Percomorpha is the major branch of Actinopteri, comprising most of the acanthopterygian fishes. The relationships among different Percomorpha groups remain uncertain because of high species diversity, thereby creating challenges for phylogenetic studies on teleosts. The phylogenetic problems of Percomorpha have not been solved using mitochondrial genes and a few nuclear genes. In this study, genomes from 34 representative species from the 7 major taxa of Percomorpha were selected to solve this problem. In all, 29592 conserved amino acid sites from 206 single-copy orthologous genes were chosen for the reconstruction of phylogenetic trees. The results showed that Gobiaria, whose position is different from that in previous studies, was the earliest branching lineage. The phylogenetic groups in this study were consistent with previous results using mitochondrial DNA and nuclear genes. Thus, this study provides a new perspective and directions for further research on the Percomorpha branch and other higher-order meta-taxonomic relationships of fish. The genome data obtained may be essential for future investigations of phylogeny and molecular evolution.

Genome-wide characterisation and correlation analysis between gene families and environmental stresses are important for understanding the adaptive evolution of marine animals to various environments. Heat shock protein 70 (Hsp70) and heat shock transcription factor (Hsf) are two important gene families that are associated with abiotic stresses and immune responses. In this study, the evolutionary history and function of Hsp70 and Hsf family genes were investigated in Cynoglossus semilaevis through an exhaustive search of all genomic resources. In addition, their regulatory mechanisms and cooperative relationship in marine fishes were investigated in response to various degrees of salinity stress. Gene structure, motif analysis and phylogenetic trees among various organisms provide references for biological and evolutionary studies of these genes. Most Hsp70 genes were upregulated under low salinity stress, especially heat shock protein family A member 5 (hspa5), whereas hsf1 and hsf2 were downregulated. The expression profile of Hsp70 genes under low salinity stress decreased the activity of hsf1 and hsf2, suggesting that transcriptional repression of Hsf occurs when a certain level of Hsp70 is reached. These findings may improve our understanding the regulatory mechanisms between Hsp70 and Hsf gene families in response to environmental stress and provide useful resources for future studies on these gene families.

Our understanding of phylogenetic relationships among Gadiformes fish is obtained through the analysis of a small number of genes, but uncertainty remains around critical nodes. A series of phylogenetic controversial exists at the suborder, family, subfamily, and species levels. A total of 1105 orthologous exon sequences and translated amino acid sequences from 36 genomes and 12 transcriptomes covering 33 species were applied to investigate the phylogenetic relationships within Gadiformes and address these problems. Phylogenetic trees reconstructed with the amino acid data set using different tree-building methods (RAxML and MrBayes) showed consistent topology. The monophyly of Gadifromes was confirmed in our study. However, the three suborders Muraenolepidoidei, Macrouroidei, and Gadoidei were not well recovered by our phy-logenomic study, rejecting the validity of suborder Muraenolepidoidei. Four major lineages were revealed in this study. The family Bregmacerotidae forming clade I was the basal lineage of Gadiformes. The family Merluciidae formed clade II. Clade III contained families Melanonidae, Muraenolepididae, Macrouridae (with subfamilies Trachyrincinae, Macrourinae, and Bathygadinae), and Moridae. Clade IV contained at least three families of suborder Gadoidei, i.e., Gadidae, Phycidae, and Ranicipitidae. The subspecies of Lota lota from Amur River were confirmed, indicating that exon markers were a valid high-resolution method for delimiting subspecies or distinct lineages within species level. The PSMC analysis of different populations of L. lota suggests a continuous decline since 2 Myr.

The marbled rockfish, Sebastiscus marmoratus, belongs to the euryhaline fish and is an oviparous scleractinian fish. There are few studies on the adaptation mechanism, functional genes, and related pathways of S. marmoratus and salinity. The results showed that a total of 72.1 GB of clean reads were obtained and all clean reads annotated a total of 25,278 Unigenes, of which 2160 were novel genes. Compared to 20‰, 479 and 520 differential genes were obtained for 35‰ and 10‰, respectively. Gene ontology (GO) enrichment analysis revealed significant enrichment in protein binding, ion binding, ATP binding, and catalytic activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that differentially expressed genes significantly expressed under salinity stress were mainly involved in the pathways of the cytochrome P450 metabolism of xenobiotics, tryptophan metabolism, cellular senescence, and calcium signaling pathways. Among them, pik3r6b, cPLA2γ-like, and WSB1 were differentially expressed in all three groups, and they were associated with apoptosis, inflammation, DNA damage, immune regulation, and other physiological processes. Six differentially expressed genes were randomly selected for qRT-PCR validation, and the results showed that the transcriptomic data were of high confidence.