Dataset Information

Complete Genome Sequence of a Betanodavirus Isolated from Half-Smooth Tongue Sole (Cynoglossus semilaevis).

ABSTRACT: Betanodavirus, commonly called nervous necrosis virus (NNV) of fish, has emerged as a major constraint on marine aquaculture worldwide. Here, we report the complete genome sequence of a betanodavirus (strain CsCN128) isolated from diseased half-smooth tongue sole (Cynoglossus semilaevis) in China. The genome sequence of strain CsCN128 shares ?98.7% similarity with seven-band grouper nervous necrosis virus from Japan. Phylogenetic analysis indicates that strain CsCN128 belongs to the red-spotted grouper nervous necrosis virus (RGNNV) genotype of betanodavirus. The genome of the strain CsCN128 will facilitate further study on the molecular epidemiology and natural susceptible host range of betanodaviruses.

SUBMITTER: Li J

PROVIDER: S-EPMC4271161 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature

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Complete Genome Sequence of a Betanodavirus Isolated from Half-Smooth Tongue Sole (Cynoglossus semilaevis).

Li Jin J Shi Cheng Yin CY Huang Jie J Geng Wei Guang WG Wang Sheng Qiang SQ Su Zi Dan ZD

Genome announcements 20141218 6

Betanodavirus, commonly called nervous necrosis virus (NNV) of fish, has emerged as a major constraint on marine aquaculture worldwide. Here, we report the complete genome sequence of a betanodavirus (strain CsCN128) isolated from diseased half-smooth tongue sole (Cynoglossus semilaevis) in China. The genome sequence of strain CsCN128 shares ≥98.7% similarity with seven-band grouper nervous necrosis virus from Japan. Phylogenetic analysis indicates that strain CsCN128 belongs to the red-spotted ...[more]

PMID: 25523771

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Project description:Cathepsins are a family of lysosomal proteases that play an important role in protein degradation, antigen presentation, apoptosis, and inflammation. Cathepsins are divided into three groups, i.e., cysteine protease, serine protease, and aspartic protease. Cathepsin D and cathepsin L, which are aspartic protease and cysteine protease respectively, have been identified in a number of teleosts; however, the immunological relevance of fish cathepsins is largely unknown. In this study, we cloned and analyzed the expression profiles of a cathepsin D (CsCatD) and a cathepsin L (CsCatL) homologs from half-smooth tongue sole (Cynoglossus semilaevis). CsCatD is composed of 396 amino acid residues and shares 67.6-88.4% overall sequence identities with fish and human cathepsin D. Structurally CsCatD possesses an aspartic endopeptidase domain, which contains two conserved aspartic acid residues that form the catalytic site. CsCatL is 336 residues in length and shares 64.7-90.2% overall sequence identities with fish and human cathepsin L. CsCatL has an N-terminal cathepsin propeptide inhibitor domain followed by a Papain family cysteine protease domain, the latter containing four conserved catalytic residues: Gln-133, Cys-139, His-279, and Asn-303. Recombinant CsCatL purified from Escherichia coli exhibited apparent protease activity. Quantitative real time RT-PCR analysis detected constitutive expression of CsCatD and CsCatL in multiple tissues, with the lowest level found in heart and the highest level found in liver. Experimental challenge of tongue sole with the bacterial pathogen Vibrio anguillarum and megalocytivirus caused significant inductions of both CsCatD and CsCatL expression in kidney and spleen in time-dependent manners. Immunization of the fish with a subunit vaccine also enhanced CsCatD and CsCatL expression in the first week post-vaccination. These results suggest involvement of CsCatD and CsCatL in host immune reactions to bacterial and viral infections and in the process of antigen-induced immune response.

Project description:BACKGROUND: Half-smooth tongue sole (Cynoglossus semilaevis Günther) has been exploited as a commercially important cultured marine flatfish, and female grows 2-3 times faster than male. Genetic studies, especially on the chromosomal sex-determining system of this species, have been carried out in the last decade. Although the genome of half-smooth tongue sole was relatively small (626.9 Mb), there are still some difficulties in the high-quality assembly of the next generation genome sequencing reads without the assistance of a physical map, especially for the W chromosome of this fish due to abundance of repetitive sequences. The objective of this study is to construct a bacterial artificial chromosome (BAC)-based physical map for half-smooth tongue sole with the method of high information content fingerprinting (HICF). RESULTS: A physical map of half-smooth tongue sole was constructed with 30, 294 valid fingerprints (7.5 × genome coverage) with a tolerance of 4 and an initial cutoff of 1e-60. A total of 29,709 clones were assembled into 1,485 contigs with an average length of 539 kb and a N50 length of 664 kb. There were 394 contigs longer than the N50 length, and these contigs will be a useful resource for future integration with linkage map and whole genome sequence assembly. The estimated physical length of the assembled contigs was 797 Mb, representing approximately 1.27 coverage of the half-smooth tongue sole genome. The largest contig contained 410 BAC clones with a physical length of 3.48 Mb. Almost all of the 676 BAC clones (99.9%) in the 21 randomly selected contigs were positively validated by PCR assays, thereby confirming the reliability of the assembly. CONCLUSIONS: A first generation BAC-based physical map of half-smooth tongue sole was constructed with high reliability. The map will promote genetic improvement programs of this fish, especially integration of physical and genetic maps, fine-mappings of important gene and/or QTL, comparative and evolutionary genomics studies, as well as whole genome sequence assembly.

Dataset Information

Complete Genome Sequence of a Betanodavirus Isolated from Half-Smooth Tongue Sole (Cynoglossus semilaevis).

Publications

Complete Genome Sequence of a Betanodavirus Isolated from Half-Smooth Tongue Sole (Cynoglossus semilaevis).

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