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Transcriptome analysis of eyestalk and hemocytes in the ridgetail white prawn Exopalaemon carinicauda: assembly, Annotation and Marker Discovery

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Abstract

The ridgetail white prawn Exopalaemon carinicauda is one of major economic mariculture species in eastern China. The deficiency of genomic and transcriptomic data is becoming the bottleneck of further researches on its good traits. In the present study, 454 pyrosequencing was undertaken to investigate the transcriptome profiles of E. carinicauda. A collection of 1,028,710 sequence reads (459.59 Mb) obtained from cDNA prepared from eyestalk and hemocytes was assembled into 162,056 expressed sequence tags (ESTs). Of these, 29.88 % of 48,428 contigs and 70.12 % of 113,628 singlets possessed high similarities to sequences in the GenBank non-redundant database, with most significant (E value <1e−10) unigenes matches occurring with crustacean and insect sequences. KEGG analysis of unigenes identified putative members of biological pathways related to growth and immunity. In addition, we obtained a total of putative 125,112 SNPs and 13,467 microsatellites. These results will contribute to the understanding of the genome makeup and provide useful information for future functional genomic research in E. carinicauda.

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Acknowledgments

This project was financially supported by the earmarked fund for National ‘‘863’’ Project of China (No. 2012AA10A409), Modern Agro-industry Technology Research System (No. CARS-47), National Natural Science Foundation of China (No. 31472275), Independent Innovation in Shandong Province (No. 2013CXC80202) and Special Fund for Agro-scientific Research in the Public Interest (No. 201103034).

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Authors and Affiliations

  1. Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China

    Jitao Li, Jian Li, Ping Chen, Ping Liu & Yuying He

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  1. Jitao Li
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  2. Jian Li
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Correspondence to Jian Li.

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Li, J., Li, J., Chen, P. et al. Transcriptome analysis of eyestalk and hemocytes in the ridgetail white prawn Exopalaemon carinicauda: assembly, Annotation and Marker Discovery. Mol Biol Rep 42, 135–147 (2015). https://doi.org/10.1007/s11033-014-3749-6

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  • DOI: https://doi.org/10.1007/s11033-014-3749-6

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