Transcriptome Analysis of Immune-Related Gene in Hybrid Yellow Catfish in Reaction to Peptidoglycan Challenge
Fishery Institute of Anhui Academy of Agricultural Sciences, Hefei 230061, China
| Abstract: | Hybrid yellow catfish (Tachysurus vachelli x Tachysurus fulvidraco) is one of the most important freshwater fish in China, intensive culturing has caused increased susceptibility to bacteria, viruses, and parasites. However, little is known about its adaptation mechanisms to pathogen infection. To better understand its immune system and immune related gene under pathogen infection, the transcriptome was analyzed by comparing the data of hybrid yellow catfish spleen stimulated by PGN and PBS. Fish in experimental group were injected with 100 μl baccilus subminis PGN (1mg/ml, 69,554, Sigma) intraperitoneally, and the fish in control group injected with 100 ul phosphate buffered solution (PBS). After 24 h injection, spleens were collected and immediately frozen in liquid nitrogen, then stored in -80°C refrigerator. Total RNA from spleens of hybrid yellow catfish were extracted using Trizol reagent (Sangon, China) according to the manufacturer’s instructions. The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, USA) and sequenced on an Illumina HiSeq X Ten platform. There were 285 differentially expressed genes (DEGs) between PGN treated experimental groups and PBS control groups at 24 h, including 213 up regulated and 72 down regulated DEGs. The expression of qRT-PCR from five up regulated DEGs and five down regulated DEGs were consistent with RNA-Seq. In the analysis of GO enrichment, DEGs in the spleens of PGN treated hybrid yellow catfish were significantly enriched in GO items, including Biological Process, Cellular Component, and Molecular Function items. The identified DEGs and enriched GO terms and KEGG pathways were useful for understanding the physical and biochemical performances, and the transcriptome data greatly enriched the genetic information of hybrid yellow catfish. |
| Keywords: | Differentially Expressed Genes, Genes and Genomes, Transcriptome, Ontology |
| DOI: | 10.57237/j.jaf.2022.01.006 |
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收稿日期: 2022-08-25
接受日期: 2022-11-1 00:00:00
在线出版日期: 2023-01-14
参考文献
| [1] | Wolf AJ, Underhill DM (2018) Peptidoglycan recognition by the innate immune system. Nature Reviews Immunology 18: 243-254. |
| [2] | Kondo H, Kikumoto T, Yoshii K, Murase N, Yamada H, Fukuda Y, Hirono I (2021) Effects of Peptidoglycan and Polyinosinic: Polycytidylic Acid on the Recombinant Subunit Vaccine Efficacy Against Edwardsiella tarda in Japanese Flounder Paralichthys olivaceus. Fish Pathology 56: 149-155. |
| [3] | Kono T, Ponpornpisit A, Sakai M (2004) The analysis of expressed genes in head kidney of common carp Cyprinus carpio L. stimulated with peptidoglycan. Aquaculture 235: 37-52. |
| [4] | Su Y (2011) Isolation and identification of pelteobagrin, a novel antimicrobial peptide from the skin mucus of yellow catfish (Pelteobagrus fulvidraco). Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology 158: 149-154. |
| [5] | Abo-Al-Ela HG (2018) An introduction to selected innate immune-relevant genes in fish. Applied Ecology and Environmental Research 16: 955-976. |
| [6] | Flajnik MF (2018) A cold-blooded view of adaptive immunity. Nature Reviews Immunology 18: 438-453. |
| [7] | Mebius RE, Kraal G (2005) Structure and function of the spleen. Nature reviews immunology 5: 606-616. |
| [8] | Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome research 18: 1509-1517. |
| [9] | Chen X, Mei J, Wu J, Jing J, Ma W, Zhang J, Dan C, Wang W, Gui J-F (2015) A comprehensive transcriptome provides candidate genes for sex determination/differentiation and SSR/SNP markers in yellow catfish. Marine Biotechnology 17: 190-198. |
| [10] | Liu Y, Xin Z-Z, Zhang D-Z, Wang Z-F, Zhu X-Y, Tang B-P, Jiang S-H, Zhang H-B, Zhou C-L, Chai X-Y (2017) Transcriptome analysis of yellow catfish (Pelteobagrus fulvidraco) liver challenged with polyriboinosinic polyribocytidylic acid (poly I: C). Fish & Shellfish Immunology 68: 395-403. |
| [11] | Tao Y-F, Qiang J, Dagoudo M, Zhu H-J, Bao J-W, Ma J-L, Li M-X, Xu P (2021) Transcriptome profiling reveals differential expression of immune-related genes in gills of hybrid yellow catfish (Tachysurus fulvidraco♀× Pseudobagrus vachellii♂) under hypoxic stress: Potential NLR-mediated immune response. Fish & Shellfish Immunology 119: 409-419. |
| [12] | Zhang J, Ma W, Song X, Lin Q, Gui J-F, Mei J (2014) Characterization and development of EST-SSR markers derived from transcriptome of yellow catfish. Molecules 19: 16402-16415. |
| [13] | Bian L, Liu C, Chen S, Zhao F, Ge J, Tan J (2018) Transcriptome analysis of gene expression patterns during embryonic development in golden cuttlefish (Sepia esculenta). Genes & genomics 40: 253-263. |
| [14] | Kim W-J, Lee K, Lee D, Kim H-C, Nam B-H, Jung H, Yi S-J, Kim K (2021) Transcriptome profiling of olive flounder responses under acute and chronic heat stress. Genes & Genomics 43: 151-159. |
| [15] | Yang L, Wang Y, Zhang Z, He S (2015) Comprehensive transcriptome analysis reveals accelerated genic evolution in a Tibet fish, Gymnodiptychus pachycheilus. Genome biology and evolution 7: 251-261. |
| [16] | Carruthers M, Yurchenko AA, Augley JJ, Adams CE, Herzyk P, Elmer KR (2018) De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species. BMC genomics 19: 1-17. |
| [17] | Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120. |
| [18] | Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nature methods 12: 357-360. |
| [19] | Anders S, Huber W (2012) Differential expression of RNA-Seq data at the gene level–the DESeq package. Heidelberg, Germany: European Molecular Biology Laboratory (EMBL) 10: f1000research. |
| [20] | Anders S, Pyl PT, Huber W (2015) HTSeq—a Python framework to work with high-throughput sequencing data. bioinformatics 31: 166-169. |
| [21] | Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T (2007) KEGG for linking genomes to life and the environment. Nucleic acids research 36: D480-D484. |
| [22] | Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2− ΔΔCT method. methods 25: 402-408. |
| [23] | Liu Q-N, Xin Z-Z, Chai X-Y, Jiang S-H, Li C-F, Zhang H-B, Ge B-M, Zhang D-Z, Zhou C-L, Tang B-P (2016) Characterization of immune-related genes in the yellow catfish Pelteobagrus fulvidraco in response to LPS challenge. Fish & Shellfish Immunology 56: 248-254. |
| [24] | Chu X-H, Yang T-T, Liu Y, Hong L, Jiao T, Meng X, Zhang D-Z, Wang J-L, Tang B-P, Zhou C-L (2019) Transcriptome analysis of differential expressed genes in hepatopancreas of Procambarus clarkii challenged with peptidoglycan. Fish & Shellfish Immunology 86: 311-318. |
| [25] | Li Y-T, Tang B-P, Zhang S-P, Tang Y-Y, Wang G, Jiang S-H, Ge B-M, Zhang D-Z, Zhou C-L, Liu Q-N (2021) Transcriptome analysis of immune-related genes in Sesarmops sinensis hepatopancreas in reaction to peptidoglycan challenge. Genomics 113: 946-954. |
| [26] | Mao Y, Wang J, Zhang Z, Ding S, Su Y (2010) Cloning, mRNA expression, and recombinant expression of peptidoglycan recognition protein II gene from large yellow croaker (Pseudosciaena crocea). Molecular biology reports 37: 3897-3908. |
| [27] | Choi K-M, Joo M-S, Cho DH, Bae J-S, Jung J-M, Hwang JY, Kwon M-G, Seo JS, Hwang SD, Jee B-Y (2019) Characterization of gene expression profiles and functional analysis of peptidoglycan recognition protein 2 from rock bream (Oplegnathus fasciatus). Fish & Shellfish Immunology 84: 1068-1074. |
| [28] | Li X, Wang S, Qi J, Echtenkamp SF, Chatterjee R, Wang M, Boons G-J, Dziarski R, Gupta D (2007) Zebrafish peptidoglycan recognition proteins are bactericidal amidases essential for defense against bacterial infections. Immunity 27: 518-529. |
| [29] | Niu J, Song W, Li R, Yu H, Guan J, Qi J, He Y (2021) The Bdkrb2 gene family provides a novel view of viviparity adaptation in Sebastes schlegelii. BMC ecology and evolution 21: 1-11. |
| [30] | Stefanova NA, Maksimova KY, Rudnitskaya EA, Muraleva NA, Kolosova NG (2018) Association of cerebrovascular dysfunction with the development of Alzheimer’s disease-like pathology in OXYS rats. BMC genomics 19: 51-63. |
| [31] | Umasuthan N, Xue X, Caballero-Solares A, Kumar S, Westcott JD, Chen Z, Fast MD, Skugor S, Nowak BF, Taylor RG (2020) Transcriptomic profiling in fins of Atlantic salmon parasitized with sea lice: evidence for an early imbalance between chalimus-induced immunomodulation and the host’s defense response. International journal of molecular sciences 21: 2417. |
