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Comparative analysis of expressed sequence tags (ESTs) between normal group and softness syndrome group in Halocynthia roretzi

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Abstract

To identify the cause of mass mortality in ascidians, we constructed cDNA libraries of both the normal and softness syndrome group in Halocynthia roretzi. To perform comparative analysis of transcripts between the two groups, we sequenced about 1,000 random clones. All the sequences obtained from the clones were processed to remove the vector region and low quality sequences through base calling and vector trimming. We collected 906 sequences with average length of 463 bp in the normal group and 1014 sequences in the softness syndrome group with an average length of 696 bp. Clustering and assembling of EST sequences using TGICL package resulted in 906 distinct sequences composed of 517 singletons and 77 contigs in 75 clusters in normal group and 1014 distinct sequences composed of 707 singletons and 120 contigs in 120 clusters in the softness syndrome group. All sequences derived from the two groups were compared against the NCBI Non-redundant database using BLASTX algorithms. As a result, 493 sequences in the normal group and 861 sequences in the softness syndrome group had significant hits within the database. In addition, we listed genes that showed differential expression in the softness syndrome group. Transcript levels of calponin increased by 11-fold and both E3 ubiquitin-protein ligase MARCH3 and selenium dependent salivary glutathione peroxidase by 5-fold in the softness syndrome group. Also, the expression of four genes including muscle actin increased by 4-fold. In contrast, we observed down-regulation of genes encoding trypsinogen 1, cathepsin D protein, serine protease, and halocidin precursor, decreasing by more than 6-fold. Herein, we identified differential expression of genes involved in the contraction and regulation of muscle cells and immune reaction in H. roretzi with softness syndrome. This study is the first report on gene expression changes occurring in H. roretzi with softness syndrome and would be useful in further studies.

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Authors and Affiliations

  1. Department of Parasitology, College of Medicine and UHRC, Inje University, Gaegum-dong, Busanjin-gu, Busan, 614-735, Korea

    Ji Eun Jeong, Se Won Kang & Yong Seok Lee

  2. Aquaculture Management Division, NFRDI, 408-1, Gijang, Busan, 619-902, Korea

    Yun Kyung Shin & Je Cheon Jun

  3. Biotechnology Research Division, NFRDI, 408-1, Gijang, Busan, 619-902, Korea

    Young-Ok Kim

  4. Southeast Sea Fisheries Research Institute, NFRDI, Tongyeong, Gyeongsangnam-do, 650-943, Korea

    Young Baek Hur

  5. Dong-il Shimadzu Biotech., 393-4, Doryong-dong, Yuseong-gu, Daejeon, 305-340, Korea

    Jae-Hyung Kim

  6. Research Institute, GnC BIO Co., LTD., 621-6 Banseok-dong, Yuseong-gu, Daejeon, 305-150, Korea

    Sung-Hwa Chae

  7. Institute of Environmental Research, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 200-701, Korea

    Jun-Sang Lee

  8. School of Biotechnology, Yeungnam University, 214-1 Dae-dong, Gyeongsan-si, Gyeongsangbuk-do, 712-749, Korea

    In ho Choi

  9. College of Agriculture and Life Science, Chonnam National University, 300 Yongbong-Dong, Buk-Gu, Gwangju, 500-757, Korea

    Yeon Soo Han

  10. Department of Biochemistry, College of Medicine, Inje University, Gaegum-dong, Busanjin-gu, Busan, 614-735, Korea

    Dae-Hyun Seog

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  1. Ji Eun Jeong
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Correspondence to Yong Seok Lee.

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Jeong, J.E., Kang, S.W., Shin, Y.K. et al. Comparative analysis of expressed sequence tags (ESTs) between normal group and softness syndrome group in Halocynthia roretzi . Mol. Cell. Toxicol. 7, 357–365 (2011). https://doi.org/10.1007/s13273-011-0045-6

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  • DOI: https://doi.org/10.1007/s13273-011-0045-6

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