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PeerJ
2016 Jan 01;4:e1779. doi: 10.7717/peerj.1779.
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Comparative transcriptome analysis of papilla and skin in the sea cucumber, Apostichopus japonicus.
Zhou X
,
Cui J
,
Liu S
,
Kong D
,
Sun H
,
Gu C
,
Wang H
,
Qiu X
,
Chang Y
,
Liu Z
,
Wang X
.
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Papilla and skin are two important organs of the sea cucumber. Both tissues have ectodermic origin, but they are morphologically and functionally very different. In the present study, we performed comparative transcriptome analysis of the papilla and skin from the sea cucumber (Apostichopus japonicus) in order to identify and characterize gene expression profiles by using RNA-Seq technology. We generated 30.6 and 36.4 million clean reads from the papilla and skin and de novo assembled in 156,501 transcripts. The Gene Ontology (GO) analysis indicated that cell part, metabolic process and catalytic activity were the most abundant GO category in cell component, biological process and molecular funcation, respectively. Comparative transcriptome analysis between the papilla and skin allowed the identification of 1,059 differentially expressed genes, of which 739 genes were expressed at higher levels in papilla, while 320 were expressed at higher levels in skin. In addition, 236 differentially expressed unigenes were not annotated with any database, 160 of which were apparently expressed at higher levels in papilla, 76 were expressed at higher levels in skin. We identified a total of 288 papilla-specific genes, 171 skin-specific genes and 600 co-expressed genes. Also, 40 genes in papilla-specific were not annotated with any database, 2 in skin-specific. Development-related genes were also enriched, such as fibroblast growth factor, transforming growth factor-β, collagen-α2 and Integrin-α2, which may be related to the formation of the papilla and skin in sea cucumber. Further pathway analysis identified ten KEGG pathways that were differently enriched between the papilla and skin. The findings on expression profiles between two key organs of the sea cucumber should be valuable to reveal molecular mechanisms involved in the development of organs that are related but with morphological differences in the sea cucumber.
Figure 1. The distribution of the size of transcripts and unigenes.Length distribution of assembled transcripts (A) and unigenes (B) of sea cucumber (Apostichopus japonicus).
Figure 2. The distribution of annotated unigenes across database.Venn diagram display of the proportion of annotated unigenes in NR, Pfam, Swiss-Prot and GO.
Figure 3. Distribution of the most common GO term categories.
Figure 4. The DEGs in the papilla and skin of sea cucumber.(A) M-A plots showing gene expression in papilla and skin. The x-axis represents the logarithm of FPKM and y-axis represents the logarithm of foldchange; (B) Venn diagram displays the number of papilla-specific, skin-specific, and co-expressed genes.
Figure 5. Comparison between RNA-Seq results and qRT-PCR validation results.X-axis shows genes in two tissues validated in this study; Y-axis shows Log2 Ratio of expression of SK (skin) versus YZ (papilla). AAC4PL, AAC-rich mRNA clone AAC4 protein-like; Hsp26, heat shock protein 26; NP, novel protein; TN, Tenascin; EMI, EMI domain; Hp TTRE, hypothetical protein TTRE_0000953901; FGL, Fibrinogen-like protein A; HpX975-24482, hypothetical protein X975_24482, partial; PP2A, Serine/threonine-protein phosphatase; FIL2L, Fibrinogen-like protein A; Col-α FiCollagen gen-like protein A; Col-l-ase; FIL2L, Fibrinogen-like proteiphosphatealdolase; ITGA2, Integrin alpha 2; MAD2A, Mitotic spindle assembly checkpoint protein.
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