Transcription profiling using RNA-Seq demonstrates expression differences in the body walls of juvenile albino and normal sea cucumbers Apostichopus japonicus

• Published in: Chinese journal of oceanology and limnology Vol. 32; no. 1; pp. 34 - 46
• Main Author: 马得友 杨红生 孙丽娜 陈慕雁
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer-Verlag 2014; Springer Berlin Heidelberg; Springer Nature B.V
• Subjects: Albinism; albino; Apoptosis; Apostichopus japonicus; Aquaculture; Aquatic life; Biology; Body walls; breeding; cDNA libraries; Cell adhesion; Coagulation; color; complement; Complementary DNA; Cytokines; Earth and Environmental Science; Earth Sciences; Gene expression; gene expression regulation; Gene sequencing; Genes; high-throughput nucleotide sequencing; Holothurioidea; Holothuroidea; Juveniles; Marine; Marine invertebrates; Next-generation sequencing; Nucleic acids; Nucleotide sequence; Nucleotides; Oceanography; PCR; Phagocytosis; Polyculture (aquaculture); quantitative polymerase chain reaction; Receptors; Ribonucleic acid; RNA; Strains; Transcription; transcription (genetics); transcriptome; Transcriptomes; Vegetables; 刺参; 差异表达基因; 测序; 海参; 白化病; 表达差异; 转录水平; China, People's Rep; real-time PCR; gene expression profiling; albino; RNA-Seq
• ISSN: 0254-4059; 2096-5508; 1993-5005; 2523-3521
• DOI: 10.1007/s00343-014-3041-6

Sea cucumbers Apostichopus japonicus are one of the most important aquaculture species in China. Their normal body color is black to fit their surroundings. Wild albinos are rare and hard to breed. To understand the differences between albino and normal （control） sea cucumbers at the transcriptional level, we sequenced the transcriptomes in their body-wall tissues using RNA-Seq high-throughput sequencing. Approximately 4.876 million （M） and 4.884 M 200-nucleotide-long cDNA reads were produced in the cDNA libraries derived from the body walls of albino and control samples, respectively. A total of 9 561 （46.89%） putative genes were identified from among the RNA-Seq reads in both libraries. After filtering, 837 significantly differentially regulated genes were identified in the albino library compared with in the control library, and 3.6% of the differentially expressed genes （DEGs） were found to have changed those more than five-fold. The expression levels of 10 DEGs were checked by real-time PCR and the results were in full accord with the RNA-Seq expression trends, although the amplitude of the differences in expression levels was lower in all cases. A series of pathways were significantly enriched for the DEGs. These pathways were closely related to phagocytosis, the complement and coagulation cascades, apoptosis-related diseases, cytokine-cytokine receptor interaction, and cell adhesion. The differences in gene expression and enriched pathways between the albino and control sea cucumbers offer control targets for cultivating excellent albino A. japonicus strains in the future.