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Genome-wide mining, characterization, and development of microsatellite markers in Marsupenaeus japonicus by genome survey sequencing

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An Erratum to this article was published on 07 March 2017

Abstract

The kuruma prawn, Marsupenaeus japonicus, is one of the most cultivated and consumed species of shrimp. However, very few molecular genetic/genomic resources are publically available for it. Thus, the characterization and distribution of simple sequence repeats (SSRs) remains ambiguous and the use of SSR markers in genomic studies and marker-assisted selection is limited. The goal of this study is to characterize and develop genome-wide SSR markers in M. japonicus by genome survey sequencing for application in comparative genomics and breeding. A total of 326 945 perfect SSRs were identified, among which dinucleotide repeats were the most frequent class (44.08%), followed by mononucleotides (29.67%), trinucleotides (18.96%), tetranucleotides (5.66%), hexanucleotides (1.07%), and pentanucleotides (0.56%). In total, 151 541 SSR loci primers were successfully designed. A subset of 30 SSR primer pairs were synthesized and tested in 42 individuals from a wild population, of which 27 loci (90.0%) were successfully amplified with specific products and 24 (80.0%) were polymorphic. For the amplified polymorphic loci, the alleles ranged from 5 to 17 (with an average of 9.63), and the average PIC value was 0.796. A total of 58 256 SSR-containing sequences had significant Gene Ontology annotation; these are good functional molecular marker candidates for association studies and comparative genomic analysis. The newly identified SSRs significantly contribute to the M. japonicus genomic resources and will facilitate a number of genetic and genomic studies, including high density linkage mapping, genome-wide association analysis, marker-aided selection, comparative genomics analysis, population genetics, and evolution.

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

    Xia Lu  (卢霞), Sheng Luan  (栾生), Jie Kong  (孔杰) & Longyang Hu  (胡龙洋)

  2. College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China

    Yong Mao  (毛勇) & Shengping Zhong  (钟声平)

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Correspondence to Jie Kong  (孔杰).

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Supported by the National High Technology Research and Development Program of China (863 Program) (No. 2012AA10A409)

LU Xia and LUAN Sheng contributed equally to this work.

An erratum to this article is available at http://dx.doi.org/10.1007/s00343-017-7466-6.

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Lu, X., Luan, S., Kong, J. et al. Genome-wide mining, characterization, and development of microsatellite markers in Marsupenaeus japonicus by genome survey sequencing. Chin. J. Ocean. Limnol. 35, 203–214 (2017). https://doi.org/10.1007/s00343-016-5250-7

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