Effect of nutrient restriction and re-feeding on calpain family genes in skeletal muscle of Channel catfish (Ictalurus punctatus).

Background: Calpains, a superfamily of intracellular calcium-dependent cysteine proteases, are involved in the cytoskeletal remodeling and wasting of skeletal muscle. Calpains are generated as inactive proenzymes which are activated by Nterminal autolysis induced by calcium-ions. Methodology/Principal Findings: In this study, we characterized the full-length cDNA sequences of three calpain genes, clpn1, clpn2, and clpn3 in channel catfish, and assessed the effect of nutrient restriction and subsequent re-feeding on the expression of these genes in skeletal muscle. The clpn1 cDNA sequence encodes a protein of 704 amino acids, Clpn2 of 696 amino acids, and Clpn3 of 741 amino acids. Phylogenetic analysis of deduced amino acid sequences indicate that catfish Clpn1 and Clpn2 share a sequence similarity of 61%; catfish Clpn1 and Clpn3 of 48%, and Clpn2 and Clpn3 of only 45%. The domain structure architectures of all three calpain genes in channel catfish are similar to those of other vertebrates, further supported by strong bootstrap values during phylogenetic analyses. Starvation of channel catfish (average weight, 15\u201320 g) for 35 days influenced the expression of clpn1 (2.3-fold decrease, P,0.05), clpn2 (1.3-fold increase, P,0.05), and clpn3 (13.0- fold decrease, P,0.05), whereas the subsequent refeeding did not change the expression of these genes as measured by quantitative real-time PCR analysis. Calpain catalytic activity in channel catfish skeletal muscle showed significant differences only during the starvation period, with a 1.2- and 1.4- fold increase (P,0.01) after 17 and 35 days of starvation, respectively. Conclusion/Significance: We have assessed that fasting and refeeding may provide a suitable experimental model to provide us insight into the role of calpains during fish muscle atrophy and how they respond to changes in nutrient supply

The catfish genome database cBARBEL: an informatic platform for genome biology of ictalurid catfish

The catfish genome database, cBARBEL (abbreviated from catfish Breeder And Researcher Bioinformatics Entry Location) is an online open-access database for genome biology of ictalurid catfish (Ictalurus spp.). It serves as a comprehensive, integrative platform for all aspects of catfish genetics, genomics and related data resources. cBARBEL provides BLAST-based, fuzzy and specific search functions, visualization of catfish linkage, physical and integrated maps, a catfish EST contig viewer with SNP information overlay, and GBrowse-based organization of catfish genomic data based on sequence similarity with zebrafish chromosomes. Subsections of the database are tightly related, allowing a user with a sequence or search string of interest to navigate seamlessly from one area to another. As catfish genome sequencing proceeds and ongoing quantitative trait loci (QTL) projects bear fruit, cBARBEL will allow rapid data integration and dissemination within the catfish research community and to interested stakeholders. cBARBEL can be accessed at http://catfishgenome.org

A pilot study for channel catfish whole genome sequencing and de novo assembly

<p>Abstract</p> <p>Background</p> <p>Recent advances in next-generation sequencing technologies have drastically increased throughput and significantly reduced sequencing costs. However, the average read lengths in next-generation sequencing technologies are short as compared with that of traditional Sanger sequencing. The short sequence reads pose great challenges for <it>de novo </it>sequence assembly. As a pilot project for whole genome sequencing of the catfish genome, here we attempt to determine the proper sequence coverage, the proper software for assembly, and various parameters used for the assembly of a BAC physical map contig spanning approximately a million of base pairs.</p> <p>Results</p> <p>A combination of low sequence coverage of 454 and Illumina sequencing appeared to provide effective assembly as reflected by a high N50 value. Using 454 sequencing alone, a sequencing depth of 18 X was sufficient to obtain the good quality assembly, whereas a 70 X Illumina appeared to be sufficient for a good quality assembly. Additional sequencing coverage after 18 X of 454 or after 70 X of Illumina sequencing does not provide significant improvement of the assembly. Considering the cost of sequencing, a 2 X 454 sequencing, when coupled to 70 X Illumina sequencing, provided an assembly of reasonably good quality. With several software tested, Newbler with a seed length of 16 and ABySS with a K-value of 60 appear to be appropriate for the assembly of 454 reads alone and Illumina paired-end reads alone, respectively. Using both 454 and Illumina paired-end reads, a hybrid assembly strategy using Newbler for initial 454 sequence assembly, Velvet for initial Illumina sequence assembly, followed by a second step assembly using MIRA provided the best assembly of the physical map contig, resulting in 193 contigs with a N50 value of 13,123 bp.</p> <p>Conclusions</p> <p>A hybrid sequencing strategy using low sequencing depth of 454 and high sequencing depth of Illumina provided the good quality assembly with high N50 value and relatively low cost. A combination of Newbler, Velvet, and MIRA can be used to assemble the 454 sequence reads and the Illumina reads effectively. The assembled sequence can serve as a resource for comparative genome analysis. Additional long reads using the third generation sequencing platforms are needed to sequence through repetitive genome regions that should further enhance the sequence assembly.</p

Generation of the first BAC-based physical map of the common carp genome

<p>Abstract</p> <p>Background</p> <p>Common carp (<it>Cyprinus carpio</it>), a member of Cyprinidae, is the third most important aquaculture species in the world with an annual global production of 3.4 million metric tons, accounting for nearly 14% of the all freshwater aquaculture production in the world. Apparently genomic resources are needed for this species in order to study its performance and production traits. In spite of much progress, no physical maps have been available for common carp. The objective of this project was to generate a BAC-based physical map using fluorescent restriction fingerprinting.</p> <p>Result</p> <p>The first generation of common carp physical map was constructed using four- color High Information Content Fingerprinting (HICF). A total of 72,158 BAC clones were analyzed that generated 67,493 valid fingerprints (5.5 × genome coverage). These BAC clones were assembled into 3,696 contigs with the average length of 476 kb and a N50 length of 688 kb, representing approximately 1.76 Gb of the common carp genome. The largest contig contained 171 BAC clones with the physical length of 3.12 Mb. There are 761 contigs longer than the N50, and these contigs should be the most useful resource for future integrations with linkage map and whole genome sequence assembly. The common carp physical map is available at <url>http://genomics.cafs.ac.cn/fpc/WebAGCoL/Carp/WebFPC/</url>.</p> <p>Conclusion</p> <p>The reported common carp physical map is the first physical map of the common carp genome. It should be a valuable genome resource facilitating whole genome sequence assembly and characterization of position-based genes important for aquaculture traits.</p

Identification and Characterization of Full-Length cDNAs in Channel Catfish (Ictalurus punctatus) and Blue Catfish (Ictalurus furcatus)

Background: Genome annotation projects, gene functional studies, and phylogenetic analyses for a given organism all greatly benefit from access to a validated full-length cDNA resource. While increasingly common in model species, fulllength cDNA resources in aquaculture species are scarce. Methodology and Principal Findings: Through in silico analysis of catfish (Ictalurus spp.) ESTs, a total of 10,037 channel catfish and 7,382 blue catfish cDNA clones were identified as potentially encoding full-length cDNAs. Of this set, a total of 1,169 channel catfish and 933 blue catfish full-length cDNA clones were selected for re-sequencing to provide additional coverage and ensure sequence accuracy. A total of 1,745 unique gene transcripts were identified from the full-length cDNA set, including 1,064 gene transcripts from channel catfish and 681gene transcripts from blue catfish, with 416 transcripts shared between the two closely related species. Full-length sequence characteristics (ortholog conservation, UTR length, Kozak sequence, and conserved motifs) of the channel and blue catfish were examined in detail. Comparison of gene ontology composition between full-length cDNAs and all catfish ESTs revealed that the full-length cDNA set is representative of the gene diversity encoded in the catfish transcriptome. Conclusions: This study describes the first catfish full-length cDNA set constructed from several cDNA libraries. The catfish full-length cDNA sequences, and data gleaned from sequence characteristics analysis, will be a valuable resource fo

A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer

10.1186/1471-2164-12-174BMC Genomics12-BGME

Phylogenetic relationships of nine mullet species (Mugilidae) in the Mediterranean Sea

Phylogenetic relationships among four genera and nine species (Mugil cephalus, Mugil soiuy, Liza ramada, Liza aurata, Liza abu, Liza saliens, Liza carinata, Chelon labrosus, Oedalechilus labeo) of the Mediterranean mullets (Mugilidae) were investigated by means of allozyme electrophoresis using a seven-enzyme system (CK*, GAPDH*, G3PDH*, IDHP*, ME*, MDH*, PGM*) comprising eleven putative loci. The highest genetic divergence was 1.299, detected between M. cephalus and L. aurata and the lowest (0.280) was found between L. carinata and L. saliens. The amount of genetic divergence between the genera Chelon and Oedalechilus did not appear to be high (0.285). In a UPGMA tree, all nine species were grouped in two main branchings. In the first branch, C. labrosus and O. labeo clustered as closest taxa and were sister group to L. ramada. The other four Liza species produced two sub-branching in this group; L. carinata branched together with L. saliens, and L. aurata branched together with L. abu. In the second branch the two species of the genus Mugil, M. cephalus and M. soiuy, clustered together and were clearly isolated from the other three genera