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

Jiafeng Wang; Haigang Qi; Li Li; Guofan Zhang

doi:10.1007/s00343-014-3064-z

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

OriginalPaper | Updated：2023-05-16

- Genome-wide survey and analysis of microsatellites in the Pacific oyster genome: abundance, distribution, and potential for marker development
- Genome-wide survey and analysis of microsatellites in the Pacific oyster genome: abundance, distribution, and potential for marker development
- 海洋湖沼学报（英文） 2014年32卷第1期页码：8-21
- Affiliations：
  
  1. Institute of Oceanology Chinese Academy of Sciences
  2. University of Chinese Academy of Sciences
- Author bio：
- Funds：
  
  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
- DOI：10.1007/s00343-014-3064-z
  中图分类号：
- 网络首发：2013-11-16，
  
  纸质出版：2014
- Accepted：
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Genome-wide survey and analysis of microsatellites in the Pacific oyster genome: abundance, distribution, and potential for marker development[J]. 海洋湖沼学报（英文）, 2014,32(1):8-21.

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
Genome-wide survey and analysis of microsatellites in the Pacific oyster genome: abundance, distribution, and potential for marker development[J]. 海洋湖沼学报（英文）, 2014,32(1):8-21. DOI： 10.1007/s00343-014-3064-z.

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 DOI：

摘要

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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