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Transcriptome analysis of the critically endangered Dabry's sturgeon (Acipenser dabryanus) head kidney response to Aeromonas hydrophila.
Fish Shellfish Immunol. 2018 Dec; 83:249-261.FS

Abstract

Dabry's sturgeon (Acipenser dabryanus), as a living fossil, is considered a critically endangered aquatic animal in China. To date, the immune system of this species remains largely unknown, with limited available sequence information. In addition, increasing incidence of bacterial pathogenic diseases has been reported. Hence, the present study aimed to characterize comprehensively transcriptome profile of the head kidney from Dabry's sturgeon infected with Aeromonas hydrophila using Illumina platform. Over 42 million high-quality reads were obtained and de novo assembled into a final set of 195240 unique transcript fragments (unigenes), with an average length of 564 bp. Approximately 41702 unigenes were annotated in the NR NCBI database. Dabry's sturgeon unigenes had the highest number of hits with 14365 (34.45%) to Lepisosteus oculatus. The 195240 unigenes were assigned to three Gene Ontology (GO) categories: biological process, cellular component, and molecular function. Among them, 27770 unigenes were clustered into 26 Eukaryotic Orthologous Group (KOG) functional categories, and 36031 unigenes were mapped to 335 known Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. After A. hydrophila administration, 1728 differentially expressed unigenes were identified, including 980 upregulated and 748 downregulated unigenes. Further KEGG enrichment analysis of these unigenes identified 16 immune-related pathways, including the Toll-like receptor signaling pathway, chemokine signaling pathway, complement and coagulation pathway, RIG-I-like receptor signaling pathway, and NOD-like receptor signaling pathway. 20 DEGs were selected and their expression patterns are largely consistent with the transcriptome profile analysis, which clearly validated the reliability of the DEGs in transcriptome analysis. This work revealed novel gene expression patterns of Dabry's sturgeon host defense and contributes to a better understanding of the immune system and defense mechanisms of Dabry's sturgeon in response to bacterial infection. The results provide valuable references for studies in sturgeons that lack complete genomic sequences, and could also be helpful for the analyzing evolution among cartilaginous and teleost fish.

Authors+Show Affiliations

School of Animal Science, Yangtze University, Jingzhou, 434020, China; State Key Laboratory of Developmental Biology of Freshwater Fish, Changsha, 410081, China.Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education of China, Southwest University, Chongqing, 400715, China.School of Animal Science, Yangtze University, Jingzhou, 434020, China.Key Lab of Freshwater Biodiversity Conservation Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China.School of Animal Science, Yangtze University, Jingzhou, 434020, China.School of Animal Science, Yangtze University, Jingzhou, 434020, China.School of Animal Science, Yangtze University, Jingzhou, 434020, China.School of Animal Science, Yangtze University, Jingzhou, 434020, China.School of Animal Science, Yangtze University, Jingzhou, 434020, China; State Key Laboratory of Developmental Biology of Freshwater Fish, Changsha, 410081, China. Electronic address: xuqiaoqing@yangtzeu.edu.cn.Key Lab of Freshwater Biodiversity Conservation Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China. Electronic address: weiqw@yfi.ac.cn.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

30219387

Citation

Luo, Kai, et al. "Transcriptome Analysis of the Critically Endangered Dabry's Sturgeon (Acipenser Dabryanus) Head Kidney Response to Aeromonas Hydrophila." Fish & Shellfish Immunology, vol. 83, 2018, pp. 249-261.
Luo K, Di J, Han P, et al. Transcriptome analysis of the critically endangered Dabry's sturgeon (Acipenser dabryanus) head kidney response to Aeromonas hydrophila. Fish Shellfish Immunol. 2018;83:249-261.
Luo, K., Di, J., Han, P., Zhang, S., Xia, L., Tian, G., Zhang, W., Dun, D., Xu, Q., & Wei, Q. (2018). Transcriptome analysis of the critically endangered Dabry's sturgeon (Acipenser dabryanus) head kidney response to Aeromonas hydrophila. Fish & Shellfish Immunology, 83, 249-261. https://doi.org/10.1016/j.fsi.2018.09.044
Luo K, et al. Transcriptome Analysis of the Critically Endangered Dabry's Sturgeon (Acipenser Dabryanus) Head Kidney Response to Aeromonas Hydrophila. Fish Shellfish Immunol. 2018;83:249-261. PubMed PMID: 30219387.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Transcriptome analysis of the critically endangered Dabry's sturgeon (Acipenser dabryanus) head kidney response to Aeromonas hydrophila. AU - Luo,Kai, AU - Di,Jun, AU - Han,Panpan, AU - Zhang,Shuhuan, AU - Xia,Lihai, AU - Tian,Guangming, AU - Zhang,Wenbing, AU - Dun,Dan, AU - Xu,Qiaoqing, AU - Wei,Qiwei, Y1 - 2018/09/14/ PY - 2018/04/18/received PY - 2018/09/11/revised PY - 2018/09/12/accepted PY - 2018/9/17/pubmed PY - 2019/2/15/medline PY - 2018/9/17/entrez KW - Aeromonas hydrophila KW - Dabry's sturgeon KW - Head kidney KW - Immune response SP - 249 EP - 261 JF - Fish & shellfish immunology JO - Fish Shellfish Immunol. VL - 83 N2 - Dabry's sturgeon (Acipenser dabryanus), as a living fossil, is considered a critically endangered aquatic animal in China. To date, the immune system of this species remains largely unknown, with limited available sequence information. In addition, increasing incidence of bacterial pathogenic diseases has been reported. Hence, the present study aimed to characterize comprehensively transcriptome profile of the head kidney from Dabry's sturgeon infected with Aeromonas hydrophila using Illumina platform. Over 42 million high-quality reads were obtained and de novo assembled into a final set of 195240 unique transcript fragments (unigenes), with an average length of 564 bp. Approximately 41702 unigenes were annotated in the NR NCBI database. Dabry's sturgeon unigenes had the highest number of hits with 14365 (34.45%) to Lepisosteus oculatus. The 195240 unigenes were assigned to three Gene Ontology (GO) categories: biological process, cellular component, and molecular function. Among them, 27770 unigenes were clustered into 26 Eukaryotic Orthologous Group (KOG) functional categories, and 36031 unigenes were mapped to 335 known Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. After A. hydrophila administration, 1728 differentially expressed unigenes were identified, including 980 upregulated and 748 downregulated unigenes. Further KEGG enrichment analysis of these unigenes identified 16 immune-related pathways, including the Toll-like receptor signaling pathway, chemokine signaling pathway, complement and coagulation pathway, RIG-I-like receptor signaling pathway, and NOD-like receptor signaling pathway. 20 DEGs were selected and their expression patterns are largely consistent with the transcriptome profile analysis, which clearly validated the reliability of the DEGs in transcriptome analysis. This work revealed novel gene expression patterns of Dabry's sturgeon host defense and contributes to a better understanding of the immune system and defense mechanisms of Dabry's sturgeon in response to bacterial infection. The results provide valuable references for studies in sturgeons that lack complete genomic sequences, and could also be helpful for the analyzing evolution among cartilaginous and teleost fish. SN - 1095-9947 UR - https://www.unboundmedicine.com/medline/citation/30219387/Transcriptome_analysis_of_the_critically_endangered_Dabry's_sturgeon__Acipenser_dabryanus__head_kidney_response_to_Aeromonas_hydrophila_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1050-4648(18)30588-6 DB - PRIME DP - Unbound Medicine ER -