Comparative Biochemistry and Physiology Part D: Genomics and Proteomics
Differentially expressed lncRNAs involved in immune responses of Haliotis diversicolor and H. discus hannai challenged with Vibrio parahaemolyticus
Introduction
LncRNA is a non-coding RNA with a length of more than 200 bases(Isin et al., 2014). lncRNA often originated from the intron or exon promoter region (Valadkhan and Gunawardane, 2016) of some coding genes through gene locating. According to different characteristics of lncRNAs, lncRNAs can be classified into cis-lncRNAs, and trans-lncRNAs (Ma et al., 2013). cis-LncRNAs can regulate the same allele's target genes, which are close to lncRNAs (Dykes and Emanueli, 2017). trans-LncRNAs can guide the changes of coding genes far away and drive the chromatin changes of the nucleus by binding to target genes in the way of RNA heteroduplex or RNA:DNA:DNA triplex (Wang and Chang, 2011). At the same time, lncRNAs may be involved in the splicing, translation, and degradation in the process of post-transcription (Shi et al., 2015).
LncRNAs can regulate many biological processes such as stress response (Huo et al., 2020; Li et al., 2018), cell development (Huang et al., 2018), Oxidation-Reduction reactions (Huang et al., 2019) in different aquatic animals. In addition, lncRNAs play an important role in the immune response of large yellow croaker, Epinephelus coioides, Penaeus vannamei, and sea cucumber (Mu et al., 2016; Liu et al., 2019; Tang et al., 2019; Ren et al., 2020). Although studies have shown that lncRNAs were extensively involved in the immune response of other aquatic animals, while studies on the immune regulation of non-model organisms, especially marine mollusks, are still relatively rare.
Haliotis diversicolor and H. discus hannai are two different most important aquaculture abalone species in China and have high commercial value. However, their aquaculture industry suffers from different diseases cuasing mass mortality of cultured abalone due to the increasing density and scale of mariculture. V. parahaemolyticus is a prominent pathogenic microorganism in marine, estuarine and aquacultural ecosystems (Srinivasan et al., 2020), and it is one of the main pathogenic bacteria causing vibriosis that results in high morbidity and mortality in aquaculture (Liu and De Mitcheson, 2008). The outbreak of pathogenic infectious diseases dominated by V. parahaemolyticus would cause a large number of abalone deaths (Cheng et al., 2004; Hasrimi et al., 2018). Therefore, the purpose of our study is to explore the role of lncRNA in the immunomodulatory response of abalone injected with V. parahaemolyticus.
Our study was the first to identify the lncRNA expression profiles of H. diversicolor and H. discus hannai infected by V. parahaemolyticus. By screening the unique and common lncRNAs in two abalone species and exploring their function, it was found that lncRNAs were widely involved in the immune process, cell differentiation process, and stress process of the two species of abalones by targeting mRNAs. Meanwhile, we also identified some lncRNAs and their target genes that may be related to the immune response in the two species of abalone. Our results may provide essential resources for further understanding the interaction mechanism between lncRNAs-mRNAs in abalone and help explore the molecular function of lncRNAs in the immune response of abalone infected by V. parahaemolytic.
Section snippets
Animals and sample preparation
Two different adult abalone with a weight of 16.45 ± 2.50 g and body length of 6.00 ± 0.50 cm were obtained from the Peiyang abalone plant (Xiamen, Fujian Province). As described in our previous publication (Sun et al., 2016), these abalones were remained at a flowing air stream and a circulating seawater system (salinity was kept at 30‰) with a constant temperature of 25 °C and dissolved oxygen (DO) of 6.2 mg/L, and they were fed with Laminaria japonica once a day. Seawater temperature and DO
Sequence assembly and identification of lncRNA characterization
After sequencing and bioinformatics analysis of the hemocyte samples, 158,937,667 and 170,082,258 raw reads were generated in H. discus hanai and H. diversicolor, respectively. After removing adaptor and low-quality reads, 154,241,843 (97.04%) and 165,613,084 (97.37%) clean reads for the two abalone species were obtained, respectively. Then the assembly of these clean reads was performed, and 367,162 contigs were produced in the H. diversicolor transcriptome, and 316,734 contigs were produced
Discussion
LncRNA as a non-coding RNA molecule has been found to play an important role in various biological processes, and its role in immunity has become one of the focuses of people studies. Of note, Valenzuela-Muñoz et al. (2019) reported that lncRNAs were involved in the immune defense process of zebrafish infected with Spring viremia of carp virus via targeting adjacent coding genes. Sun and Feng (2018) also showed that lncRNA was widely involved in the initial antiviral immune response of
Conclusion
We identified the expression profile of lncRNAs for the first time in H. diversicolor and H. discus hannai infected with V. parahaemolyticus. It is also the first time use of the non-referenced transcriptome method for comparing the functional difference of lncRNAs in H. diversicolor and H. discus hannai. This study found some differentially expressed lncRNAs related to the genes involved in immune response in abalone infected with V. parahaemolyticus. The result indicated that lncRNAs might
Declaration of competing interest
All authors have read and approved the manuscript. None of the authors had a conflict of interest that interfered with our work.
Acknowledgments
This research was funded by the National Key Research and Development Program of China (Grant Number: 2018YFD0900304–5, 2021YFE0106100); Discipline Development Grant from College of Animal Sciences FAFU (712018R0404), Open fund project of Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture (DF20902); the Natural Science Foundation of China (No. 41176152); International Science and Technology Cooperation and Communication Grant of Fujian Agriculture and Forestry
CRediT authorship contribution statement
G.L participated in the experimental design, experimental data processing and drawing, and wrote the manuscript. C·Y participated in the experimental data processing and qRT-PCR drawing, X.Z and Y·S designed the experiment and participated in the sample collection, Z.Z and Y·W edited the manuscript and supervised the study. All the authors reviewed the manuscript.
References (36)
- et al.
Transcriptional and post-transcriptional gene regulation by long non-coding RNA
Genom. Proteom. Bioinf.
(2017) - et al.
The regulation mechanism of lncRNAs and mRNAs in sea cucumbers under global climate changes: defense against thermal and hypoxic stresses
Sci. Total Environ.
(2020) - et al.
Investigation of circulating lncRNAs in B-cell neoplasms
Clin. Chim. Acta
(2014) - et al.
Recombinant engineered phage-derived enzybiotic in Pichia pastoris X-33 as whole cell biocatalyst for effective biocontrol of Vibrio parahaemolyticus in aquaculture
Int. J. Biol. Macromol.
(2020) - et al.
Differential lncRNA expression profiles reveal the potential roles of lncRNAs in antiviral immune response of Crassostrea gigas
Fish Shellfish Immunol.
(2018) - et al.
lncRNA-mediated regulation of the interferon response
Virus Res.
(2016) - et al.
Molecular mechanisms of long noncoding RNAs
Mol. Cell
(2011) - et al.
A novel C-type lectin from abalone, Haliotis discus discus, agglutinates Vibrio alginolyticus
Dev. Comp. Immunol.
(2008) - et al.
Trimmomatic: a flexible trimmer for Illumina sequence data
Bioinformatics
(2014) - Cheng, W., Hsiao, I.S., Chen, J.C., 2004. Effect of ammonia on the immune response of Taiwan abalone Haliotis...
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Nat. Biotechnol.
Detection of tlh and tdh genes in Vibrio Parahaemolyticus inhabiting farmed water ecosystem used for L. Vannamei aquaculture
J. Phys. Conf. Ser.
Identification, characterization, and expression of the genes TektinA1 and axonemal protein 66.0 in the tropical abalone Haliotis asinina
Zool. Sci.
Genome-wide identification and differentially expression analysis of lncRNAs in tilapia
BMC Genomics
Profile of a fishery collapse: why mariculture failed to save the large yellow croaker
Fish Fish.
Cited by (5)
Leveraging lncRNA-miRNA-mRNA network to reveal anti-Spiroplasma eriocheiris infection mechanisms in Macrobrachium nipponense
2022, AquacultureCitation Excerpt :Long non-coding RNAs (lncRNAs) are a class of non-protein coding RNAs with a length longer than 200 nucleotides, playing critical roles in the host immune defense against pathogens in aquatic organisms (Wang et al., 2018). For instance, through comparative transcriptome analysis, it is found that a number of lncRNAs from Oncorhynchus mykiss (Paneru et al., 2016), Oncorhynchus kisutch (Valenzuela-Muñoz et al., 2018), Larimichthys crocea (Liu et al., 2019), Danio rerio (Valenzuela-Muñoz et al., 2019), Oreochromis niloticus (Xiu et al., 2019), Haliotis diversicolor (Lu et al., 2021), and some crustaceans like whiteleg shrimp (Ren et al., 2020) and Litopenaeus vannamei (Zhang et al., 2019) were differentially expressed after pathogen infections. Further functional enrichment analysis showed that these lncRNAs were mainly involved in immune or stress responses by modulating their target genes (Pereiro et al., 2020; Valenzuela-Muñoz et al., 2018).
Transcriptomic analysis and discovery of genes involving in enhanced immune protection of Pacific abalone (Haliotis discus hannai) in response to the re-infection of Vibrio parahaemolyticus
2022, Fish and Shellfish ImmunologyCitation Excerpt :Moreover, these unannotated genes were most likely noncoding RNAs. In our previous study, it has shown that long non-coding RNAs (lncRNAs) were expressed in H. discus hannai and H. diversicolor after infection with V. parahaemolyticus, and that lncRNAs influenced the immune response of abalone [77]. Further research can analyze these unannotated genes and the regulation effect of lncRNAs on immune enhancement in H. discus hannai, in order to supplement the relevant research findings.
The potential role of eyestalk in the immunity of Litopenaeus vannamei to Vibrio parahaemolyticus infection II. From the perspective of long non-coding RNA
2022, Fish and Shellfish ImmunologyCitation Excerpt :Furthermore, lncRNAs have an important role in the immune responses of various aquatic organisms. Following V. parahaemolyticus infection, 34,240 and 23,022 lncRNAs were sequenced in H. diversicolor and H. discus hannai, respectively, and some of them were shown to be engaged in abalone immune response by targeting coding genes [18]. In wild-type zebrafish infected with spring viraemia of carp virus (SVCV), the most important biological activities controlled by lncRNAs are metabolism, growth, and redox mechanisms [19].
Long non-coding RNAs in the physiology of aquaculture animals: a perspective update
2022, Reviews in Fish Biology and Fisheries