Transcriptome analysis identifies immune-related genes and antimicrobial peptides in Siamese fighting fish (Betta splendens)

Unveiling the multifaceted role of toll-like receptors in immunity of aquatic animals: pioneering strategies for disease management

The pattern recognition receptor (PRR), which drives innate immunity, shields the host against invasive pathogens. Fish and other aquatic species with poorly developed adaptive immunity mostly rely on their innate immunity, regulated by PRRs such as inherited-encoded toll-like receptors (TLRs). The discovery of 21 unique TLR variations in various aquatic animals over the past several years has sparked interest in using TLRs to improve aquatic animal's immune response and disease resistance. This comprehensive review provides an overview of the latest investigations on the various characteristics of TLRs in aquatic animals. It emphasizes their categorization, insights into 3D architecture, ligand recognition, signaling pathways, TLRs mediated immune responses under biotic and abiotic stressors, and expression variations during several developmental stages. It also highlights the differences among aquatic animals' TLRs and their mammal counterparts, which signifies the unique roles that TLRs play in aquatic animal's immune systems. This article summarizes current aquaculture research to enhance our understanding of fish immune systems for effective aquaculture -related disease management.

Nanopore-based full-length transcriptome sequencing of the skin in Pseudopleuronectes yokohamae identifies novel antimicrobial peptide genes

The marbled flounder (Pseudopleuronectes yokohamae) is highly esteemed for its exceptional nutritional value and delicious taste. However, this species has extremely limited transcriptome data, which can offer priceless information for disease protection. In the study, the skin transcriptomic sequencing of P. yokohamae revealed 7.72 GB of clean data using the Nanopore sequencing platform. The results revealed 30,498 transcripts of functional annotations in the P. yokohamae transcriptome. All transcripts were searched in eight functional databases. A total of 10,337 ORFs were obtained, of which 6081 complete ORFs accounted for 58.83% of all predicted CDS. Moreover, 10,195 SSRs were detected. Meanwhile, the non-pecific immunity pathways were investigated for better understanding of the immunological reaction in P. yokohamae, and seven innate immune pathways were identified. The innate-immune related genes were highly expressed in the NOD-like receptor signaling pathway, followed by the C-type lectin receptor signaling pathway, Toll-like receptor signaling pathway, RIG-I-like receptor signaling pathway and Cytosolic DNA-sensing pathway. In this study, four families of antimicrobial peptides (AMPs) in P. yokohamae were analysed for the first time, including piscidins, hepcidins, liver-expressed antimicrobial peptide and defensins. Seven AMPs, including Pypleurocidin-like WF3, Pypleurocidin-like WFX, Pyhepcidin 1, Pyhepcidin-like 1, PyLEAP-2, Pybeta-defensin and Pybeta-defensin-like 1, were further identified. The seven AMPs showed a highly identity in their cDNA and genomic structures and an inducible expression pattern preferable to skin in response to pathogens. The transcriptomic data and investigation of AMPs from P. yokohamae promote a deeper awareness of fish mucosal immunity and provide information in the prevention of fish diseases.

Transcriptomic profiling revealed immune-related signaling pathways in response to experimental infection of Leishmania donovani in two desert lizards from Northwest China

Little is known about the immune response of lizards to Leishmania parasties. In this study, we conducted the first liver transcriptome analysis of two lizards (Phrynocephalus przewalskii and Eremias multiocellata) challenged with L. donovani, endemic to the steppe desert region of northwestern China. Our results revealed that multiple biological processes and immune-related signaling pathways are closely associated with the immune response to experimental L. donovani infection in the two lizards, and that both lizards show similar changes to mammals in terms of immunity to Leishmania. However, the interspecific divergence of the two lizards leads to different transcriptomic changes. In particular, in contrast to P. przewalskii, the challenged E. mutltiocellata was characterized by the induction of down-regulation of most DEGs. These findings will contribute to the scarce resources on lizard immunity and provide a reference for further research on immune mechanisms in reptiles.

Effects of clove oil concentrations on blood chemistry and stress-related gene expression in Siamese fighting fish (Betta splendens) during transportation

Siamese fishing fish (Betta splendens) or betta are usually subjected to a special method of transportation for global trade, where they are individually conveyed in plastic bags containing just enough water to cover their bodies. This study aimed to investigate the effects of transportation on their stress response by measuring hematological values, stress hormone levels, glucose levels, and stress-related gene expression. Betta fish (average body weight 1.91 ± 0.42 g; n = 30) were exposed to simulated transport in a water volume of 40 mL for 12, 24, and 48 h. Baseline levels (pre-transport) were measured prior to the experiment. The control group was transported using water without adding clove oil. Two treatment groups were transported using water with the addition of 1 and 3 mg/L concentrations of clove oil, respectively. The results revealed that transportation can be a factor that affects water quality. The pH and dissolved oxygen levels were significantly lower than baseline, while nitrite and total ammonia concentrations significantly increased. Correlating to the stress responses, significantly increasing total red blood cell counts, plasma cortisol levels, and up-regulating the expression of stress-related genes, including HSP70, GR, MR, and HIF-1α. The addition of 1 mg/L clove oil was found to reduce stress during the transport simulation, as evidenced by a reduction in these stress parameters. Conversely, increasing the concentration of clove oil to 3 mg/L significantly increased plasma cortisol after 12 h of simulated transport, and up-regulated GR, MR, and HIF-1α expression. This study revealed that the transport process can stimulates stress in betta fish but adding a concentration of 1 mg/L clove oil to the transport water could mitigate this stress response and promote animal welfare during their transportation.

Antifungal Efficacy of Antimicrobial Peptide Octominin II against Candida albicans

Most clinically isolated Candida albicans strains are drug-resistant, emphasizing the urgent need to discover alternative therapies. In this study, the previously characterized Octominin was modified into a shorter peptide with an 18 amino acid sequence (1GWLIRGAIHAGKAIHGLI18) and named Octominin II. The secondary structure of Octominin II is a random coil with a helical turn and a positive charge (+2.46) with a hydrophobic ratio of 0.46. Octominin II inhibited C. albicans, C. auris, and C. glabrata with minimum inhibitory and fungicidal concentrations against C. albicans of 80 and 120 µg/mL, respectively. Field emission scanning electron microscopy confirmed that Octominin II treatment caused ultra-structural changes in C. albicans cells. Furthermore, membrane permeability results for the fluorescent indicator propidium iodide revealed modifications in cell wall integrity in Octominin II-treated C. albicans. Octominin II treatment increases the production of reactive oxygen species (ROS) in C. albicans. Gene expression studies revealed that Octominin II suppresses virulence genes of C. albicans such as CDR1, TUP1, AGE3, GSC1, SAP2, and SAP9. In addition, a nucleic acid binding assay revealed that Octominin II degraded genomic DNA and total RNA in a concentration-dependent manner. Additionally, Octominin II inhibited and eradicated C. albicans biofilm formation. Octominin II showed relatively less cytotoxicity on raw 264.7 cells (0-200 µg/mL) and hemolysis activity on murine erythrocytes (6.25-100 µg/mL). In vivo studies confirmed that Octominin II reduced the pathogenicity of C. albicans. Overall, the data suggests that Octominin II inhibits C. albicans by employing different modes of action and can be a promising candidate for controlling multidrug-resistant Candida infections.

Transcriptomic Analysis of Liver Tissue of Black Sea Bass (Centropristis striata) Exposed to High Nitrogen Environment

The black sea bass, Centropristis striata, is a potential candidate for commercial aquaculture. Due to inadequate removal of nitrogen in its breeding environment, C. striata exhibits increased nitrate concentration, which can cause acute toxicity, including energy metabolism damage and tissue damage. Therefore, RNA-seq technology was applied to characterize genes associated with toxicity tolerance under nitrate stress. The nitrate treatment caused significant changes in a total of 8920 genes, of which 2949 genes were up-regulated and 5971 genes were down-regulated. It was found that significantly enriched GO terms and KEGG were associated with blood microparticles, inhibitors of enzyme activity, and complement and coagulation cascade pathways. Furthermore, through bioinformatics analysis, it was found that these different pathways obtained in GO and KEGG enrichment analysis were mostly related to the immune and inflammatory response of fish. This study expands our understanding of the mechanism of nitrate stress affecting the liver function of C. striata.

Tannin alleviates glyphosate exposure-induced apoptosis, necrosis and immune dysfunction in hepatic L8824 cell line by inhibiting ROS/PTEN/PI3K/AKT pathway

Glyphosate can cause tissue damage such as liver and kidney in mammals. Tannin has anti-inflammatory, antibacterial and anti-inflammatory properties. However, the effect of glyphosate on the growth of L8824 cell line and the effect of tannin on antagonism of glyphosate through the ROS/PTEN/PI3K/AKT axis are unclear. In this study, L8824 cells were treated with glyphosate (50 μg/mL) and/or tannin (4.5 μM) for 24 h to establish a model. The results showed that glyphosate exposure increased ROS and MDA levels, decreased CAT and SOD activities. PTEN was activated and the PI3K/AKT signaling pathway was inhibited. The P53/Bcl-2/Bax/CytC/Caspase3 and RIPK1/RIPK3/MLKL pathways were also activated. In addition, the cytokines and antimicrobial peptides LEAP-2, TNF-α and IL-1β were increased while β-defensin, Hepcidin, IL-2 and IFN-γ were decreased. The use of tannin reduced the adverse effects of glyphosate exposure on L8824 cells significantly. In conclusion, tannin can trigger oxidative stress via PTEN/PI3K/AKT pathway to cause apoptosis, necroptosis and immune dysfunction of L8824 cells.

Transcriptome analysis of largemouth bass (Micropterus salmoides) challenged with LPS and polyI:C

Largemouth bass (Micropterus salmoides) is a worldwide commercially important aquatic species. In recent years, pathogenic diseases cause great economic losses and hinder the industry of largemouth bass. To further understand the immune response against pathogens in largemouth bass, splenic transcriptome libraries of largemouth bass were respectively constructed at 12 h post-challenged with phosphate-buffered saline (PBS), lipopolysaccharide (LPS) and polyinosinic-polycytidylic acid (polyI:C) by using RNA sequencing technology (RNA-seq). RNA libraries were constructed using 9 RNA splenic samples isolated from three biological replicates of the three groups and sequenced on the DNBSEQ platform. A total number of 86,306 unigenes were obtained. Through pairwise comparisons among the three groups, we identified 11,295 different expression genes (DEGs) exhibiting significant differences at the transcript level. There were 7, 7, and 13 signal pathways were significantly enriched in LPS-PBS comparison, polyI:C-PBS comparison, and LPS-polyI:C comparison, respectively, indicating that the immune response to different pathogens was distinct in largemouth bass. To the best of our knowledge, this is the first report on the immune response of largemouth bass against different pathogen-associated molecular patterns (PAMPs) stimuli using transcriptomic analysis. Our results provide a valuable resource and new insights to understanding the immune characteristics of largemouth bass against different pathogens.

Transcriptome analysis and gene expression analysis related to salinity-alkalinity and low temperature adaptation of Triplophysa yarkandensis

T. yarkandensis is a common species of Triplophysa, and it is distributed in Shule river of Hexi Corridor, of Gansu province in China. In order to enrich gene database resources and explore the environment adaptation of T. yarkandensis, fifteen tissues were collected from three adult T. yarkandensis for transcriptome sequencing and de novo assembly. Nine major international gene annotation databases (NR, COG, egg_NOG, TrEMBL, Pfam, KOG, Swiss prot, KEGG and Gene Ontology) were utilized to annotate unigenes. A detailed study was conducted to explore the gene expression and the differentially expressed genes among five tissues (brain, heart, kidney, liver and spleen). In addition, the current study showed that candidate genes involved in salinity-alkalinity and low temperature adaptation were differentially expressed in tissues of T. yarkandensis. Precisely, mapk1, abcc1, gpx1, gpx4, cat and aqp1 genes participated in the regulation process of salinity-alkalinity adaptation, and elovl4, acaca, fasn, acaa2, acox1 and acox3 genes were involved in fatty acid metabolism and closely associated with low temperature adaptation. On the one hand, it was found that the expression of these genes varied among different tissues, and the important pathways involved in these genes were mapped. Furthermore, we analyzed mapk1 and acox1 genes in depth to obtain the predicted gene structure and important amino acid sites. The transcriptome information in this study will be conducive to provide further understanding for the molecular level research and exploration of the environmental adaptation of T. yarkandensis.

Transcriptome characterization and SSR discovery in the giant spiny frog Quasipaa spinosa

The giant spiny frog Quasipaa spinosa (Amphibia: Ranidae) is a large unique frog species found mainly in southern China with a low amount of fat and high protein, and it has become one of the most important aquaculture animal species in China. To better understand its genetic background and screen potential molecular markers for artificial breeding and species conservation, we constructed an expression profile of Q. spinosa with high-throughput RNA sequencing and acquired potential SSR markers. Approximately 81.7 Gb of data and 93,887 unigenes were generated. The transcriptome contains 2085 (80.7 %) complete BUSCOs, suggesting that our assembly methods were effective and accurate.These unigenes were functionally classified using 7 functional databases, yielding 17,482 Pfam-, 12,752 Sting-, 17,526 KEGG-, 24,341 Swiss-Prot-, 28,604 Nr-, 16,287 GO- and 12,752 COG-annotated unigenes. Among several amphibian species, Q. spinosa unigenes had the highest number of hits to Xenopus tropicalis (35.25 %), followed by Xenopus laevis (12.68 %). 1417 unigenes were assigned to the immune system. In addition, a total of 33,019 candidate SSR markers were identified from the constructed library. Further tests with 20 loci and 118 large-scale breeding specimens gathered from four culture farms in China showed that 15 (75 %) loci were polymorphic, with the number of alleles per locus varying from 3 to 9 (mean of 4.3). The PIC values for the SSR markers ranged from 0.19 to 0.82, with an average value of 0.43, indicating moderate polymorphism in Q. spinosa. The transcriptomic profile and SSR repertoire obtained in the present study will facilitate population genetic studies and the selective breeding of amphibian species.

RNA-seq transcriptome analysis and identification of the theromacin antimicrobial peptide of the copepod Apocyclops royi

Copepods, including Apocyclops royi, are small aquatic crustaceans and one of the important foods for fish and shellfish larvae. However, studies of the host-pathogen interactions and understanding of infectious disease in copepods are still very limited, yet they are likely to be a significant factor in the sustainable development of copepod aquaculture. In the present study, we performed de novo RNA sequence analysis of A. royi-TH (a Thai isolate of A. royi), which yielded 4.80 Gb bases of clean data and a total of 29,786 unigenes. Annotation was then performed by comparison against seven functional databases, yielding 17,617 (NR: 59.15%), 2,969 (NT: 9.97%), 15,023 (SwissProt: 50.44%), 14,543 (KOG: 48.82%), 15,077 (KEGG: 50.62%), 6,763(GO: 22.71%), and 15,841 (InterPro: 53.18%) unigenes. In comparison to the components of the shrimp Toll pathway, LGBP, Spätzle, Toll receptors, MyD88, Pelle, TRAF6, Dorsal, and Cactus homologs were successfully identified in A. royi-TH. Additionally, a novel antimicrobial peptide (Theromacin-like) was characterized in A. royi (ArTM-like). The ArTM-like ORF was 279 bp and predicted to encode for 92 amino acid residues, with a mature peptide of 75 amino acids and a molecular mass of 8.56 kDa. The genomic organization of the ArTM-like gene consisted of three exons and two introns. Expression analysis indicated that ArTM-like mRNA was abundantly expressed in copepodid and adult stages as an immune responsive gene after infection with the pathogenic Vibrio parahaemolyticus-(AHPND)-causing strain. Altogether, the knowledge obtained in this study will provide a basis for future functional studies of the molecular mechanisms in copepod immunity that may eventually be applied for disease prevention in copepod aquaculture.

Transcriptome comparison for identification of pigmentation-related genes in different color varieties of Siamese fighting fish Betta splendens

Transcriptome comparison was performed to identify genes expressed in skin, muscle and tails of mono-color (Red, Blue, Black, White and Yellow), bi-color (Cambodian) and multi-color (Marble) varieties of Siamese fighting fish Betta splendens. In total, 163,140 unigenes covering 26.348 Gb were found. Of these, 93,899 (57.55 %) unigenes significantly matched at least one database. In total, 5039 differentially expressed genes (DEGs) were found where 2415 genes (47.93 %) showed higher expression and 2624 genes (52.07 %) showed lower expression for all pairwise comparisons. DEGs between paired color varieties were 133-443. Of these, 38-220 genes were more highly expressed while 37-280 genes were more lowly expressed relative to the compared varieties. A total of 897 sequences (148 genes) significantly matched pigmentation-related genes of Danio rerio (E-value < 1e-06). Of these, 19 DEGs were identified. Examples are tyrosinase-related protein 1a (BsTyrp1a), epidermal growth factor receptor (BsEgfr) and neurofibronin 1a (BsNf1a). Moreover, 711,123 SNPs were identified and 1365 of these were located in pigmentation-related genes. Interestingly, an A > C₄₇₄ SNP in the gene BsTrpm7 and an indel (position 3571) in the BsItgb1a gene were found only in Cambodian. A C > T₂₅₂₀ SNP in BsFzd4 and 10 of 11 SNPs in BsTyrp1a were found only in Black. Different expression levels (P < 0.05) were found for tyrosinase (BsTyr), BsTyrp1a, BsNf1a and BsEgf1 among skin, body muscle and tails of the same variety and among the same tissues of different varieties (Red, Green, Blue, Black, Cambodian and Multi-colors, N = 5 each).

Comprehensive transcriptome profiling and functional analysis of the meagre (Argyrosomus regius) immune system

Meagre (Argyrosomus regius) belongs to the family Sciaenidae and is a promising candidate for Mediterranean aquaculture diversification. As a relatively recent species in aquaculture, the physiological consequences of the immune system activation in meagre are understudied. Spleen, as a primary lymphoid organ has an essential role in meagre immune and inflammatory responses. In this study, we have evaluated the in vivo effects of lipopolysaccharide (LPS) on the spleen transcriptome of meagre by RNA-seq analysis at 4 and 24 h after injection.

Transcriptome Sequencing Reveals the Antiviral Innate Immunity by IFN-γ in Chinese Sturgeon Macrophages

To further study the biological function of interferon-gamma (IFN-γ) in the Chinese sturgeon (Acipenser sinensis), we conducted a transcriptome analysis of primary macrophages induced by IFN-γ using Illumina sequencing technology. We obtained 88,879 unigenes, with a total length of 93,919,393 bp, and an average length of 1,057bp. We identified 8,490 differentially expressed genes (DEGs) between the untreated and IFN-γ-treated macrophages, with 4,599 upregulated and 3,891 downregulated. Gene ontology (GO) analysis showed that 4,044 DEGs were enriched in the biological, cellular components, and molecular function categories. Kyoto Encyclopedia of Genes and Genomes (KEGG) identified 278 immunity-related pathways enriched for the DEGs. According to the GO enrichment results, eight key immunity-related genes were screened for verification using qPCR. Results indicate that IFN-γ can activate macrophage Interferon Regulatory Factors (IRFs) and type I interferon (IFN-I), activate RIG-I-like and Toll-like receptor-related pathways, and improve the antiviral ability of macrophages in Chinese sturgeon.

The dynamic immune responses of Mandarin fish (Siniperca chuatsi) to ISKNV in early infection based on full-length transcriptome analysis and weighted gene co-expression network analysis

Mandarin fish (Siniperca chuatsi) been seriously harmed by infectious spleen and kidney necrosis virus (ISKNV) in recent years, but the early immune response mechanism of infection is still unknown. Here, we performed RNA sequencing on the spleens of mandarin fish infected with ISKNV at 0, 12, 24, 48, and 72 h post-infection (hpi) using short-read Illumina RNA sequencing and long-read Pacific Biosciences isoform sequencing to generate a full-length transcriptome. The immune responses of mandarin fish infected with ISKNV at the molecular level were characterized by RNA-seq analysis and weighted gene co-expression network analysis (WGCNA). A total of 26,528 full-length transcript sequences were obtained. There were 2,729 (1,680 up-regulated and 1,112 down-regulated), 1,874 (1,136 up-regulated and 738 down-regulated), 2,032 (1,158 up-regulated and 847 down-regulated), and 4,176 (2,233 up-regulated and 1,943 down-regulated) differentially expressed genes (DEGs) in mandarin fish at 12, 24, 48, and 72 hpi, compared with uninfected fish, respectively. A total of four modules of co-expressed DEGs identified by WGCNA were significantly positively correlated to the four time points after infection, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the immune-related DEGs in all these modules were mainly enriched in Phagosome, Endocytosis, Herpes simplex infection, and Cytokine-cytokine receptor interaction pathways. Further analysis showed that oher signaling pathways, including CAMs, NOD-like receptor and ER protein processing, Intestinal immune network for IgA production, TLR pathway, and Apoptosis significantly enriched in four modules corresponding to 12, 24, 48, and 72 hpi respectively, had specifically participated in the immune response. Hub genes identified based on the high-degree nodes in the WGCN, including CAM3, IL-8, CCL21, STING, SNX1, PFR and TBK1, and some DEGs such as MHCI, MHCII, TfR, STING, TNF α, TBK1, IRF1, and NF-kB, BCR, IgA and Bcl-XL had involved in dynamic molecular response of mandarin fish to ISKNV infection. In sum, this study provides a set of full-length transcriptome of the spleen tissue of mandarin fish for the first time and revealed a group of immune genes and pathways involved in different temporal responses to ISKNV infection, which has implications for resource conservation and aiding the development of strategies to prevent virus early infection for mandarin fish.

Recurrent expansions of B30.2-associated immune receptor families in fish

B30.2 domains, also known as PRY/SPRY, are key components of specific subsets of two large families of proteins involved in innate immunity: the tripartite motif proteins (TRIMs) and the Nod-like receptors (NLRs). TRIM proteins are important, often inducible factors of antiviral innate immunity, targeting multiple steps of viral cycles through a variety of mechanisms. NLRs prime and regulate systemic innate defenses, especially against bacteria, and control inflammation. Large TRIM and NLR subsets characterized by the presence of a B30.2 domain have been reported from a few fish species including zebrafish and seem to be strongly prone to gene duplication/expansion. Here, we performed a large-scale survey of these receptors across about 150 fish genomes, focusing on ray-finned fishes. We assessed the number and genomic distribution of domains and domain combinations associated with TRIMs, NLRs, and other genes containing B30.2 domains and looked for gene expansion patterns across fish groups. We then used a model to test the impact of taxonomy, genome size, and environmental variables on the copy numbers of these genes. Our findings reveal novel domain structures, clade-specific gains and losses. They also assist with the timing of the gene expansions, reveal patterns associated with the MHC, and lay the groundwork for further studies delving deeper into the forces that drive the copy number variation of immune genes on a species level.

Antimicrobial Peptides: Novel Source and Biological Function With a Special Focus on Entomopathogenic Nematode/Bacterium Symbiotic Complex

The rapid emergence of multidrug resistant microorganisms has become one of the most critical threats to public health. A decrease in the effectiveness of available antibiotics has led to the failure of infection control, resulting in a high risk of death. Among several alternatives, antimicrobial peptides (AMPs) serve as potential alternatives to antibiotics to resolve the emergence and spread of multidrug-resistant pathogens. These small proteins exhibit potent antimicrobial activity and are also an essential component of the immune system. Although several AMPs have been reported and characterized, studies associated with their potential medical applications are limited. This review highlights the novel sources of AMPs with high antimicrobial activities, including the entomopathogenic nematode/bacterium (EPN/EPB) symbiotic complex. Additionally, the AMPs derived from insects, nematodes, and marine organisms and the design of peptidomimetic antimicrobial agents that can complement the defects of therapeutic peptides have been used as a template.

Transcriptome analysis of immune response against Siniperca chuatsi rhabdovirus infection in mandarin fish Siniperca chuatsi

As one of the piscine rhabdoviruses, Siniperca chuatsi rhabdovirus (SCRV) has caused considerable losses to mandarin fish aquaculture industry. RNA-seq, as efficient transcriptome research method, has been widely used to study the immune response of fish to pathogens. This study reported the effect of SCRV infection at 0, 24 and 60 hr on S. chuatsi at the transcriptome level. A total of 61,527 unigenes with high quality were obtained, and 3,095, 1,854 and 227 differentially expressed genes (DEGs) were labelled between the Sc24 and Sc0 groups, the Sc60 and Sc0 groups and the Sc60 and Sc24 groups, respectively. Genes involved in innate and adaptive immunity were highlighted. In Gene Ontology analysis, the DEGs that participated in immune response, innate immune response and the regulation of apoptotic process were identified as enriched classes. Kyoto Encyclopedia of Genes and Genomes pathway results indicated that most DEGs caused by SCRV infection were identified in the immune system (retinoic acid-inducible gene-I-like receptor/Toll-like receptor/nucleotide-binding oligomerization domain-like receptor/C-type lectin receptor signalling pathway), cellular processes, cell growth and death (p53 signalling pathway, cellular senescence, apoptosis and phagosome), and metabolism. Quantitative real-time PCR was used to further verify the expression levels of 15 immune-related DEGs. The transcriptome database obtained in this study provided further in-depth insight into the immune response of S. chuatsi against SCRV.

Comprehensive analysis of full-length transcriptomes of Schizothorax prenanti by single-molecule long-read sequencing

Schizothorax prenanti (S. prenanti) is one of the most important aquaculture species in the southwest of China. However, information of the full-length transcripts in S. prenanti remains unknown. In this study, single-molecule real-time (SMRT) sequencing was performed to generate full-length transcriptomes of S.prenanti. In total, 23.26 Gb of clean reads were generated. A total of 312,587 circular consensus sequences (CCS) were obtained with average lengths of 2634 bp and 84.16% (270,662) of CCS were full-length non-chimeric reads. After being corrected with Illumina library sequencing, 18,005 contigs were obtained, with 17,797 (98.81%) successfully annotated in eight public databases, including 15,839 complete open reading frames (ORFs) with an average length of 1330 bp. Furthermore, a total of 4152 alternative splicing (AS) events and 250 long non-coding RNA (lncRNA) transcripts were detected. Additionally, a total of 1129 putative transcription factors (TFs) members from 56 TF families and 11,660 simple sequence repeats (SSRs) were identified. This study provided a valuable resource of full-length transcripts for further research on S. prenanti.

Transcriptome analysis reveals potential immune function-related regulatory genes/pathways of female Lubo goat submandibular glands at different developmental stages

Background

The submandibular glands, as major salivary glands, participate in rumen digestion in goats. Sialic acid, lysozyme, immunoglobulin A (IgA), lactoferrin and other biologically active substances secreted in the submandibular glands were reported in succession, which suggests that the submandibular gland may have immune functions in addition to participating in digestion. The aim of this study was to map the expression profile of differentially expressed genes (DEGs) at three different stages by transcriptome sequencing, screen immune-related genes and pathways by bioinformatics methods, and predict the immune function of submandibular glands at different developmental stages.

Methods

Nine submandibular gland tissue samples were collected from groups of 1-month-old kids, 12-month-old adolescent goats and 24-month-old adult goats (3 samples from each group), and high-throughput transcriptome sequencing was conducted on these samples. The DEGs among the three stages were screened and analysed. Key genes and signalling pathways were selected via protein-protein interaction (PPI) network analysis.

Results

The results revealed 2,706, 2,525 and 52 DEGs between 1-month-old and 12-month-old goats, between 1-month-old and 24-month-old goats, and between 12-month-old and 24-month-old goats, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that most of the DEGs were enriched in immune- related GO terms and pathways. Based on functional enrichment analysis and network analysis, 10 genes (PTPRC, CD28, SELL, LCP2, MYC, LCK, ZAP70, ITGB2, SYK and CCR7), two signalling pathways (the T cell receptor signalling pathway and the NF-κβ signalling pathway) and eight GO terms (T cell receptor signalling pathway, neutrophil mediated immunity, B cell mediated immunity, regulation of alpha-beta T cell activation, positive regulation of T cell proliferation, regulation of leukocyte differentiation, positive regulation of antigen receptor-mediated signalling pathway, positive regulation of lymphocyte proliferation) that may play key roles in the immune functions of the goat submandibular glands at different developmental stages were identified. Moreover, we found that eight antibacterial peptide-encoding genes were downregulated in the tuberculosis and salivary secretion pathways, while all immunoglobulins were upregulated in 10 immune system pathways. These findings indicate that the submandibular glands may be important immunological organs during the growth process of goats and that the immune function of these glands gradually weakens with age up to 12 months but remains relatively stable after 12 months of age. Overall, this study will improve our understanding of transcriptional regulation related to goat submandibular gland immune function.