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Int J Mol Sci
2015 Jul 17;167:16347-77. doi: 10.3390/ijms160716347.
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Transcriptome Analysis and Discovery of Genes Involved in Immune Pathways from Coelomocytes of Sea Cucumber (Apostichopus japonicus) after Vibrio splendidus Challenge.
Gao Q
,
Liao M
,
Wang Y
,
Li B
,
Zhang Z
,
Rong X
,
Chen G
,
Wang L
.
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Vibrio splendidus is identified as one of the major pathogenic factors for the skin ulceration syndrome in sea cucumber (Apostichopus japonicus), which has vastly limited the development of the sea cucumber culture industry. In order to screen the immune genes involving Vibrio splendidus challenge in sea cucumber and explore the molecular mechanism of this process, the related transcriptome and gene expression profiling of resistant and susceptible biotypes of sea cucumber with Vibrio splendidus challenge were collected for analysis. A total of 319,455,942 trimmed reads were obtained, which were assembled into 186,658 contigs. After that, 89,891 representative contigs (without isoform) were clustered. The analysis of the gene expression profiling identified 358 differentially expression genes (DEGs) in the bacterial-resistant group, and 102 DEGs in the bacterial-susceptible group, compared with that in control group. According to the reported references and annotation information from BLAST, GO and KEGG, 30 putative bacterial-resistant genes and 19 putative bacterial-susceptible genes were identified from DEGs. The qRT-PCR results were consistent with the RNA-Seq results. Furthermore, many DGEs were involved in immune signaling related pathways, such as Endocytosis, Lysosome, MAPK, Chemokine and the ERBB signaling pathway.
Figure 1. The length distribution of assembled contigs in the sequenced cDNA library.
Figure 2. The length distribution of representative contigs in the sequenced cDNA library.
Figure 3. Species distribution of the BLAST matches of the transcriptome representative contigs.
Figure 4. Classification of the gene ontology (GO) for the sea cucumber coelomocytes transcriptome representative contigs.
Figure 5. Clusters of Orthologous Groups (COG) classification of the sea cucumber coelomocytes transcriptome representative contigs.
Figure 6. KEGG classification of the sea cucumber coelomocytes transcriptome representative contigs.
Figure 7. Summary of simple sequence repeat (SSR) identified from the sea cucumber coelomocytes transcriptome.
Figure 8. Differentially expressed genes from disease-resistant group (A), comparing with control group (K). Red points represent 13 up-regulated genes, and green points represent 345 down-regulated genes.
Figure 9. Differentially expressed genes from susceptibility group (S) comparing with control group (K). Red points represent 86 up-regulated genes, green point represents 16 down-regulated genes.
Figure 10. MAPK signaling pathway. Red boxes represent up-regulated genes, and green boxes represent down-regulated genes.
Figure 11. ERBB signaling pathway. Red boxes represent up-regulated genes, and green boxes represent down-regulated genes.
Figure 12. Lysosome signaling pathway. Red boxes represent up-regulated genes, and green boxes represent down-regulated genes.
Figure 13. Endocytosis signaling pathway. Red boxes represent up-regulated genes, and green boxes represent down-regulated genes.
Figure 14. Chemokine signaling pathway. Red boxes represent up-regulated genes, green boxes represent down-regulated genes, and blue box includes two genes of which one is an up-regulated gene and the other is a down-regulated gene.
Figure 15. Comparison of 22 putative disease-resistant gene expression levels between RNA-Seq (blue bar) and RT-PCR (red bar). “−”indicates down-regulation.
Figure 16. Comparison of 14 putative susceptibility gene expression levels between RNA-Seq (blue bar) and RT-PCR (red bar). “−”indicates down-regulation.
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