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Data Brief. 2018 February; 16: 466–469.
Published online 2017 November 13. doi:  10.1016/j.dib.2017.11.024
PMCID: PMC5724979

Transcriptome data of Epinephelus fuscoguttatus infected by Vibrio vulnificus

Abstract

Vibriosis disease by Vibrio spp. greatly reduced productivity of aquaculture, such as brown-marbled grouper (Epinephelus fuscoguttatus), which is an economically important fish species in Malaysia. Preventive measures and immediate treatment are critical to reduce the mortality of E. fuscoguttatus from vibriosis. To investigate the molecular mechanisms associated with immune response and host-bacteria interaction, a transcriptomic analysis was performed to compare between healthy and Vibrio-infected groupers. This permits the discovery of immune-related genes, specifically the resistance genes upon infection. Herein, we provide the raw transcriptome data from Illumina HiSeq. 4000 that have been deposited into NCBI SRA database with the BioProject accession number PRJNA396437. A total of 493,403,076 raw sequences of 74.5 Gb were obtained. Trimming of the raw data produced 437,186,232 clean reads of ~58 Gb. These datasets will be useful to elucidate the defence mechanisms of E. fuscoguttatus against Vibrio vulnificus infection for future development of effective prevention and treatment of vibriosis.

Keywords: Transcriptome, Grouper, Vibriosis, Epinephelus fuscoguttatus

Specifications Table

Table thumbnail

Value of the data

  • • This dataset provides the transcriptome sequences from gill and whole-body tissues of control (healthy) and Vibrio-infected E. fuscoguttatus.
  • • Downstream analysis will allow the identification of genes involved in the mechanism of host immune response against Vibrio infection.
  • • This study will provide a better understanding on the molecular mechanisms associated with immune defense and host-pathogen interaction.
  • • The data can be a reference transcriptome for grouper and useful for comparative analysis with other fish diseases.

1. Data

This article reports the transcriptome data from gill and whole-body tissues of control (healthy) and V. vulnificus-infected E. fuscoguttatus at day 31 post infection. The raw data were deposited in the NCBI SRA database as detailed in Table 1.

Table 1
SRA accession links for brown-marbled group data.

2. Experimental design, materials and methods

2.1. Fish sampling and infection experiment

Brown-marbled grouper (Epinephelus fuscoguttatus) fingerlings were obtained from Fisheries Research Institute (FRI) Tanjung Demong, Besut in Terengganu, Malaysia (5°46'09.0"N 102°33'02.6"E). Fingerlings with length of ~5 cm were acclimatised in aerated seawater (25 °C, salinity ~35 parts per thousand (PPT), pH 7.9) for one week. For experimental infection, healthy fingerlings were randomly selected and immersed in 20 L seawater containing 1×107 CFU mL−1 of Vibrio vulnificus for 30 min, whereas the controls were immersed in clean seawater. Both control and infected fingerlings were then transferred independently into new aquarium containing fresh seawater, and observed daily for 30 days. At day 31-post-infection, fingerlings that survived from the experimental infection and the controls were collected and flash frozen in liquid nitrogen respectively. Samples were then kept at −80 °C prior to RNA extraction.

2.2. Total RNA Extraction and quality control, library preparation and RNA-seq

Total RNA was extracted from gills and whole-body tissues using modified hexadecyltrimethylammonium bromide (CTAB) method [1]. Ten biological replicates from each tissue were used for the RNA extraction. The quality and integrity of the isolated RNA were quantified using NanoDrop spectrophotometer (Thermo Fisher Scientific Inc., United States) and Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., United States), respectively. Only three replicates from each tissue with the highest RIN score were chosen for RNA sequencing. The cDNA poly (A)-containing mRNA libraries were then prepared according to the SureSelect Strand-Specific RNA Library Prep for Illumina Multiplexed Sequencing (mRNA Library Preparation Protocol) Version E0, March 2017. Libraries were then sequenced using Illumina HiSeq. 4000 platform at Theragene Etex Bio Institute (Gyeonggi-do, Republic of Korea).

2.3. Transcriptome de novo assembly

Raw reads obtained were filtered by trimming the adapter sequences using cutadapt v1.14 program [2] with the Phred quality score of 30 (nucleotide accuracy: 99.9%) (Table 2). Clean reads were then de novo assembled using Trinity v2.4.0 [3].

Table 2
Statistics of gill and whole-body sequence reads.

Acknowledgements

This work was supported by Research University Grants from Universiti Kebangsaan Malaysia (UKM-GUP-2014-083 and DIP-2015-024) awarded to Syarul Nataqain Baharum. We acknowledged Azhani Abdul-Rahman for the technical support.

Footnotes

Transparency documentSupplementary data associated with this article can be found in the online version at doi:10.1016/j.dib.2017.11.024.

Transparency document. Supplementary material

Supplementary material

.

References

1. Abdul-Rahman A., Suleman N.I., Zakaria W.A., Goh H.-H., Noor N.M., Aizat W.M. RNA extractions of mangosteen (Garcinia mangostana L.) pericarps for sequencing. Sains Malays. 2017;46:1231–1240.
2. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 2011;17:10–12.
3. Haas B.J., Papanicolaou A., Yassour M., Grabherr M., Philip D., Bowden J., Couger M.B., Eccles D., Li B., Lieber M., MacManes M.D., Ott M., Orvis J., Pochet N., Strozzi F., Weeks N., Westerman R., William T., Dewey C.N., Henschel R., LeDuc R.D., Friedman N., Regev A. De novo transcript sequence reconstruction from RNA-seq: reference generation and analysis with Trinity. Nat. Protoc. 2014;8:1–43. [PMC free article] [PubMed]

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