A High-Quality Genome Assembly of Striped Catfish (Pangasianodon hypophthalmus) Based on Highly Accurate Long-Read HiFi Sequencing Data.

The HiFi sequencing technology yields highly accurate long-read data with accuracies greater than 99.9% that can be used to improve results for complex applications such as genome assembly. Our study presents a high-quality chromosome-scale genome assembly of striped catfish (Pangasianodon hypophthalmus), a commercially important species cultured mainly in Vietnam, integrating HiFi reads and Hi-C data. A 788.4 Mb genome containing 381 scaffolds with an N50 length of 21.8 Mb has been obtained from HiFi reads. These scaffolds have been further ordered and clustered into 30 chromosome groups, ranging from 1.4 to 57.6 Mb, based on Hi-C data. The present updated assembly has a contig N50 of 14.7 Mb, representing a 245-fold and 4.2-fold improvement over the previous Illumina and Illumina-Nanopore-Hi-C based version, respectively. In addition, the proportion of repeat elements and BUSCO genes identified in our genome is remarkably higher than in the two previously released striped catfish genomes. These results highlight the power of using HiFi reads to assemble the highly repetitive regions and to improve the quality of genome assembly. The updated, high-quality genome assembled in this work will provide a valuable genomic resource for future population genetics, conservation biology and selective breeding studies of striped catfish.

Salinity significantly affects intestinal microbiota and gene expression in striped catfish juveniles.

In the present study, juvenile striped catfish (Pangasianodon hypophthalmus), a freshwater fish species, have been chronically exposed to a salinity gradient from freshwater to 20 psu (practical salinity unit) and were sampled at the beginning (D20) and the end (D34) of exposure. The results revealed that the intestinal microbial profile of striped catfish reared in freshwater conditions were dominated by the phyla Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia. Alpha diversity measures (observed OTUs (operational taxonomic units), Shannon and Faith's PD (phylogenetic diversity)) showed a decreasing pattern as the salinities increased, except for the phylogenetic diversity at D34, which was showing an opposite trend. Furthermore, the beta diversity between groups was significantly different. Vibrio and Akkermansia genera were affected differentially with increasing salinity, the former being increased while the latter was decreased. The genus Sulfurospirillium was found predominantly in fish submitted to salinity treatments. Regarding the host response, the fish intestine likely contributed to osmoregulation by modifying the expression of osmoregulatory genes such as nka1a, nka1b, slc12a1, slc12a2, cftr, and aqp1, especially in fish exposed to 15 and 20 psu. The expression of heat shock proteins (hsp) hsp60, hsp70, and hsp90 was significantly increased in fish reared in 15 and 20 psu. On the other hand, the expression of pattern recognition receptors (PRRs) were inhibited in fish exposed to 20 psu at D20. In conclusion, the fish intestinal microbiota was significantly disrupted in salinities higher than 10 psu and these effects were proportional to the exposure time. In addition, the modifications of intestinal gene expression related to ion exchange and stressful responses may help the fish to adapt hyperosmotic environment. KEY POINTS: • It is the first study to provide detailed information on the gut microbiota of fish using the amplicon sequencing method. • Salinity environment significantly modified the intestinal microbiota of striped catfish. • Intestinal responses may help the fish adapt to hyperosmotic environment.

Salinity affects growth performance, physiology, immune responses and temperature resistance in striped catfish (Pangasianodon hypophthalmus) during its early life stages.

In this study, striped catfish larvae were gradually exposed to the increase of different salinities, and then they reached the levels of 0, 5, 10, 15, and 20 psu after 10 days, followed by heat shock at 39 °C to determine stress tolerance. After the 10-day experiment, the survival rate of fish exposed to the 20 psu treatment was only 28.6 ± 4%, significantly lower than that of the other treatments. The results showed that the osmolality of the whole-body (WB) homogenate was gradually and significantly increased with salinity elevation, except in fish exposed to freshwater and 5 psu treatments, while there were no significant changes in WB Na+/K+-ATPase activity. Digestive enzymatic activities, i.e., pepsin, α-amylase, alkaline phosphatase, and leucine alanine peptidase (leu-ala) generally increased with salinity, but not aminopeptidase and trypsin. Lysozyme and peroxidase activities increased in fish larvae exposed to 15 and 20 psu. These increases proportionally improved growth performance, with the lowest and the highest final weights observed in fish reared at 0 psu (0.08 ± 0.03 g/larvae) and 20 psu (0.11 ± 0.02 g/larvae), respectively, although the average growth recorded at 20 psu could be biased by the high mortality in this group. Occurrence of skeleton deformities, such as in caudal vertebrae and branchiostegal rays, was significantly higher in fish exposed to the higher osmotic conditions (15.0 ± 1.2% and 10.3 ± 2.1% respectively at 0 psu vs. 31.0 ± 2.9% and 49.0 ± 5.6%, respectively at 15 psu). After the 12.5-h heat shock, survival rates significantly differed between treatments with the highest survival observed in fish submitted to 5 psu (68.9%), followed by those exposed to 0 (27%) and 10 (20%) while all fish died at 15 psu. These findings suggest that the striped catfish larvae could be reared in salinity up to 5 to 10 psu with a higher survival and tolerance to thermal stress when compared to fish maintained in freshwater.