical environmental stages, such as spores or flagellated cells, have been observed. The life cycles for these parasites have not been demonstrated and it remains unknown how transmission to a new host occurs. In the present study, pseudobranchial pseudotumours from Atlantic cod, Gadus morhua, in Iceland and epidermal pseudotumours from the northern black flounder, Pseudopleuronectes obscurus, in Japan were used in experimental transmission studies to establish whether direct transmission of the parasite is achievable. In addition, X-cells from Atlantic cod were sequenced to confirm whether they are phylogenetically related to other X-cells and epidermal pseudotumours from the northern black flounder were analysed to establish whether the same parasite is responsible for infecting different flatfish species in Japan.ResultsPhylogenetic analyses of small subunit ribosomal DNA (SSU rDNA) sequence data from Atlantic cod X-cells show that they are a related parasite that occupies a basal position to the clade containing other X-cell parasites. The X-cell parasite causing epidermal pseudotumours in P. obscurus is the same parasite that causes pseudotumours in H. dubius. Direct, fish to fish, transmission of the X-cell parasites used in this study, via oral feeding or injection, was not achieved. Non-amoeboid X-cells are contained within discrete sac-like structures that are loosely attached to epidermal pseudotumours in flatfish; these X-cells are able to tolerate exposure to seawater. A sensitive nested PCR assay was developed for the sub clinical detection of both parasites and to assist in future life cycle studies. PCR revealed that the parasite in P. obscurus was detectable in non-pseudotumourous areas of fish that had pseudotumours present in other areas of the body.ConclusionsThe inability to successfully transmit both parasites in this study suggests that either host detachment combined with a period of independent development or an alternate host is required to complete the life cycle for X-cell parasites. Phylogenetic analyses of SSU rDNA confirm a monophyletic grouping for all sequenced X-cell parasites, but do not robustly support their placement within any established protist phylum. Analysis of SSU rDNA from X-cells in Japanese flatfish reveals that the same parasite can infect more than one species of fish.
| S-EPMC3045979 | biostudies-literature
Project description:The full-length mitochondrial genome of Muraenolepis orangiensis (Vaillant, 1888) was studied using PacBio platform and it is first report in a Muraenolepididae family. The circular form of mitochondria genome is 16,833 bp including 13 protein-coding genes, two rRNA, and 22 tRNA. Start codon of 13 protein-coding genes was only ATG but three types of stop codons (TAA, T(AA), and TAG) were detected. To evaluate evolutionary position of M. orangiensis, the phylogenetic tree with other 13 Antarctic fishes belonged to five families were showed that M. orangiensis is unique cluster as a Muraenolepididae family and this study would provide fundamental data to understand the evolutionary relationship of fishes founded in Antarctic area.
| S-EPMC7782825 | biostudies-literature
Project description:The mitochondrial DNA (mtDNA) from the Atlantic cod, Gadus morhua, was mapped using 11 different restriction enzymes and cloned into plasmid vectors. Sequence data obtained from more than 10 kilobases of cod mtDNA show that the genome organization, genetic code, and the overall codon usage have been conserved throughout the evolution of vertebrates. Comparison of the derived amino acid sequences of proteins encoded by cod mtDNA to the ones encoded by Xenopus laevis mtDNA revealed that the amino acid identity range from 46% to 93% for the different proteins. ND4L is most divergent while COI is most conserved. GUG was found as the translation initiation codon of the COI gene, indicating a dual coding function for this codon. The sequences of the 997 base pair displacement-loop (D-loop)-containing region and the origin of L-strand replication (oriL), are presented. Only few of the primary and secondary structure features found to be conserved among mammalian mitochondrial D-loops, can be identified in cod. Presence of CSB-2 in the D-loop-containing region and the conserved hairpin structure at oriL, indicates that replication of bony fish mtDNA may follow the same general scheme as described for higher vertebrates.
| S-EPMC333442 | biostudies-other
Project description:Gadus macrocephalus (Pacific cod) is an economically important species on the northern coast of the Pacific. Although numerous studies on G. macrocephalus exist, there are few reports on its genomic data. Here, we used whole-genome sequencing data to elucidate the genomic characteristics and phylogenetic relationship of G. macrocephalus. From the 19-mer frequency distribution, the genome size was estimated to be 658.22 Mb. The heterozygosity, repetitive sequence content and GC content were approximately 0.62%, 27.50% and 44.73%, respectively. The draft genome sequences were initially assembled, yielding a total of 500,760 scaffolds (N50 = 3565 bp). A total of 789,860 microsatellite motifs were identified from the genomic data, and dinucleotide repeat was the most dominant simple sequence repeat motif. As a byproduct of whole-genome sequencing, the mitochondrial genome was assembled to investigate the evolutionary relationships between G. macrocephalus and its relatives. On the basis of 13 protein-coding gene sequences of the mitochondrial genome of Gadidae species, the maximum likelihood phylogenetic tree showed that complicated relationships and divergence times among Gadidae species. Demographic history analysis revealed changes in the G. macrocephalus population during the Pleistocene by using the pairwise sequentially Markovian coalescent model. These findings supplement the genomic data of G. macrocephalus, and make a valuable contribution to the whole-genome studies on G. macrocephalus.
| S-EPMC9289796 | biostudies-literature
Project description:Codfish genome sequencing
| PRJNA301002 | ENA
Project description:The complete mitochondrial genome of Macrourus witsoni was determined in this study by the Long-read Technology, such as PacBio Sequel System. The Long-read Technology, which can sequence continuously the whole vertebrate mitochondrial genome, allows more accurate genomes to be completed. The circular form of its mitochondrial genome was 16,714bp, which contained 13 protein-coding genes, 22 tRNA, and 2 rRNA. The gene orders of M.witsoni was identical to that of the other species of Macrouridae family. Phylogenetic analysis indicated M. witsoni was mostly close to C.kishinouyei in the Macrouridae family.
| S-EPMC7782029 | biostudies-literature
Project description:UNLABELLED: BACKGROUND: Although numerous studies on parasites of the Atlantic cod, Gadus morhua L. have been conducted in the North Atlantic, comparative analyses on local cod parasite faunas are virtually lacking. The present study is based on examination of large samples of cod from six geographical areas of the North East Atlantic which yielded abundant baseline data on parasite distribution and abundance. MATERIALS AND METHODS: A total of 826 fish was sampled in the Baltic, Celtic, Irish and North seas, Icelandic waters and Trondheimsfjord (Norway) in 2002 (spring and autumn) and 2003 (spring). The gills and internal organs (oesophagus, stomach, intestine, pyloric caeca, liver, heart, spleen, gall bladder and gonads) were examined for macroparasites following a standardised protocol. The taxonomic consistency of the identification was ensured thorough the entire study. RESULTS: We discuss some problems in parasite identification, outline the composition of the parasite faunas in cod in the six North East Atlantic regions, provide novel data on parasite prevalence and abundance and a comparative assessment of the structure of the regional parasite faunas with respect to the higher-level taxonomic groupings, host specificity and zoogeographical distribution of the parasites. Altogether 57 different parasite forms were found including seven new host records (Diclidophora merlangi, Rhipidocotyle sp., Fellodistomum sp., Steringotrema sp., Cucullanus sp., Spinitectus sp., and Chondracanthus ornatus). The predominant groups of cod parasites were trematodes (19 species) and nematodes (13 species) including larval anisakids which comprised 58.2% of the total number of individuals. CONCLUSION: Our study reveals relatively rich regional parasite faunas in cod from the North East Atlantic which are dominated by generalist parasites with Arcto-Boreal distribution. Further, it provides more detailed data on the distribution in the North East Atlantic of the majority of cod parasites which may serve as baselines for future studies on the effect of climate change. Based on the faunal comparisons, predictions can be made in relation to the structure and diversity of the parasite communities in the North East Atlantic regions studied.
| S-EPMC2503959 | biostudies-literature
Project description:The endangered giant root-rat (Tachyoryctes macrocephalus, also known as giant mole rat) is a fossorial rodent endemic to the afro-alpine grasslands of the Bale Mountains in Ethiopia. The species is an important ecosystem engineer with the majority of the global population found within 1000 km2. Here, we present the first complete mitochondrial genome of the giant root-rat and the genus Tachyoryctes, recovered using shotgun sequencing and iterative mapping. A phylogenetic analysis including 15 other representatives of the family Spalacidae placed Tachyoryctes as sister genus to Rhizomys with high support. This position is in accordance with a recent study revealing the topology of the Spalacidae family. The full mitochondrial genome of the giant root-rat presents an important resource for further population genetic studies.
| S-EPMC8253177 | biostudies-literature