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Characterization and analysis of ribosomal proteins in two marine calanoid copepods

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Abstract

Copepods are among the most abundant and successful metazoans in the marine ecosystem. However, genomic resources related to fundamental cellular processes are still limited in this particular group of crustaceans. Ribosomal proteins are the building blocks of ribosomes, the primary site for protein synthesis. In this study, we characterized and analyzed the cDNAs of cytoplasmic ribosomal proteins (cRPs) of two calanoid copepods, Pseudodiaptomus poplesia and Acartia pacifica. We obtained 79 cRP cDNAs from P. poplesia and 67 from A. pacifica by cDNA library construction/sequencing and rapid amplification of cDNA ends. Analysis of the nucleic acid composition showed that the copepod cRP-encoding genes had higher GC content in the protein-coding regions (CDSs) than in the untranslated regions (UTRs), and single nucleotide repeats (>3 repeats) were common, with “A” repeats being the most frequent, especially in the CDSs. The 3′-UTRs of the cRP genes were significantly longer than the 5′-UTRs. Codon usage analysis showed that the third positions of the codons were dominated by C or G. The deduced amino acid sequences of the cRPs contained high proportions of positively charged residues and had high pI values. This is the first report of a complete set of cRP-encoding genes from copepods. Our results shed light on the characteristics of cRPs in copepods, and provide fundamental data for further studies of protein synthesis in copepods. The copepod cRP information revealed in this study indicates that additional comparisons and analysis should be performed on different taxonomic categories such as orders and families.

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Authors and Affiliations

  1. Key Laboratory of Marine Environment and Ecology (Ocean University of China), Ministry of Education, Qingdao, 266100, China

    Feifei Yang  (杨菲菲), Yousong Huang  (黄有松), Xiaoyan Yi  (衣晓燕), Hongju Chen  (陈洪举), Guangxing Liu  (刘光兴) & Huan Zhang  (张寰)

  2. College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China

    Feifei Yang  (杨菲菲), Donghui Xu  (徐东会), Yunyun Zhuang  (庄昀筠), Xiaoyan Yi  (衣晓燕), Hongju Chen  (陈洪举), Guangxing Liu  (刘光兴) & Huan Zhang  (张寰)

  3. Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA

    Huan Zhang  (张寰)

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  1. Feifei Yang  (杨菲菲)
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  2. Donghui Xu  (徐东会)
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  3. Yunyun Zhuang  (庄昀筠)
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  4. Yousong Huang  (黄有松)
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  5. Xiaoyan Yi  (衣晓燕)
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  6. Hongju Chen  (陈洪举)
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  7. Guangxing Liu  (刘光兴)
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  8. Huan Zhang  (张寰)
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Correspondence to Guangxing Liu  (刘光兴) or Huan Zhang  (张寰).

Additional information

Supported by the National Natural Science Foundation of China (Nos. 31372509, 41328009) and the National Science Foundation for Young Scientists of China (No. 41106095)

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Yang, F., Xu, D., Zhuang, Y. et al. Characterization and analysis of ribosomal proteins in two marine calanoid copepods. Chin. J. Ocean. Limnol. 34, 1258–1268 (2016). https://doi.org/10.1007/s00343-016-5129-7

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  • DOI: https://doi.org/10.1007/s00343-016-5129-7

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