BackgroundThe channel catfish (Ictalurus punctatus), a species native to North America, is one of the most important commercial freshwater fish in the world, especially in the United States’ aquaculture industry. Since its introduction into China in 1984, both cultivation area and yield of this species have been dramatically increased such that China is now the leading producer of channel catfish. To aid genomic research in this species, data sets such as genetic linkage groups, long-insert libraries, physical maps, bacterial artificial clones (BAC) end sequences (BES), transcriptome assemblies, and reference genome sequences have been generated. Here, using diverse assembly methods, we provide a comparable high-quality genome assembly for a channel catfish from a breeding stock inbred in China for more than three generations, which was originally imported to China from North America.FindingsApproximately 201.6 gigabases (Gb) of genome reads were sequenced by the Illumina HiSeq 2000 platform. Subsequently, we generated high quality, cost-effective and easily assembled sequences of the channel catfish genome with a scaffold N50 of 7.2 Mb and 95.6 % completeness. We also predicted that the channel catfish genome contains 21,556 protein-coding genes and 275.3 Mb (megabase pairs) of repetitive sequences.ConclusionsWe report a high-quality genome assembly of the channel catfish, which is comparable to a recent report of the “Coco” channel catfish. These generated genome data could be used as an initial platform for molecular breeding to obtain novel catfish varieties using genomic approaches.

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After feeding female Eriocheir sinensis on an optimized formulated diet or fresh razor clam Sinonovacula constricta for 7 months, their reproductive performance and o¡spring quality were compared. To evaluate diet nutrient contents, the proximate, fatty acid and amino acid compositions of the formulated diet and the razor clam were analysed. The nutritional value of the diets was determined by assessing survival, gonadosomatic index (GSI) and hepatosomatic index (HSI) of female crabs from both diet treatments, together with the percentage of females that spawned, total egg production per female and fecundity (number of eggs g À 1 female wet weight). Furthermore, the quality of eggs and newly hatched larvae from the two dietary treatments were determined using the following parameters: egg diameter, wet weight and dry weight, hatchability, proximate and fatty acid pro¢le of eggs, larval carapace length, resistant to starvation and osmotic shock, larval survival and development to the zoea II stage.Higher protein, phospholipids (PL) and amino acids (AA) contents were found in the razor clam while the formulated diet contains higher levels of ash, total lipid (TL) and 18:1n-9, 18:2n-6 and 22:6n-3 fatty acids. Although female crabs fed the two di¡er-ent diets showed similar reproductive performances, newly hatched zoea I larvae produced by the crabs fed the formulated diet had signi¢cantly longer mean carapace length and shorter development time to the zoea II stage under identical culture condition (Po0.05). Moreover, dietary fatty acid appeared to have more signi¢cant e¡ects on the fatty acid composition of the hepatopancreas than it did on mature ovaries or eggs. This suggests that the fatty acid pro-¢le of mature ovaries is indicative of the speci¢c fatty acid required for ovarian development in E. sinensis.In conclusion, our results show that the optimized formulated diet developed in this laboratory can totally replace the razor clam, a broodstock food widely used in E. sinensis hatcheries in China. This encouraging result should facilitate more reliable hatchery production of this important aquaculture species.

A high-density genetic linkage map is of particular importance in the fine mapping for important economic traits and whole genome assembly in aquaculture species. The channel catfish ( Ictalurus punctatus ), a species native to North America, is one of the most important commercial freshwater fish in the world. Outside of the United States, China has become the major producer and consumer of channel catfish after experiencing rapid development in the past three decades. In this study, based on restriction site associated DNA sequencing (RAD-seq), a high-density genetic linkage map of channel catfish was constructed by using single nucleotide polymorphisms (SNPs) in a F 1 family composed of 156 offspring and their two parental individuals. A total of 4,768 SNPs were assigned to 29 linkage groups (LGs), and the length of the linkage map reached 2,480.25 centiMorgans (cM) with an average distance of 0.55 cM between loci. Based on this genetic linkage map, 223 genomic scaffolds were anchored to the 29 LGs of channel catfish, and a total length of 704.66 Mb was assembled. Quantitative trait locus (QTL) mapping and genome-wide association analysis identified 10 QTLs of sex-related and six QTLs of growth-related traits at LG17 and LG28, respectively. Candidate genes associated with sex dimorphism, including spata2, spata5, sf3, zbtb38 , and fox , were identified within QTL intervals on the LG17. A sex-linked marker with simple sequence repeats (SSR) in zbtb38 gene of the LG17 was validated for practical verification of sex in the channel catfish. Thus, the LG17 was considered as a sex-related LG. Potential growth-related genes were also identified, including important regulators such as megf9, npffr1 , and gas1 . In a word, we constructed the high-density genetic linkage map and developed the sex-linked marker in channel catfish, which are important genetic resources for future marker-assisted selection (MAS) of this economically important teleost.

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Herein, the complete mitochondrial genome of Odontobutis haifengensis was sequenced for the first time. The O. haifengensis mitogenome was 17,016bp in length and included 13 protein-coding genes, 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region (CR). The genome organization, base composition, codon usage, and gene rearrangement was similar to other Odontobutis species. Furthermore, a tRNA gene rearrangement within the SLH cluster was found to be identical to other Odontobutis species. Moreover, the gene order and the positions of additional intergenic non-coding regions suggests that the observed unique gene rearrangement resulted from a tandem duplication and random loss of large-scale gene regions. Additionally, phylogenetic analysis showed that Odontobutis species form a monophyletic clade due to the conserved mitochondrial gene rearrangement. This study provides useful information that aids in a better understanding of mitogenomic diversity and evolutionary patterns of Odontobutidae species.