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

Updated：2023-05-16

- Genome-wide survey and analysis of microsatellites in the Pacific oyster genome: abundance, distribution, and potential for marker development
- Journal of Oceanology and Limnology Vol. 32, Issue 1, Pages: 8-21(2014)
- Affiliations：
  
  1. Institute of Oceanology Chinese Academy of Sciences
  2. University of Chinese Academy of Sciences
- Author bio：
- Funds：
- DOI：10.1007/s00343-014-3064-z
  CLC：
- Online First：16 November 2013，
  
  Published：2014
- Accepted：
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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
DOI：

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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