Genome-wide identification of the Na+/H+ exchanger gene family in Lateolabrax maculatus and its involvement in salinity regulation

Genome-wide identification of the NHE gene family in Coilia nasus and its response to salinity challenge and ammonia stress

Background

In aquatic environments, pH, salinity, and ammonia concentration are extremely important for aquatic animals. NHE is a two-way ion exchange carrier protein, which can transport Na⁺ into cells and exchange out H⁺, and also plays key roles in regulating intracellular pH, osmotic pressure, and ammonia concentration.

Results

In the present study, ten NHEs, the entire NHE gene family, were identified from Coilia nasus genome and systemically analyzed via phylogenetic, structural, and synteny analysis. Different expression patterns of C. nasus NHEs in multiple tissues indicated that expression profiles of NHE genes displayed tissue-specific. Expression patterns of C. nasus NHEs were related to ammonia excretion during multiple embryonic development stages. To explore the potential functions on salinity challenge and ammonia stress, expression levels of ten NHEs were detected in C. nasus gills under hypotonic stress, hypertonic stress, and ammonia stress. Expression levels of all NHEs were upregulated during hypotonic stress, while they were downregulated during hypertonic stress. NHE2 and NHE3 displayed higher expression levels in C. nasus larvae and juvenile gills under ammonia stress.

Conclusions

Our study revealed that NHE genes played distinct roles in embryonic development, salinity stress, and ammonia exposure. Syntenic analysis showed significant difference between stenohaline fish and euryhaline fishes. Our findings will provide insight into effects of C. nasus NHE gene family on ion transport and ammonia tolerance and be beneficial for healthy aquaculture of C. nasus.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08761-9.

Genome-wide identification and expression analysis of serine hydroxymethyltransferase (SHMT) gene family in tomato (Solanum lycopersicum)

Serine hydroxymethyltransferase (SHMT) is one of the most important enzyme families in one-carbon metabolic pathway and photorespiration within plant cells. Recently studies reported the active roles of plant SHMTs in defending abiotic stresses. However, genome-scale analysis of SHMT in tomato is currently unknown. In this study, seven SHMT genes were identified in the tomato genome using a genome-wide search approach. In addition, their physicochemical properties, protein secondary structure, subcellular localization, gene structure, conserved motifs, phylogenetic and collinear relationships were analyzed. Our results demonstrated that tomato SHMT members were divided into two group and four subgroups, and they were conserved with the orthologs of other plants. Analysis of cis-acting elements showed that each of the SlSHMT genes contained different kinds of hormones and stress-related cis-acting elements in their promoter regions. Finally, qRT-PCR analysis indicated that SlSHMTs were expressed at different levels in different tissues, and they responded to UV, cold, heat, NaCl, H₂O₂, ABA and PEG treatments. These results provided definite evidence that SlSHMTs might involve in growth, development and stress responses in tomato, which laid a foundation for future functional studies of SlSHMTs.

Full-length transcriptomic analysis reveals osmoregulatory mechanisms in Coilia nasus eyes reared under hypotonic and hyperosmotic stress

In recent years, sea-level rise, caused by global warming, will trigger salinity changes. This will threaten the survival of aquatic animals. Till now, the osmoregulatory mechanism of Coilia nasus eyes has not been yet explored. Oxford Nanopore Technologies (ONT) sequencing was performed in C. nasus eyes during hypotonic and hyperosmotic stress for the first time. 22.5G clean reads and 26,884 full-length non-redundant sequences were generated via ONT sequencing. AS events, APA, TF, and LncRNA were identified. During hypotonic stress, 46 up-regulated DEGs and 28 down-regulated DEGs were identified. During hypertonic stress, 190 up-regulated DEGs and 182 down-regulated DEGs were identified. These DEGs were associated with immune, metabolism, and transport responses. The expression of these DEGs indicated that apoptosis and inflammation were triggered during hypotonic and hyperosmotic stress. To resist hypotonic stress, polyamines metabolism and transport of Na⁺ and Cl^- from inter-cellular to extra-cellular were activated. During hyperosmotic stress, amino acids metabolism and transport of myo-inositol and Na⁺ from extra-cellular to inter-cellular were activated, while Cl^- transport was inhibited. Moreover, different transcript isoforms generated from the same gene performed different expression patterns during hypotonic and hypertonic stress. These findings will be beneficial to understand osmoregulatory mechanism of C. nasus eyes, and can also improve our insights on the adaptation of aquatic animals to environmental changes.

Whole-genome resequencing of three Coilia nasus population reveals genetic variations in genes related to immune, vision, migration, and osmoregulation

Background

Coilia nasus is an important anadromous fish, widely distributed in China, Japan, and Korea. Based on morphological and ecological researches of C. nasus, two ecotypes were identified. One is the anadromous population (AP). The sexually mature fish run thousands of kilometers from marine to river for spawning. Another one is the resident population which cannot migrate. Based on their different habitats, they were classified into landlocked population (LP) and sea population (SP) which were resident in the freshwater lake and marine during the entire lifetime, respectively. However, they have never been systematically studied. Moreover, C. nasus is declining sharply due to overfishing and pollution recently. Therefore, further understandings of C. nasus populations are needed for germplasm protection.

Results

Whole-genome resequencing of AP, LP, and SP were performed to enrich the understanding of different populations of C. nasus. At the genome level, 3,176,204, 3,307,069, and 3,207,906 single nucleotide polymorphisms (SNPs) and 1,892,068, 2,002,912, and 1,922,168 insertion/deletion polymorphisms (InDels) were generated in AP, LP, and SP, respectively. Selective sweeping analysis showed that 1022 genes were selected in AP vs LP; 983 genes were selected in LP vs SP; 116 genes were selected in AP vs SP. Among them, selected genes related to immune, vision, migration, and osmoregulation were identified. Furthermore, their expression profiles were detected by quantitative real-time PCR. Expression levels of selected genes related to immune, and vision in LP were significantly lower than AP and SP. Selected genes related to migration in AP were expressed significantly more highly than LP. Expression levels of selected genes related to osmoregulation were also detected. The expression of NKAα and NKCC1 in LP were significantly lower than SP, while expression of NCC, SLC4A4, NHE3, and V-ATPase in LP was significantly higher than SP.

Conclusions

Combined to life history of C. nasus populations, our results revealed that the molecular mechanisms of their differences of immune, vision, migration, and osmoregulation. Our findings will provide a further understanding of different populations of C. nasus and will be beneficial for wild C. nasus protection.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08182-0.

Genome-wide identification and expression analysis of the trehalose-6-phosphate synthase (TPS) gene family in cucumber (Cucumis sativus L.)

Trehalose-6-phosphate synthase (TPS) is significant in the growth, development and stress resistance of plants. We identified the cucumber TPS family and its physicochemical properties, domains, gene structures, evolutionary relationships, gene locations, cis-acting elements, conserved motifs, and expression patterns using bioinformatics. Our results uncovered seven CsTPS genes in the cucumber genome and named CsTPS1-CsTPS7 according to their locations in the chromosomes. Seven CsTPS genes were randomly distributed in six cucumber chromosomes. Domain analysis showed that the TPS and TPP domains exist in all CsTPSs, and an additional hydrolase-3 domain exist in CsTPS3, CsTPS5 and CsTPS6. Phylogenetic analysis showed that TPS proteins from Arabidopsis, rice, soybean, and cucumber were divided into two subfamilies (Class I and Class II) and they were further divided into seven subgroups. TPS proteins from Arabidopsis and cucumber were grouped together, suggesting a close evolutionary relationship. Gene structure analysis indicated that most Class I genes contained 16-17 introns, while Class II genes (except CsTPS7) had two introns. Motif analysis showed that Class II genes had 10 complete conserved motifs, while Class I genes lacked motif 8 and motif 9. Furthermore, CsTPS genes possessed numerous cis-acting elements related to stress, hormone, and light response in the promoter regions. GO analysis indicated multiple functions for the CsTPS proteins. Expression analysis of CsTPS genes in different tissues found that they were expressed in roots, stems and leaves, with the highest expression levels in roots. The expression analysis of CsTPSs under different treatments showed that CsTPS genes may participate in the response to abiotic stress, plant hormones and sugar treatments.

Effects of Vibrio harveyi infection on serum biochemical parameters and expression profiles of interleukin-17 (IL-17) / interleukin-17 receptor (IL-17R) genes in spotted sea bass

Vibrio harveyi is regarded as serious pathogen for marine fishes. To evaluate the physiological responses of spotted sea bass (Lateolabrax maculatus) after V. harveyi infection, four biochemical biomarkers including alanine amino transferase (ALT), albumin (ALB), total protein (TP) and glucose (GLU) were measured in serum. Our results showed that V. harveyi infection significantly influenced the concentration of ALT, ALB and GLU. Additionally, five interleukin-17 (IL-17) and five IL-17 receptors (IL-17R) genes were identified in spotted sea bass and their gene structures were characterized. Furthermore, the expression patterns of IL-17 and IL-17R genes were determined by qPCR in liver, intestine, spleen and head kidney after V. harveyi infection. All IL-17 and IL-17R genes exhibited time- and tissue-dependent expressions. Several tested genes were dramatically induced by V. harveyi treatment, particularly IL-17A/F1 in liver and head kidney, IL-17A/F2 in head kidney, IL-17RC in spleen with more than 10-fold increases, which suggested their potential essential roles against bacterial infection.

First High-Density Linkage Map and QTL Fine Mapping for Growth-Related Traits of Spotted Sea bass (Lateolabrax maculatus)

Possessing powerful adaptive capacity and a pleasant taste, spotted sea bass (Lateolabrax maculatus) has a broad natural distribution and is one of the most popular mariculture fish in China. However, the genetic improvement program for this fish is still in its infancy. Growth is the most economically important trait and is controlled by quantitative trait loci (QTL); thus, the identification of QTLs and genetic markers for growth-related traits is an essential step for the establishment of marker-assisted selection (MAS) breeding programs. In this study, we report the first high-density linkage map of spotted sea bass constructed by sequencing 333 F1 generation individuals in a full-sib family using 2b-RAD technology. A total of 6883 SNP markers were anchored onto 24 linkage groups, spanning 2189.96 cM with an average marker interval of 0.33 cM. Twenty-four growth-related QTLs, including 13 QTLs for body weight and 11 QTLs for body length, were successfully detected, with phenotypic variance explained (PVE) ranging from 5.1 to 8.6%. Thirty potential candidate growth-related genes surrounding the associated SNPs were involved in cell adhesion, cell proliferation, cytoskeleton reorganization, calcium channels, and neuromodulation. Notably, the fgfr4 gene was detected in the most significant QTL; this gene plays a pivotal role in myogenesis and bone growth. The results of this study may facilitate marker-assisted selection for breeding populations and establish the foundation for further genomic and genetic studies investigating spotted sea bass.