Pseudobagrus ussuriensis is an aquaculture catfish with significant sexual dimorphism. In this study, a chromosome-level genome with a size of 741.97 Mb was assembled for female P. ussuriensis. A total of 26 chromosome-level contigs covering 97.34% of the whole-genome assembly were obtained with an N50 of 28.53 Mb and an L50 of 11. A total of 24,075 protein-coding genes were identified, with 91.54% (22,039) genes being functionally annotated. Based on the genome assembly, four chromosome evolution clusters of catfishes were identified and the formation process of P. ussuriensis chromosomes was predicted. A total of 55 sex-related quantitative trait loci (QTLs) with a phenotypic variance explained value of 100% were located on chromosome 8 (chr08). The QTLs and other previously identified sex-specific markers were located in a sex-determining region of 16.83 Mb (from 6.90 to 23.73 Mb) on chr08, which was predicted as the X chromosome. The sex-determining region comprised 554 genes, with 135 of which being differently expressed between males and females/pseudofemales, and 16 candidate sex-determining genes were screened out. The results of this study provided a useful chromosome-level genome for genetic, genomic and evolutionary studies of P. ussuriensis, and also be useful for further studies on sex-determination mechanism analysis and sex-control breeding of this fish.

The classification of Carassius has not been well established due to its great variability and wide distribution. Usually, Carassius is identified as three species: C. carassius, C. cuvieri and C. auratus, the latter including several subspecies, such as goldfish. Out of these subspecies, C. auratus gibelio have recently been thought of as a valid species of Carassius. In this study we collected the 5'end 651 bp segments of the mitochondrial cytochrome c oxidase I (COI) gene from 128 specimens, including C. carassius, C. cuvieri, C. auratus auratus, C. auratus gibelio and C. auratus langsdorfii. All three species of Carassius (C. carassius, C. cuvieri, C. auratus) were found to be valid, meanwhile genetic differentiation between the Eurasian C. auratus and Japanese C. auratus has reached a high level. However, several haplotypes were shared between C. auratus auratus and C. auratus gibelio. Consequently, C. auratus gibelio should be regarded as a subspecies of C. auratus rather than a valid species. Moreover, because both diploids and triploids exist in C. auratus auratus and C. auratus gibelio, ploidy level should not be used as criteria for the classification of species or subspecies in Carassius.