Transcriptome of intraperitoneal organs of starry flounder Platichthys stellatus challenged by Edwardsiella ictaluri JCM1680

Yanli Tong; Xiuqin Sun; Bo Wang; Ling Wang; Yan Li; Jinhu Tian; Fengrong Zheng; Minggang Zheng

doi:10.1007/s00343-015-3307-7

Your Location：

Home >

Browse articles >

Transcriptome of intraperitoneal organs of starry flounder Platichthys stellatus challenged by Edwardsiella ictaluri JCM1680

Updated：2023-05-16

- Transcriptome of intraperitoneal organs of starry flounder Platichthys stellatus challenged by Edwardsiella ictaluri JCM1680
- Journal of Oceanology and Limnology Vol. 33, Issue 1, Pages: 20-27(2015)
- Affiliations：
  
  1. College of Marine Life Science Ocean University of China
  2. Research Center for Marine Ecology First Institute of Oceanography State Oceanic Administration
  3. College of Chemistry and Chemical Engineering and Environment Qingdao University
- Author bio：
- Funds：
- DOI：10.1007/s00343-015-3307-7
  CLC：
- Online First：02 September 2014，
  
  Published：2015
- Accepted：
Scan QR Code
Tong, Y., Sun, X., Wang, B. et al. Transcriptome of intraperitoneal organs of starry flounder Platichthys stellatus challenged by Edwardsiella ictaluri JCM1680., Chin. J. Ocean. Limnol. 33, 20–27 (2015). https://doi.org/10.1007/s00343-015-3307-7
DOI：

Tong, Y., Sun, X., Wang, B. et al. Transcriptome of intraperitoneal organs of starry flounder Platichthys stellatus challenged by Edwardsiella ictaluri JCM1680., Chin. J. Ocean. Limnol. 33, 20–27 (2015). https://doi.org/10.1007/s00343-015-3307-7 DOI：

摘要

Abstract

Platichthys stellatus is an economically important marine bony fish species that is cultured in China on a large scale. However

very little is known about its immune-related genes. In this study

the transcriptome of the immune organs of P. stellatus that were intraperitoneally challenged with the pathogen E dwardsiella ictaluri JCM1680 is analyzed. Total RNA from four tissues (spleen

kidney

liver

and intestine) was mixed equally and then sequenced on an Illumina HiSeq 2000 platform. Overall

28 465 813 quality reads were generated and assembled into 43 061 unigenes. Similarity searches against public protein sequence databases were used to annotate 28 291 unigenes (65.7% of the total)

368 of which were associated with immunoregulation

including 188 related to immunity response. Additionally

the transcript levels of immunity response unigenes annotated as related to tumor necrosis factor (TNF)

TNF receptor

chemokine

major histocompatibility complex

and interleukin-6 were investigated in the different tissues of normal and infected P. stellatus by real-time quantitative PCR. The results confirmed that the unigenes identified in the transcriptome database were indeed expressed and up-regulated in infected P. stellatus. To our knowledge

this is the first report of the sequencing and analysis of the transcriptome of P. stellatus. These findings provide insights into the transcriptomics and immunogenetics of bony fish.

关键词

Keywords

references

Altschul S F, Madden T L, Schaffer A A, Zhang J, Zhang Z, Miller W, Lipman D J. 1997. Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res., 25(17): 3 389–3 402.

Amabile-Cuevas C F. 2010. Global Perspectives of Antibiotic Resistance. In: Sosa A J ed. Antimicrobial Resistance in Developing Countries. Springer New York, America. p.3–13.

Andreakos E T, Foxwell B M, Brennan F M, Maini R N, Feldmann M. 2002. Cytokines and anti-cytokine biologicals in autoimmunity: present and future. Cytokine Growth Factor Rev., 13(4): 299–313.

Bairoch A, Boeckmann B. 1991. The SWISS-PROT protein sequence data bank. Nucleic Acids Res., 19(Suppl): 2 247.

Bao Y Y, Wang Y, Wu W J, Zhao D, Xue J, Zhang B Q, Shen Z C, Zhang C X. 2012. De novo intestine-specific transcriptome of the brown planthopper Nilaparvata lugens revealed potential functions in digestion, detoxification and immune response. Genomics, 99(4): 256–264.

Bettencourt R, Pinheiro M, Egas C, Gomes P, Afonso M, Shank T, Santos R S. 2010. High-throughput sequencing and analysis of the gill tissue transcriptome from the deep-sea hydrothermal vent mussel Bathymodiolus azoricus. BMC Genomics, 11(1): 559.

Bo J, Cai L, Xu J H, Wang K J, Au D W. 2011. The marine medaka Oryzias melastigma—A potential marine fish model for innate immune study. Mar. Pollut. Bull., 63(5): 267–276.

Cabello F C. 2006. Heavy use of prophylactic antibiotics in aquaculture: a growing problem for human and animal health and for the environment. Environ. Microbiol., 8(7): 1 137–1 144.

Chen F, Sun H L, Li Z, Cao X R. 2003. Research progress of cytokines. Shanghai J. Anim. Husb. Vet. Med., 5: 6–8. (in Chinese)

Clarke K R, Gorley R N. 2001. Primer v5: User Manual/Tutorial. PRIMER-E, Plymouth.

Gao Y, Zhang H, Gao Q, Wang L, Zhang F, Siva V S, Zhou Z, Song L, Zhang S. 2013. Transcriptome analysis of artificial hybrid pufferfish Jiyan-1 and its parental species: implications for Pufferfish Heterosis. PloS O ne, 8(3): e58453.

Götz S, García-Gómez J M, Terol J, Williams T D, Nagaraj S H, Nueda M J, Robles M, Talón M, Dopazo J, Conesa A. 2008. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res., 36(10): 3 420–3 435.

Grabherr M G, Haas B J, Yassour M, Levin J Z, Thompson D A, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol., 29(7): 644–652.

Hampton M, Melvin R G, Kendall A H, Kirkpatrick B R, Peterson N, Andrews M T. 2011. Deep sequencing the transcriptome reveals seasonal adaptive mechanisms in a hibernating mammal. PloS One, 6(10): e27021.

Hua W P, Yuan Zhang Y, Song J, Zhao L J, Wang Z Z. 2011. De novo transcriptome sequencing in Salvia miltiorrhiza to identify genes involved in the biosynthesis of active ingredients. Genomics, 98(4): 272–279.

Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y. 2008. KEGG for linking genomes to life and the environment. Nucleic A cids R es., 36(Suppl. 1): D480–D484.

Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita K F, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M. 2006. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res., 34(Suppl. 1): D354–D357.

Livak K J, Schmittgen T D. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCt method. M ethods, 25(4): 402–408.

Magnadottir B. 2010. Immunological control of fish diseases. Mar. Biotechnol., 12(4): 361–379.

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M. 2010. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res., 20(9): 1 297–1 303.

Mestecky J, Russell M W, Elson C O. 1999. Intestinal IgA: novel views on its function in the defence of the largest mucosal surface. Gut., 44(1): 2–5.

Patel S, Malde K, Lanzén A, Olsen R H, Nerland A H. 2009. Identification of immune related genes in Atlantic halibut (Hippoglossus hippoglossus L.) following in vivo antigenic and in vitro mitogenic stimulation. Fish Shellfish Immunol., 27(6): 729–738.

Pridgeon J W, Yeh H Y, Shoemaker C A, Mu X, Klesius P H. 2012. Global gene expression in channel catfish after vaccination with an attenuated Edwardsiella ictaluri. Fish Shellfish Immunol., 32(4): 524–533.

Schaue D, Kachikwu E L, McBride W H. 2012. Cytokines in radiobiological responses: a review. Radiat. Res., 178(6): 505–523.

Spurgin L G, Richardson D S. 2010. How pathogens drive genetic diversity: MHC, mechanisms and misunderstandings. Proc. R. Soc. B, 277(1684): 979–988.

Stockhammer O W, Zakrzewska A, Hegedus Z, Spaink H P, Meijer A H. 2009. Transcriptome profiling and functional analyses of the Zebra fish embryonic innate immune response to salmonell infection. J. Immunol., 182(9): 5 641–5 653.

Tatusov R L, Fedorova N D, Jackson J D, Jacobs A R, Kiryutin B, Koonin E V, Krylov D M, Mazumder R, Mekhedov S L, Nikolskaya A N. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinf., 4(1): 41.

Tonheim T C, Bøgwald J, Dalmo R A. 2008. What happens to the DNA vaccine in fish? A review of current knowledge. Fish Shellfish Immunol., 25(1): 1–18.

Wallny H J, Rammensee H G. 1990. Identification of classical minor histocompatibility antigen as cell-derived peptide. Nature, 343: 275–278.

Wang Y P, Ma Y. 2008. Potential public hazard of using antibiotics in livestock industry. Chin. J. Antibiot., 33: 519–523. (in Chinese)

Xiang L X, He D, Dong W R, Zhang Y W, Shao J Z. 2010. Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune-relevant genes in marine fish. BMC Genomics, 11(1): 472.

Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z J, Wang J, Li S T, Li R Q, Bolund L, Wang J. 2006. WEGO: a web tool for plotting GO annotations. Nucleic Acids Res., 34(Suppl. 2): W293–W297.

Zhang Y A, Salinas I, Li J, Parra D, Bjork S, Xu Z, LaPatra S E, Bartholomew J, Sunyer J O. 2010. IgT, a primitive immunoglobulin class specialized in mucosal immunity. Nat. Immunol., 11(9): 827–835.

Zheng M G, Tian J H, Yang G P, Zheng L, Chen G G, Chen J L, Wang B. 2013. Transcriptome sequencing, annotation and expression analysis of Nannochloropsis sp. at different growth phases. Gene, 523(2): 117–121.

Views

Downloads

CSCD

Alert me when the article has been cited

Submit

Tools

Publicity Resources

Parental exposure to ocean acidification impacts the larval development and transcriptome of the Pacific oyster Crassostrea gigas

Transcriptomic insights into the adaptive mechanisms of antennal glands in mud crab (Scylla paramamosain) to acute chloride-type low-salinity alkaline water stress

Changes in induced-antipredation defense traits and transcriptome regulation of rotifer Brachionus calyciflorus in response to nanoplastics

The impacts of PVC microplastics on physiology and transcriptomic responses of pearl oyster Pinctada fucata martensii

Study on Temperature Field Characteristics of2.5D Braided Composites

Related Author

Hailun FU

Wen TENG

Shoudu ZHANG

Zhangjie PENG

Jiulin CHAN

Linlin ZHANG

Jinwei WANG

Xiaosong JIANG

Related Institution

School of Marine Science and Engineering, Qingdao Agricultural University

State Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Oceanology, Chinese Academy of Sciences

Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center

Marine Sciences Research Institute of Shandong Province, National Oceanographic Center

College of Marine Science, University of Chinese Academy of Sciences

Address：Editorial Office of JOL, 88 Haijun Rd. Qingdao, 266000, China
Tel：+86-532-82898754 Email：jol@qdio.ac.cn
Technical support is provided by Beijing Founder electronics co., LTD 京ICP备09064830号-19 京公网安备11010802024621
It is recommended to read the content of this site in Chrome&IE9+. Please switch to extreme mode in browser 360.
Cookies We use cookies to help provide and enhance our service and tailor content. By continuing, you agree to the use of cookies.

⁰