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

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Abstract

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.

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Authors and Affiliations

  1. Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China

    Deyou Ma  (马得友), Hongsheng Yang  (杨红生) & Lina Sun  (孙丽娜)

  2. University of Chinese Academy of Sciences, Beijing, 10049, China

    Deyou Ma  (马得友) & Lina Sun  (孙丽娜)

  3. Ocean University of China, Qingdao, 266071, China

    Muyan Chen  (陈慕雁)

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  1. Deyou Ma  (马得友)
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  2. Hongsheng Yang  (杨红生)
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  3. Lina Sun  (孙丽娜)
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  4. Muyan Chen  (陈慕雁)
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Correspondence to Hongsheng Yang  (杨红生).

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Supported by the National High Technology Research and Development Program of China (863 Program) (No. 2012AA10A412), the National Natural Science Foundation of China (No. 40976089), the National Key Technology Research and Development Program of China (No. 2011BAD13B02), and the National Oceanic Public Welfare Industry Special Scientific Research of China (No. 201205023)

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Ma, D., Yang, H., Sun, L. et al. Transcription profiling using RNA-Seq demonstrates expression differences in the body walls of juvenile albino and normal sea cucumbers Apostichopus japonicus . Chin. J. Ocean. Limnol. 32, 34–46 (2014). https://doi.org/10.1007/s00343-014-3041-6

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