Genome-wide survey and analysis of microsatellites in the Pacific oyster genome: abundance, distribution, and potential for marker development
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 aquacult...
Published in: | Chinese Journal of Oceanology and Limnology |
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ftchinacasciocas:oai:ir.qdio.ac.cn:337002/24217 2023-05-15T15:58:19+02:00 Genome-wide survey and analysis of microsatellites in the Pacific oyster genome: abundance, distribution, and potential for marker development Wang Jiafeng Qi Haigang Li Li Zhang Guofan Qi, HG (reprint author), Chinese Acad Sci, Inst Oceanol, Qingdao 266071, Peoples R China. 2014 http://ir.qdio.ac.cn/handle/337002/24217 https://doi.org/10.1007/s00343-014-3064-z 英语 eng CHINESE JOURNAL OF OCEANOLOGY AND LIMNOLOGY http://ir.qdio.ac.cn/handle/337002/24217 doi:10.1007/s00343-014-3064-z cn.org.cspace.api.content.CopyrightPolicy@21c7bd64 Microsatellites Genome Pacific Oyster Crassostrea Gigas Marine & Freshwater Biology Oceanography Article 期刊论文 2014 ftchinacasciocas https://doi.org/10.1007/s00343-014-3064-z 2022-06-27T05:36:52Z 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 (a parts per thousand yen24 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. Article in Journal/Newspaper Crassostrea gigas Pacific oyster Institute of Oceanology, Chinese Academy of Sciences: IOCAS-IR Pacific Chinese Journal of Oceanology and Limnology 32 1 8 21 |
institution |
Open Polar |
collection |
Institute of Oceanology, Chinese Academy of Sciences: IOCAS-IR |
op_collection_id |
ftchinacasciocas |
language |
English |
topic |
Microsatellites Genome Pacific Oyster Crassostrea Gigas Marine & Freshwater Biology Oceanography |
spellingShingle |
Microsatellites Genome Pacific Oyster Crassostrea Gigas Marine & Freshwater Biology Oceanography Wang Jiafeng Qi Haigang Li Li Zhang Guofan Qi, HG (reprint author), Chinese Acad Sci, Inst Oceanol, Qingdao 266071, Peoples R China. Genome-wide survey and analysis of microsatellites in the Pacific oyster genome: abundance, distribution, and potential for marker development |
topic_facet |
Microsatellites Genome Pacific Oyster Crassostrea Gigas Marine & Freshwater Biology Oceanography |
description |
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 (a parts per thousand yen24 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. |
format |
Article in Journal/Newspaper |
author |
Wang Jiafeng Qi Haigang Li Li Zhang Guofan Qi, HG (reprint author), Chinese Acad Sci, Inst Oceanol, Qingdao 266071, Peoples R China. |
author_facet |
Wang Jiafeng Qi Haigang Li Li Zhang Guofan Qi, HG (reprint author), Chinese Acad Sci, Inst Oceanol, Qingdao 266071, Peoples R China. |
author_sort |
Wang Jiafeng |
title |
Genome-wide survey and analysis of microsatellites in the Pacific oyster genome: abundance, distribution, and potential for marker development |
title_short |
Genome-wide survey and analysis of microsatellites in the Pacific oyster genome: abundance, distribution, and potential for marker development |
title_full |
Genome-wide survey and analysis of microsatellites in the Pacific oyster genome: abundance, distribution, and potential for marker development |
title_fullStr |
Genome-wide survey and analysis of microsatellites in the Pacific oyster genome: abundance, distribution, and potential for marker development |
title_full_unstemmed |
Genome-wide survey and analysis of microsatellites in the Pacific oyster genome: abundance, distribution, and potential for marker development |
title_sort |
genome-wide survey and analysis of microsatellites in the pacific oyster genome: abundance, distribution, and potential for marker development |
publishDate |
2014 |
url |
http://ir.qdio.ac.cn/handle/337002/24217 https://doi.org/10.1007/s00343-014-3064-z |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_relation |
CHINESE JOURNAL OF OCEANOLOGY AND LIMNOLOGY http://ir.qdio.ac.cn/handle/337002/24217 doi:10.1007/s00343-014-3064-z |
op_rights |
cn.org.cspace.api.content.CopyrightPolicy@21c7bd64 |
op_doi |
https://doi.org/10.1007/s00343-014-3064-z |
container_title |
Chinese Journal of Oceanology and Limnology |
container_volume |
32 |
container_issue |
1 |
container_start_page |
8 |
op_container_end_page |
21 |
_version_ |
1766394043524186112 |