Preliminary Exploration of Transcriptome Comparative Analysis of Muscle Tissues from Asymptomatic and Diseased Epinephelus fuscoguttatus Infected with Nervous Necrosis Virus
Preliminary Exploration of Transcriptome Comparative Analysis of Muscle Tissues from Asymptomatic and Diseased Epinephelus fuscoguttatus Infected with Nervous Necrosis Virus
Wei Fang1,2,3, Jiawei Hong1,2,3,4, Zhengyi Fu1,2,3, Jing Hu1,2,3, Gang Yu1,2,3, Zhenhua Ma1,2,3* and Humin Zong5*
ABSTRACT
Through the study of differential gene expression in the muscle tissue from asymptomatic and diseased Epinephelus fuscoguttatus infected with nervous necrosis virus (NNV), this research initially explored the main genes and key pathways related to anti-NNV. This study used the Illumina HiSeq 4000 sequencing platform to sequence the transcriptome of E. fuscoguttatus, the transcriptome data clustered by TGICL to obtain Unigene, and bioinformatics methods were then adopted to perform functional annotation classification, metabolic pathways and SSR feature analysis. The results showed that a total of 42.40 Gb data were obtained from transcriptome sequencing, and 38,817 Unigenes were obtained after assembly and de-redundancy; Using BLAST to annotate the assembled unigenes with seven functional databases (NR, NT, GO, COG, KEGG, Swissprot and Interpro), a total of 23,417 unigenes were annotated (accounting for 61.14%); A total of 253 differentially expressed genes (DEGs) were screened, with 199 up-regulated genes and 54 down-regulated genes; GO analysis showed that DEGs was mainly enriched in cellular processes, biological regulation, cell parts, membrane parts, binding and catalytic activity; COG analysis showed that DEGs was mainly related to posttranslational modification, protein turnover, chaperones, intracellular trafficking, secretion, vesicular transport, transcription, amino acid transport and metabolism; KEGG analysis showed that DEGs was mainly related to cardiac muscle contraction, renin-angiotensin system, adrenergic signaling in cardiomyocytes, oxidative phosphorylation; The distribution types of SSR sites and their characteristic analysis results showed that the most important repeat type was mononucleotide repeats (7,840, accounting for 51.31%), followed by dinucleotide repeats (4,007, accounting for 26.22%), while the number of tetranucleotide, pentanucleotide and hexanucleotide repeat was relatively small. Through the above analysis, it could be concluded that the difference in gene expression of the transcriptome between asymptomatic group and the infected group was significant. PHGDH, PASAT1, RPL38, RPS2, ATP6V1D, ATP6V11, etc. may be the key genes that affect the expression of anti-NNV for E. fuscoguttatus, which mainly related to the inhibition of the capsid protein encoded by NNV’s RNA2. This research not only provided a theoretical basis for the breeding of anti-NVV, but also made up for the gap in the research field of anti-NVV of E. fuscoguttatus.
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