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Genome-wide survey and analysis of microsatellites in the Pacific oyster genome: abundance, distribution, and potential for marker development

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Abstract

Microsatellites are a ubiquitous component of the eukaryote genome and constitute one of the most popular sources of molecular markers for genetic studies. However, no data are currently available regarding microsatellites across the entire genome in oysters, despite their importance to the aquaculture industry. We present the first genome-wide investigation of microsatellites in the Pacific oyster Crassostrea gigas by analysis of the complete genome, resequencing, and expression data. The Pacific oyster genome is rich in microsatellites. A total of 604 653 repeats were identified, in average of one locus per 815 base pairs (bp). A total of 12 836 genes had coding repeats, and 7 332 were expressed normally, including genes with a wide range of molecular functions. Compared with 20 different species of animals, microsatellites in the oyster genome typically exhibited 1) an intermediate overall frequency; 2) relatively uniform contents of (A)n and (C)n repeats and abundant long (C)n repeats (≥24 bp); 3) large average length of (AG)n repeats; and 4) scarcity of trinucleotide repeats. The microsatellite-flanking regions exhibited a high degree of polymorphism with a heterozygosity rate of around 2.0%, but there was no correlation between heterozygosity and microsatellite abundance. A total of 19 462 polymorphic microsatellites were discovered, and dinucleotide repeats were the most active, with over 26% of loci found to harbor allelic variations. In all, 7 451 loci with high potential for marker development were identified. Better knowledge of the microsatellites in the oyster genome will provide information for the future design of a wide range of molecular markers and contribute to further advancements in the field of oyster genetics, particularly for molecular-based selection and breeding.

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Authors and Affiliations

  1. Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China

    Jiafeng Wang  (王家丰), Haigang Qi  (亓海刚), Li Li  (李莉) & Guofan Zhang  (张国范)

  2. University of Chinese Academy of Sciences, Beijing, 100049, China

    Jiafeng Wang  (王家丰)

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  1. Jiafeng Wang  (王家丰)
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  2. Haigang Qi  (亓海刚)
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  3. Li Li  (李莉)
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  4. Guofan Zhang  (张国范)
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Correspondence to Haigang Qi  (亓海刚) or Guofan Zhang  (张国范).

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Supported by the National Basic Research Program of China (973 Program) (No. 2010CB126402), the National Natural Science Foundation of China (Nos. 41206149, 40730845), the National High Technology Research and Development Program of China (863 Program) (No. 2012AA10A405), the Mollusc Research and Development Center, CARS, the Taishan Scholar Program of Shandong Province, and the Taishan Scholars Climbing Program of Shandong Province of China

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Wang, J., Qi, H., Li, L. et al. Genome-wide survey and analysis of microsatellites in the Pacific oyster genome: abundance, distribution, and potential for marker development. Chin. J. Ocean. Limnol. 32, 8–21 (2014). https://doi.org/10.1007/s00343-014-3064-z

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