The First Report on Chromosome Analysis of F1 Hybrid Catfish: Mekong Giant Catfish (Pangasianodon gigas)×Striped Catfish (Pangasianodon hypophthalmus) and Spot Pangasius (Pangasius larnaudii)×Pangasianodon hypophthalmus (Siluriformes, Pangasiidae)

Range extension of the Mexican-endemic killifish Profundulus chimalapensis (Cyprinodontiformes: Profundulidae), with comments on its phylogenetic placement and possible intergeneric hybridization with Tlaloc Álvarez & Carranza 1951

Recent ichthyological surveys in southern Mexico resulted in the unexpected discovery of populations of P. chimalapensis outside its distribution range, broadening its extent of occurrence to a total of three river basins (Coatzacoalcos [original], Grijalva, Ostuta) and two versants (Atlantic [original] and Pacific). The taxonomic nature of these populations was further investigated using comparative genetic data in a phylogenetic framework. Our results include the first assessment of the phylogenetic position of P. chimalapensis with respect to other Profundulus species and imply a sister-group relationship with P. oaxacae. Remarkably, our results also imply a close phylogenetic affinity of some P. chimalapensis samples with the genus Tlaloc, which we interpret as possible evidence of intergeneric hybridization, a phenomenon previously unreported in the family. If our interpretation in this regard is correct, it raises several broader evolutionary and taxonomic questions, such as the role that introgressive hybridization might be playing as a driver of speciation in profundulid fishes. From a historical biogeographic perspective, the proposed expanded geographic range could be explained by inter-basin dispersal enabled by recent or historical events (e.g., paleodrainage connections, headwaters stream capture, floodings) in the same fashion as these have been invoked to explain distribution patterns in other Middle American freshwater fishes.

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.

A chromosome-level genome assembly of the striped catfish (Pangasianodon hypophthalmus)

Striped catfish (Pangasianodon hypophthalmus), belonging to the Pangasiidae family, has become an economically important fish with wide cultivation in Southeast Asia. Owing to the high-fat trait, it is always considered as an oily fish. In our present study, a high-quality genome assembly of the striped catfish was generated by integration of Illumina short reads, Nanopore long reads and Hi-C data. A 731.7-Mb genome assembly was finally obtained, with a contig N50 of 3.5 Mb, a scaffold N50 of 29.5 Mb, and anchoring of 98.46% of the assembly onto 30 pseudochromosomes. The genome contained 36.9% repeat sequences, and a total 18,895 protein-coding genes were predicted. Interestingly, we identified a tandem triplication of fatty acid binding protein 1 gene (fabp1; thereby named as fabp1-1, fabp1-2 and fabp1-3 respectively), which may be related to the high fat content in striped catfish. Meanwhile, the FABP1-2 and -3 isoforms differed from FABP1-1 by several missense mutations including R126T, which may affect the fatty acid binding properties. In summary, we report a high-quality chromosome-level genome assembly of the striped catfish, which provides a valuable genetic resource for biomedical studies on the high-fat trait, and lays a solid foundation for practical aquaculture and molecular breeding of this international teleost species.