A Chromosome-Level Genome Assembly of the Mandarin Fish (Siniperca chuatsi)

A chromosome-level genome of electric catfish (Malapterurus electricus) provided new insights into order Siluriformes evolution

The electric catfish (Malapterurus electricus), belonging to the family Malapteruridae, order Siluriformes (Actinopterygii: Ostariophysi), is one of the six branches that has independently evolved electrical organs. We assembled a 796.75 Mb M. electricus genome and anchored 88.72% sequences into 28 chromosomes. Gene family analysis revealed 295 expanded gene families that were enriched on functions related to glutamate receptors. Convergent evolutionary analyses of electric organs among different lineage of electric fishes further revealed that the coding gene of rho guanine nucleotide exchange factor 4-like (arhgef4), which is associated with G-protein coupled receptor (GPCR) signaling pathway, underwent adaptive parallel evolution. Gene identification suggests visual degradation in catfishes, and an important role for taste in environmental adaptation. Our findings fill in the genomic data for a branch of electric fish and provide a relevant genetic basis for the adaptive evolution of Siluriformes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-023-00197-8.

Genome-wide identification, evolution and expression of TGF-β signaling pathway members in mandarin fish (Siniperca chuatsi)

Members of the transforming growth factor β (TGF-β) signaling pathway regulate diverse cellular biological processes in embryonic and tissue development. We took mandarin fish (Siniperca chuatsi) as the research object to identify all members of the TGF-β signaling pathway, measure their expression pattern in the key period post hatching, and further explore their possible role in the process of sex regulation. Herein, we identified eighty-three TGF-β signaling pathway members and located them on chromosomes based on the genome of mandarin fish. TGF-β signaling pathway members were highly conserved since each TGF-β subfamily clustered with orthologs from other species. Transcriptome analysis, qRT-PCR and in situ hybridization demonstrated that most mandarin fish TGF-β signaling pathway members presented stage-specific and/or sex-dimorphic expression during gonadal development, and different members of the TGF-β signaling pathway participated in different stages of gonadal development. Taken together, our results provide new insight into the role of TGF-β signaling pathway members in the sex regulation of mandarin fish.

Genome-wide identification and expression patterns of opsin genes during larval development in Chinese perch (Siniperca chuatsi)

Vision is important for fish to forage food and fishes express opsin genes to receive visual signals. Chinese perch (Siniperca chuatsi) larvae prey on other fish species larvae at firstfeeding but donoteat any zooplankton, the expression of opsin genes in S. chuatsilarvae is unknown. In this study, we conducted a whole-genome analysis and demonstrated that S. chuatsihave5cone opsin genes (sws1, sws2Aα, sws2Aβ, rh2and lws)and 2 rod opsin genes (rh1and rh1-exorh). The syntenicanalysisshowedthe flanking genes ofall opsin genes were conserved during fish evolution, but the ancestorof S. chuatsimightlost some opsin gene copies duringtheevolution.The phylogeneticanalysisshowed sws1of S. chuatsiwas closest to those of Lates calcariferwhich had a truncated sws1gene; the sws2Aα, sws2Aβ,lws,rh2,rh1 andrh1-exorh of S. chuatsihad a closer relationship with those of Percomorpha fishes.Importantly, results of in situhybridization showed the sws1 opsingene,which is related to forage zooplankton,had extremely low levelexpression in retinaat early stages.Surprisingly, the rh2 opsin gene had a high level expression at firstfeeding stage. The sws2Aα, sws2Aβand lwshad a little expression at early stages but the lwsshowed a increasing trend with larval development, rh1 opsin gene expression appeared at15 dph. In thisstudy, we found a specialpattern of visual opsin genes expression in S. chuatsi, it might influence the larval first feeding and feeding habit.