Comparative transcriptome analysis of papilla and skin in the sea cucumber, Apostichopus japonicus

Xiaoxu Zhou; Jun Cui; Shikai Liu; Derong Kong; He Sun; Chenlei Gu; Hongdi Wang; Xuemei Qiu; Yaqing Chang; Zhanjiang Liu; Xiuli Wang

doi:10.7717/peerj.1779

Comparative transcriptome analysis of papilla and skin in the sea cucumber, Apostichopus japonicus

PeerJ. 2016 Mar 7:4:e1779. doi: 10.7717/peerj.1779. eCollection 2016.

Authors

Xiaoxu Zhou^#^{1

2}, Jun Cui^#², Shikai Liu^#³, Derong Kong², He Sun², Chenlei Gu², Hongdi Wang², Xuemei Qiu^{1

2}, Yaqing Chang^{1

2}, Zhanjiang Liu³, Xiuli Wang^{1

2}

Affiliations

¹ Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China.
² College of Fisheries and Life Science, Dalian Ocean University, Dalian, China.
³ The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States.

^# Contributed equally.

Abstract

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.

Keywords: Comparative transcriptome; Gene expression; High-throughput sequencing; Papilla; Sea cucumber (Apostichopus japonicus); Skin.

Grants and funding

This project was supported by the State 863 High-Technology R & D Project of China (No. 2012AA10A412) and the Program for Liaoning Excellent Talents in University, China (No. LR2014022). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.