Transcriptome-Based Identification and Molecular Evolution of the Cytochrome P450 Genes and Expression Profiling under Dimethoate Treatment in Amur Stickleback (Pungitius sinensis)

Cytochrome P450 superfamily in spotted sea bass: Genome-wide identification and expression profiles under trichlorfon and environmental stresses

Cytochrome P450s (CYPs), as one of the most diverse enzyme superfamilies in nature, play critical functions in antioxidant reactions against endogenous and exogenous compounds. In this study, we performed genome-wide characterization of CYP superfamily members and analyzed their expression patterns under several abiotic stresses in spotted sea bass, which is known as an economically important fish species in the Chinese aquaculture industry. A total of 55 CYP genes were identified and divided into 17 families within 10 clans. The analysis of phylogeny, gene structure, and syntenic relationships provided evidence for the evolution of CYP genes and confirmed their annotation and orthology. The expression of CYP genes was examined in the liver during trichlorfon stress using quantitative real-time PCR. The results showed that 20 tested CYP genes displayed significant mRNA expression changes, indicating that they may play crucial roles in the metabolism of trichlorfon and can be potential biomarkers for trichlorfon pollution. Moreover, by screening transcriptomic databases, 10, 3 and 19 CYP genes exhibited differential expression patterns in response to hypoxia, alkalinity and heat stress, respectively. Taken together, this study provided insights into the regulation of CYP genes by toxicological and environmental stresses, laid basis for extensive functional studies of the CYP superfamily in spotted sea bass and other teleost species.

Functional Divergence of the N-Lobe and C-Lobe of Transferrin Gene in Pungitius sinensis (Amur Stickleback)

Transferrin is an important iron-binding glycosylated protein and plays key roles in iron-binding and immune response. Here, a 2037-bp open reading frame was obtained from our previous transcriptome sequencing data of Amur stickleback, which encoded a 679 amino acid putative transferrin protein harbored obvious N-lobe and C-lobe domains. The tissue-specific expression pattern showed that the transcript was detected in a variety of tissues, with the highest signal in liver. Moreover, Streptococcus iniae pathogen stimulation can increase the expression level of this transcript, implying important immune properties for organisms. Next, N-lobes and C-lobes were obtained from 45 fish species. The phylogenetic tree showed that N-lobes and C-lobes were in two different evolutionary branches, and they had different motif composition. Functional divergence indicated a higher evolutionary rate or site-specific alteration among the N-lobe and C-lobe groups. Ka/Ks value of C-lobe group was relatively higher than that of N-lobe group, indicating a faster change rate of C-lobe sequences in evolution. Moreover, some sites experiencing positive selection were also found, which may be involved in the iron- or anion-binding, pathogen resistance and diversification of transferrin protein. Differential iron-binding activity was also detected between N-lobe and C-lobe of Amur stickleback transferrin protein with Chrome Azurol S assay. Compared with the C-lobe, the N-lobe showed stronger growth inhibitory activity of Escherichia coli, implying their potential antibacterial properties. This study will give a reference for subsequent research of transferrin proteins.

A chromosome-level genome assembly of the yellowfin seabream (Acanthopagrus latus; Hottuyn, 1782) provides insights into its osmoregulation and sex reversal

The yellowfin seabream Acanthopagrus latus is the economically most important Sparidae fish in the northern South China Sea. As euryhaline fish, they are perfect model for investigating osmoregulatory mechanisms in teleosts. Moreover, the reproductive biology of hermaphrodites has long been intriguing; however, little information is known about the molecular pathways underlying their sex change. Here, we report a chromosome level reference genome of A. latus generated by employing the PacBio single molecule sequencing technique (SMRT) and high-throughput chromosome conformation capture (Hi-C) technologies. The draft genome of yellowfin seabream was 806 Mb, with 732 Mb scaffolds anchored on 24 chromosomes. The contig N50 and scaffold N50 were 2.6 Mb and 30.17 Mb, respectively. The assembly is of high integrity and includes 92.23% universal single-copy orthologues based on benchmarking universal single-copy orthologs (BUSCO) analysis. A total of 19,631 protein-coding genes were functionally annotated in the reference genome. Moreover, ARRDC3 and GSTA gene families which related to osmoregulation underwent an extensive expansion in two euryhaline sparids fish genomes compared to other teleost genomes. Moreover, integrating sex-specific transcriptome analyses, several genes related to the transforming growth factor beta (TGF-β) signalling pathway involved in sex differentiation and development. This genomic resource will not only be valuable for studying the osmoregulatory mechanisms in estuarine fish and sex determination in hermaphrodite vertebrate species, but also provide useful genomic tools for facilitating breeding of the yellowfin seabream.

Characterization and molecular evolution of claudin genes in the Pungitius sinensis

Claudins are a family of integrated membrane-bound proteins involving in paracellular tightness, barrier forming, ion permeability, and substrate selection at tight junctions of chordate epithelial and endothelial cells. Here, 39 putative claudin genes were identified in the Pungitius sinensis based on the high throughput RNA-seq. Conservative motif distribution in each group suggested functional relevance. Divergence of duplicated genes implied the species' adaptation to the environment. In addition, selective pressure analyses identified one site, which may accelerate functional divergence in this protein family. Pesticides cause environmental pollution and have a serious impact on aquatic organisms when entering the water. The expression pattern of most claudin genes was affected by organophosphorus pesticide, indicating that they may be involved in the immune regulation of organisms and the detoxification of xenobiotics. Protein-protein network analyses also exhibited 439 interactions, which implied the functional diversity. It will provide some references for the functional study on claudin genes.

Molecular Evolution and Characterization of Fish Stathmin Genes

Simple Summary

Stathmin is a highly conserved microtubule remodeling protein. Here, 175 putative stathmin genes were identified in 27 species of fish. Gene organization, motif distribution, divergence of duplicated genes, functional divergence, synteny relationship, and protein-protein interaction were performed to investigate their evolutionary history. In addition, expression profiles of some stathmins were examined under dimethoate treatment. The results will provide useful references for further functional analyses.

Abstract

Stathmin is a highly conserved microtubule remodeling protein, involved in many biological processes such as signal transduction, cell proliferation, neurogenesis and so on. However, little evolutional information has been reported about this gene family in fish. In this study, 175 stathmin genes were identified in 27 species of fish. Conserved exon-intron structure and motif distributions were found in each group. Divergence of duplicated genes implied the species’ adaptation to the environment. Functional divergence suggested that the evolution of stathmin is mainly influenced by purifying selection, and some residues may undergo positive selection. Moreover, synteny relationship near the stathmin locus was relatively conserved in some fish. Network analyses also exhibited 74 interactions, implying functional diversity. The expression pattern of some stathmin genes was also investigated under pesticide stress. These will provide useful references for their functional research in the future.