Comparative Transcriptome Analysisof Papilla And Skin In The Sea Cucumber,Apostichopus Japonicus

Sea cucumber issubordinated to Echinoermata, mainly distributed in the coastal of Russia, Japan, Korea and China. At present, the development of mariculture industry of sea cucumber has become more perfect and mature. The production of sea cucumber has more than 20 billion yuan in 2013. Though many achievements of sea cucumber have been reported, such as development, disease control and breeding. The molecular research of sea cucumber remains largely unknown.The papilla of sea cucumber is a multifunctional organ, which could perform for breath and exchange information with the environment. The number of the papilla is the important economic traits of sea cucumber.Many studys of sea cucumber has performed in recent years, while the researches mainly focused on the morphology, anatomical biology and tissue function. The molecular interactions and multiple biological process of papilla is still a new field. To obtained the genes that relact to papilla, this study choose the skin of sea cucumber as the control tissue, we conducted RNA-Seq of these two organs to determine global changes in gene expression between the papilla and skin of sea cucumber, Apostichopus japonicus. The main results as follows:1. RNA-Seq was appiled to generate transcriptome data from the papilla and skin of sea cucumber. Comparative analysis between papilla and skin samples, we generated 30,657,027 and 36,444,908 clean reads from 33,504,127 and 37,384,685 raw reads, respectively. De novo assembled in 92,343 unigenes. From the annotation of 92,343 unigenes, NR was the most abundant database, which contains 33,584 unigenes. After GO analysis, the results showed that 7,056 unigenes were annotated in the cell component. 17347 unigenes were annotated in molecular function; 17,113 unigenes were annotated in biological process. KEGG analysis showed that a total of 10,058 unigenes were assigned with one or more KEGG Pathway annotations, involved 227 KEGG pathways.2. At the present study, we obtained 1,059 differentially expressed genes, of which 739 genes were expressed at higher levels in papilla, while 320 were expressed at lower levels in papilla. And we also identified 288 papilla-specific genes in all of 1,059 differentially expressed genes. Fibroblast growth factor, transforming growth factor-β, collagen-α2 and Integrin-α2, which may be related to the development of the papilla of sea cucumber are also expressedat higher levels in papilla. We also enriched several pathways, such as tight junction and p53 signaling pathway.3. A total of 166,572 potential SNPs were identified from papilla. The putative SNPs included 95,713 transitions and 70,859 tranversions. A total of 166,572 explored SSRs were identified from papilla. And 171,480 potential SNPs and 12,149 explored SSRs were also identified from skin transcriptome.This study provided comparative transcriptome analysis by using RNA–Seq. This work will excavate the sufficient growth related gene of sea cucumber, and provide valuable genomic resources to understand the molecular mechanisms of papilla and skin in sea cucumber.