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Patnaik HH, Sang MK, Park JE, Song DK, Jeong JY, Hong CE, Kim YT, Shin HJ, Ziwei L, Hwang HJ, Park SY, Kang SW, Ko JH, Lee JS, Park HS, Jo YH, Han YS, Patnaik BB, Lee YS. A review of the endangered mollusks transcriptome under the threatened species initiative of Korea. Genes Genomics 2023:10.1007/s13258-023-01389-3. [PMID: 37405596 DOI: 10.1007/s13258-023-01389-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/09/2023] [Indexed: 07/06/2023]
Abstract
Transcriptome studies for conservation of endangered mollusks is a proactive approach towards managing threats and uncertainties facing these species in natural environments. The population of these species is declining due to habitat destruction, illicit wildlife trade, and global climate change. These activities risk the free movement of species across the wild landscape, loss of breeding grounds, and restrictions in displaying the physiological attributes so crucial for faunal welfare. Gastropods face the most negative ecological effects and have been enlisted under Korea's protective species consortium based on their population dynamics in the last few years. Moreover, with the genetic resources restricted for such species, conservation by informed planning is not possible. This review provides insights into the activities under the threatened species initiative of Korea with special reference to the transcriptome assemblies of endangered mollusks. The gastropods such as Ellobium chinense, Aegista chejuensis, Aegista quelpartensis, Incilaria fruhstorferi, Koreanohadra kurodana, Satsuma myomphala, and Clithon retropictus have been represented. Moreover, the transcriptome summary of bivalve Cristaria plicata and Caenogastropoda Charonia lampas sauliae is also discussed. Sequencing, de novo assembly, and annotation identified transcripts or homologs for the species and, based on an understanding of the biochemical and molecular pathways, were ascribed to predictive gene function. Mining for simple sequence repeats from the transcriptome have successfully assisted genetic polymorphism studies. A comparison of the transcriptome scheme of Korean endangered mollusks with the genomic resources of other endangered mollusks have been discussed with homologies and analogies for dictating future research.
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Affiliation(s)
- Hongray Howrelia Patnaik
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
| | - Min Kyu Sang
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Jie Eun Park
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Dae Kwon Song
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Jun Yang Jeong
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - Chan Eui Hong
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - Yong Tae Kim
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - Hyeon Jun Shin
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - Liu Ziwei
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - Hee Ju Hwang
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - So Young Park
- Biodiversity Research Team, Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Gyeongbuk, 37242, South Korea
| | - Se Won Kang
- Biological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeonbuk, 56212, South Korea
| | - Jung Ho Ko
- Police Science Institute, Korean National Police University, Asan, Chungnam, 31539, South Korea
| | - Jun Sang Lee
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
| | - Hong Seog Park
- Research Institute, GnC BIO Co., LTD., 621-6 Banseok-dong, Yuseong-gu, Daejeon, 34069, South Korea
| | - Yong Hun Jo
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea
| | - Yeon Soo Han
- College of Agriculture and Life Science, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, South Korea
| | - Bharat Bhusan Patnaik
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
- P.G Department of Biosciences and Biotechnology, Fakir Mohan University, Odisha, 756089, Nuapadhi, Balasore, India
| | - Yong Seok Lee
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.
- Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Asan, Chungnam, South Korea.
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan,, Chungnam, 31538, South Korea.
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Wang X, Qu X, Lu X, Chen M, Ning J, Liu H, Liu G, Xu X, Zhang X, Yu K, Xu H, Liu B, Wang C. Characterization of TRAF genes and their responses to Vibrio anguillarum challenge in Argopecten scallops. Fish Shellfish Immunol 2023; 135:108675. [PMID: 36906048 DOI: 10.1016/j.fsi.2023.108675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/27/2023] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
The tumor necrosis factor receptor-related factor (TRAF) family has been reported to be involved in many immune pathways, such as TNFR, TLR, NLR, and RLR in animals. However, little is known about the roles of TRAF genes in the innate immune of Argopecten scallops. In this study, we first identified five TRAF genes, including TRAF2, TRAF3, TRAF4, TRAF6 and TRAF7, but not TRAF1 and TRAF5, from both the bay scallop A. irradians (Air) and the Peruvian scallop A. purpuratus (Apu). The phylogenetic analysis showed that the TRAF genes in Argopecten scallops (AiTRAF) belong to the branch of molluscan TRAF family, which lacks TRAF1 and TRAF5. Since TRAF6 is a key bridge factor in the tumor necrosis factor superfamily and plays an important role in innate and adaptive immunity, we cloned the ORFs of the TRAF6 gene in both A. irradians and A. purpuratus, as well as in two reciprocal hybrids (Aip for the hybrid Air × Apu and Api for the hybrid Apu × Air). Differences in conformational and post-translational modification resulted from the variation in amino acid sequences may cause differences in activity among them. Analysis of conserved motifs and protein structural domains revealed that AiTRAF contains typical structural domains similar to those of other mollusks and has the same conserved motifs. Tissue expression of TRAF in Argopecten scallops challenged by Vibrio anguillarum was examined by qRT-PCR. The results showed that AiTRAF were higher in gill and hepatopancreas. When challenged by Vibrio anguillarum, the expression of AiTRAF was significantly increased compared with the control group, indicating that AiTRAF may play an important role in the immunity of scallops. In addition, the expression of TRAF was higher in Api and Aip than in Air when challenged by Vibrio anguillarum, suggesting that TRAF may have contributed to the high resistance of Api and Aip to Vibrio anguillarum. The results of this study may provide new insights into the evolution and function of TRAF genes in bivalves and ultimately benefit scallop breeding.
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Affiliation(s)
- Xia Wang
- College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong, 266109, China
| | - Xiaoxu Qu
- College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong, 266109, China
| | - Xia Lu
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China
| | - Min Chen
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China
| | - Junhao Ning
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China
| | - Haijun Liu
- Yantai Spring-Sea AquaSeed, Co., Ltd., Yantai, 264006, China
| | - Guilong Liu
- Yantai Spring-Sea AquaSeed, Co., Ltd., Yantai, 264006, China
| | - Xin Xu
- Yantai Spring-Sea AquaSeed, Co., Ltd., Yantai, 264006, China
| | - Xiaotong Zhang
- College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong, 266109, China
| | - Kai Yu
- College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong, 266109, China
| | - He Xu
- Jiangsu Baoyuan Biotechnology Co., Ltd., Lianyungang, 222144, China; Jiangsu Haitai MariTech Co., Ltd., Lianyungang, 222144, China
| | - Bo Liu
- College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong, 266109, China.
| | - Chunde Wang
- College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China.
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Hwang HJ, Patnaik BB, Baliarsingh S, Patnaik HH, Sang MK, Park JE, Cho HC, Song DK, Jeong JY, Hong CE, Kim YT, Sin HJ, Ziwei L, Park SY, Kang SW, Jeong HC, Park HS, Han YS, Lee YS. Transcriptome analysis of the endangered dung beetle Copris tripartitus (Coleoptera: Scarabaeidae) and characterization of genes associated to immunity, growth, and reproduction. BMC Genomics 2023; 24:94. [PMID: 36864388 PMCID: PMC9979532 DOI: 10.1186/s12864-023-09122-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/09/2023] [Indexed: 03/04/2023] Open
Abstract
BACKGROUND Dung beetles recycle organic matter through the decomposition of feces and support ecological balance. However, these insects are threatened by the indiscriminate use of agrochemicals and habitat destruction. Copris tripartitus Waterhouse (Coleoptera: Scarabaeidae), a dung beetle, is listed as a class-II Korean endangered species. Although the genetic diversity of C. tripartitus populations has been investigated through analysis of mitochondrial genes, genomic resources for this species remain limited. In this study, we analyzed the transcriptome of C. tripartitus to elucidate functions related to growth, immunity and reproduction for the purpose of informed conservation planning. RESULTS The transcriptome of C. tripartitus was generated using next-generation Illumina sequencing and assembled de novo using a Trinity-based platform. In total, 98.59% of the raw sequence reads were processed as clean reads. These reads were assembled into 151,177 contigs, 101,352 transcripts, and 25,106 unigenes. A total of 23,450 unigenes (93.40%) were annotated to at least one database. The largest proportion of unigenes (92.76%) were annotated to the locally curated PANM-DB. A maximum of 5,512 unigenes had homologous sequences in Tribolium castaneum. Gene Ontology (GO) analysis revealed a maximum of 5,174 unigenes in the Molecular function category. Further, in Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, a total of 462 enzymes were associated with established biological pathways. Based on sequence homology to known proteins in PANM-DB, representative immunity, growth, and reproduction-related genes were screened. Potential immunity-related genes were categorized into pattern recognition receptors (PRRs), the Toll-like receptor signaling pathway, the MyD88- dependent pathway, endogenous ligands, immune effectors, antimicrobial peptides, apoptosis, and adaptation-related transcripts. Among PRRs, we conducted detailed in silico characterization of TLR-2, CTL, and PGRP_SC2-like. Repetitive elements such as long terminal repeats, short interspersed nuclear elements, long interspersed nuclear elements and DNA elements were enriched in the unigene sequences. A total of 1,493 SSRs were identified among all unigenes of C. tripartitus. CONCLUSIONS This study provides a comprehensive resource for analysis of the genomic topography of the beetle C. tripartitus. The data presented here clarify the fitness phenotypes of this species in the wild and provide insight to support informed conservation planning.
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Affiliation(s)
- Hee Ju Hwang
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
| | - Bharat Bhusan Patnaik
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.,PG Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore-, Odisha, 756089, India.,Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Snigdha Baliarsingh
- PG Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore-, Odisha, 756089, India
| | - Hongray Howrelia Patnaik
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
| | - Min Kyu Sang
- Research Support Center (Core-Facility) for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Jie Eun Park
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.,Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Hang Chul Cho
- iLAB, INSILICOGEN, INC. #2901~2904, Tower-Dong A, HEUNGDEOK IT VALLEY, 13, Heungdeok 1-Ro, Giheung-Gu, Yongin-Si, 16954, Gyeonggi-do, Korea
| | - Dae Kwon Song
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.,Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Jun Yang Jeong
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.,Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Chan Eui Hong
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.,Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Yong Tae Kim
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.,Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Hyeon Jun Sin
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, Chungnam, South Korea
| | - Liu Ziwei
- Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, Chungnam, South Korea
| | - So Young Park
- Biodiversity Research Team, Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Gyeongbuk, South Korea
| | - Se Won Kang
- Biological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeonbuk, South Korea
| | - Heon Cheon Jeong
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea
| | - Hong Seog Park
- Research Institute, GnC BIO Co., LTD., 621-6 Banseok-Dong, Yuseong-Gu, Daejeon, 34069, Korea
| | - Yeon Soo Han
- College of Agriculture and Life Science, Chonnam National University, 77 Yongbong-Ro, Buk-Gu, Gwangju, 61186, South Korea
| | - Yong Seok Lee
- Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea. .,Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, Chungnam, South Korea. .,Research Support Center (Core-Facility) for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Asan, Chungnam, South Korea.
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Juhász A, Lawton SP. Toll like receptors and their evolution in the lymnaeid freshwater snail species Radix auricularia and Lymnaea stagnalis, key intermediate hosts for zoonotic trematodes. Dev Comp Immunol 2022; 127:104297. [PMID: 34662684 DOI: 10.1016/j.dci.2021.104297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
One of the major evolutionarily conserved pathways in innate immunity of invertebrates is the toll-like receptor (TLR) pathway. However, little is known of the TLR protein family in gastropod molluscs despite their role in the transmission of human diseases, especially the common lymnaeid freshwater snail species Radix auricularia and Lymnaea stagnalis, key intermediate hosts of zoonotic trematodes. Using comparative genomics and gene prediction approaches utilising the freshwater snail Biomphalaria glabrata genome as a reference ten putative TLR proteins were identified in both R. auricularia and L. stagnalis. Phylogenetic analyses revealed that unlike other molluscs the lymnaeid species also possessed class 1 TLRs, previously thought to be unique to B. glabrata. Gene duplication events were also seen across the TLR classes in the lymnaeids with several of the genes appearing to exist as potential tandem elements in R. auricularia. Each predicted TLR was shown to possess the typical the leucine-rich repeat extracellular and TIR intracellular domains and both single cysteine clusters and multiple cysteine clusters TLRs were identified in both lymnaeid species. Principle component analyses of 3D models of the predicted TLRs showed that class 1 and 5 proteins did not cluster based on similarity of structure, suggested to be potential adaptation to a range of pathogens. This study provides the first detailed account of TLRs in lymnaeids and affords a platform for further research into the role of these proteins into susceptibility and compatibility of these snails with trematodes and their role in transmission.
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Affiliation(s)
- Alexandra Juhász
- Institute of Medical Microbiology, Semmelweis University, H-1089, Budapest, Hungary; Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Scott P Lawton
- Epidemiology Research Unit (ERU) Department of Veterinary and Animal Sciences, Northern Faculty, Scotland's Rural College (SRUC), An Lòchran, 10 Inverness Campus, Inverness, IV2 5NA, UK.
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Gorbushin AM. Identification of peptidoglycan recognition proteins in hemocytes and kidney of common periwinkle Littorinalittorea. Fish Shellfish Immunol 2022; 120:11-14. [PMID: 34774730 DOI: 10.1016/j.fsi.2021.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/11/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Peptidoglycan Recognition Proteins (PGRPs) are a diverse group of proteins involved in innate immunity. In particular, PGRPs have been shown to participate in immune pattern recognition in various mollusks. However, they have not been described in Caenogastropoda, a large molluscan group comprising sea, freshwater and land snails. In this study, four short PGRPs with molecular weights ranging from 21 to 34 kDa and their isoforms were identified and structurally characterized in the kidney and hemocytic transcriptomes of a caenogastropod mollusk Littorina littorea. All of them (LlPGRP1-4) are secretory, possess a signal peptide and a characteristic N-terminal N-acetylmuramoyl-l-alanine amidase (Ami) domain with conserved Zn2+ binding- and amidase catalytic sites. The shortest proteins, LlPGRP1 and LlPGRP2, have no additional conserved motifs on the N-terminus. In longer and most abundantly expressed LlPGRP3 and LlPGRP4 the Ami-domain is combined with an N-terminal SH3-domain and a cysteine-rich motif, respectively. Expression analysis showed that LlPGRPs of the common periwinkle were uninvolved in the immune response to infection with trematode Himasthla elongata though they might act in antibacterial defense.
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Affiliation(s)
- Alexander M Gorbushin
- Sechenov Institute of Evolutionary Physiology and Biochemistry (IEPhB RAS), St Petersburg, Russia.
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Gao C, Cai X, Cao M, Fu Q, Yang N, Liu X, Wang B, Li C. Comparative analysis of the miRNA-mRNA regulation networks in turbot (Scophthalmus maximus L.) following Vibrio anguillarum infection. Dev Comp Immunol 2021; 124:104164. [PMID: 34129850 DOI: 10.1016/j.dci.2021.104164] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/06/2021] [Accepted: 06/06/2021] [Indexed: 06/12/2023]
Abstract
MicroRNAs could not only regulate posttranscriptional silencing of target genes in eukaryotic organisms, but also have positive effect on their target genes as well. These microRNAs have been reported to be involved in mucosal immune responses to pathogen infection in teleost. Therefore, we constructed the immune-related miRNA-mRNA networks in turbot intestine following Vibrio anguillarum infection. In our results, 1550 differentially expressed (DE) genes and 167 DE miRNAs were identified. 113 DE miRNAs targeting 89 DE mRNAs related to immune response were used to construct miRNA-mRNA interaction networks. Functional analysis showed that target genes were associated with synthesis and degradation of ketone bodies, mucin type O-Glycan biosynthesis, homologous recombination, biotin metabolism, and intestinal immune network for IgA production that were equivalent to the function of IgT and IgM in fish intestine. Finally, 10 DE miRNAs and 7 DE mRNAs were selected for validating the accuracy of high-throughput sequencing results by qRT-PCR. The results of this study will provide valuable information for the elucidation of the regulation mechanisms of miRNA-mRNA interactions involved in disease resistance in teleost mucosal immune system.
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Affiliation(s)
- Chengbin Gao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China; Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, 90 South St, Murdoch, Perth, 6150, Australia
| | - Xin Cai
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China; Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, 90 South St, Murdoch, Perth, 6150, Australia
| | - Min Cao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qiang Fu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ning Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiaoli Liu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Beibei Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
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Gao C, Cai X, Fu Q, Yang N, Song L, Su B, Tan F, Liu B, Li C. Dynamics of MiRNA Transcriptome in Turbot (Scophthalmus maximus L.) Intestine Following Vibrio anguillarum Infection. Mar Biotechnol (NY) 2019; 21:550-564. [PMID: 31111338 DOI: 10.1007/s10126-019-09903-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/26/2019] [Indexed: 06/09/2023]
Abstract
MicroRNAs (miRNAs) are a group of small non-coding RNAs, which could bind to the 3'-untranslated regions of their target mRNAs to regulate gene expression in various biological processes, including immune-regulated signaling pathways. Turbot (Scophthalmus maximus L.), an important commercial fish species in China, has been suffering with Vibrio anguillarum infection resulted in dramatic economic loss. Therefore, we investigated the expression profiles of miRNAs, as well as the immune-related miRNA-mRNA pairs in turbot intestine at 1 h, 4 h, and 12 h following V. anguillarum infection. As a result, 266 predicted novel miRNAs and 283 conserved miRNAs belonging to 92 miRNA families were detected. A total of 44 miRNAs were differentially expressed in the intestine following V. anguillarum infection. Following prediction, the potential target genes of differentially expressed miRNAs were grouped into a wide range of functional categories, including immune defense/evasion, inflammatory responses, RIG-I signaling pathway, and Toll-like receptor signaling pathway. Moreover, we selected 15 differentially expressed immune genes and their related differentially expressed miRNAs to construct an interaction network for V. anguillarum infection in turbot. These results suggested that in teleost, as in higher vertebrates, miRNAs prominently contribute to immune responses, protecting the host against infection. In addition, this is the first report of comprehensive identification of turbot miRNAs being differentially regulated in the intestine related to V. anguillarum infection. Our results provided an opportunity for further understanding of the molecular mechanisms of miRNA regulation in turbot host-pathogen interactions.
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Affiliation(s)
- Chengbin Gao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xin Cai
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qiang Fu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ning Yang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lin Song
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Baofeng Su
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Fenghua Tan
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Baining Liu
- Menaul School Qingdao, Qingdao, 266200, China
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
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