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, Zhanjian "John" Liu, Xiuli Wang

Research output: Contribution to journalArticle

7 Citations (Scopus)

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 skinspecific 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.

Original languageEnglish (US)
Article number1779
JournalPeerJ
Volume2016
Issue number3
DOIs
StatePublished - 2016
Externally publishedYes

Fingerprint

Stichopus
Sea Cucumbers
Apostichopus japonicus
Holothuroidea
Gene Expression Profiling
transcriptomics
skin (animal)
Skin
Genes
genes
Gene Ontology
Ontology
Databases
Biological Phenomena
transforming growth factors
fibroblast growth factors
unigenes
Fibroblast Growth Factors
integrins
Transforming Growth Factors

Keywords

  • Comparative transcriptome
  • Gene expression
  • High-throughput sequencing
  • Papilla
  • Sea cucumber (Apostichopus japonicus)
  • Skin

ASJC Scopus subject areas

  • Neuroscience(all)
  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Zhou, X., Cui, J., Liu, S., Kong, D., Sun, H., Gu, C., ... Wang, X. (2016). Comparative transcriptome analysis of papilla and skin in the sea cucumber, Apostichopus japonicus. PeerJ, 2016(3), [1779]. https://doi.org/10.7717/peerj.1779

Comparative transcriptome analysis of papilla and skin in the sea cucumber, Apostichopus japonicus. / Zhou, Xiaoxu; Cui, Jun; Liu, Shikai; Kong, Derong; Sun, He; Gu, Chenlei; Wang, Hongdi; Qiu, Xuemei; Chang, Yaqing; Liu, Zhanjian "John"; Wang, Xiuli.

In: PeerJ, Vol. 2016, No. 3, 1779, 2016.

Research output: Contribution to journalArticle

Zhou, X, Cui, J, Liu, S, Kong, D, Sun, H, Gu, C, Wang, H, Qiu, X, Chang, Y, Liu, ZJ & Wang, X 2016, 'Comparative transcriptome analysis of papilla and skin in the sea cucumber, Apostichopus japonicus', PeerJ, vol. 2016, no. 3, 1779. https://doi.org/10.7717/peerj.1779
Zhou, Xiaoxu ; Cui, Jun ; Liu, Shikai ; Kong, Derong ; Sun, He ; Gu, Chenlei ; Wang, Hongdi ; Qiu, Xuemei ; Chang, Yaqing ; Liu, Zhanjian "John" ; Wang, Xiuli. / Comparative transcriptome analysis of papilla and skin in the sea cucumber, Apostichopus japonicus. In: PeerJ. 2016 ; Vol. 2016, No. 3.
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