Chromosomal-Level Genome Assembly of Silver Sillago (Sillago sihama)

Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions

BACKGROUND

Channel catfish and blue catfish are the most important aquacultured species in the USA. The species do not readily intermate naturally but F₁ hybrids can be produced through artificial spawning. F₁ hybrids produced by mating channel catfish female with blue catfish male exhibit heterosis and provide an ideal system to study reproductive isolation and hybrid vigor. The purpose of the study was to generate high-quality chromosome level reference genome sequences and to determine their genomic similarities and differences.

RESULTS

We present high-quality reference genome sequences for both channel catfish and blue catfish, containing only 67 and 139 total gaps, respectively. We also report three pericentric chromosome inversions between the two genomes, as evidenced by long reads across the inversion junctions from distinct individuals, genetic linkage mapping, and PCR amplicons across the inversion junctions. Recombination rates within the inversional segments, detected as double crossovers, are extremely low among backcross progenies (progenies of channel catfish female × F₁ hybrid male), suggesting that the pericentric inversions interrupt postzygotic recombination or survival of recombinants. Identification of channel catfish- and blue catfish-specific genes, along with expansions of immunoglobulin genes and centromeric Xba elements, provides insights into genomic hallmarks of these species.

CONCLUSIONS

We generated high-quality reference genome sequences for both blue catfish and channel catfish and identified major chromosomal inversions on chromosomes 6, 11, and 24. These perimetric inversions were validated by additional sequencing analysis, genetic linkage mapping, and PCR analysis across the inversion junctions. The reference genome sequences, as well as the contrasted chromosomal architecture should provide guidance for the interspecific breeding programs.

Genome-Wide Identification and Characterization of Olfactory Receptor Genes in Silver Sillago (Sillago sihama)

Olfactory receptor (OR) genes are essential in the specific recognition of diverse stimuli in fish. In this study, a total of 141 OR genes were identified in silver sillago (Sillago sihama), a marine fish sensitive to environmental stimuli, including 112 intact genes, 26 truncated genes, and three pseudogenes. A phylogenetic tree analysis elucidated that the OR genes of S. sihama were classified into six groups, of which β, γ, δ, ε, and ζ groups belonged to type I, and the η group belonged to type II. The type I OR genes contained almost all conserved motifs (n = 62), while type II OR genes mainly retained conserved motifs 7(3), 1, 10, 4, and 2 (n = 39). OR genes were mainly distributed on LG1, LG9, LG11, and LG12. Of all OR genes, 36.23% (50 genes) showed significant expansion in S. sihama. Ka/Ks analysis demonstrated that 227 sites were under purifying selection, while 12 sites were under positive selection, including eight genes in the OR2A12 gene subfamily. Sixty-one genes (44.20%) displayed differential expression under hypoxic stress. The identified OR genes explored the mechanism of environmental stress and ecological adaptation of S. sihama, and provided valuable genomic resources for further research on the olfaction of teleosts.

Genome-wide identification and expression profiling of glutathione S-transferase family under hypoxia stress in silver sillago (Sillago sihama)

Glutathione S-transferase (GST) is an important detoxification enzyme in organisms. GSTs play an important role in responding to environmental stresses. This study aimed to identify the GST gene superfamily in silver sillago (Sillago sihama) and analyze its expression pattern under hypoxia stress. A total of 17 GST genes were identified in silver sillago. Phylogenetic analysis showed that the GST gene family contained two subgroups (cytosolic and MAPEGs), and lacked three subgroups (i.e. Pi, Kappa, and MGST2). Phylogenetic and syntenic analysis revealed that GST genes were conserved in evolution. Eight SsGSTs were significantly differentially expressed under hypoxia stress in silver sillago by RNA-seq and qRT-PCR analysis. The expression levels of SsMGST3b, SsGSTO1, SsGSTT1b and SsGSTR2 genes were significantly up-regulated after 4 h of reoxygenation in the gill tissue. In the heart tissue, the expression of SsGSTR3 was significantly up-regulated after 1 h of hypoxia while the expression levels of SsGSTT1b and SsFLAP genes were significantly down-regulated after 4 h of hypoxia. In summary, this study provides for the first time a comprehensive analysis of the GST gene superfamily of silver sillago.