Relationship Among Intron Length, Gene Expression, and Nucleotide Diversity in the Pacific Oyster Crassostrea gigas
Crassostrea gigas is a model mollusk, but its genetic features have not been studied comprehensively. In this study, we used whole-genome resequencing data to identify and characterize nucleotide diversity and population recombination rate in a diverse collection of 21 C. gigas samples. Our analyses...
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ftchinacasciocas:oai:ir.qdio.ac.cn:337002/160263 2023-05-15T15:57:59+02:00 Relationship Among Intron Length, Gene Expression, and Nucleotide Diversity in the Pacific Oyster Crassostrea gigas Song, Kai Li, Li Zhang, Guofan 2018-10-01 http://ir.qdio.ac.cn/handle/337002/160262 http://ir.qdio.ac.cn/handle/337002/160263 https://doi.org/10.1007/s10126-018-9838-0 英语 eng SPRINGER MARINE BIOTECHNOLOGY http://ir.qdio.ac.cn/handle/337002/160262 http://ir.qdio.ac.cn/handle/337002/160263 doi:10.1007/s10126-018-9838-0 Single nucleotide polymorphism (SNP) Recombination rates Purifying selection Biotechnology & Applied Microbiology Marine & Freshwater Biology 期刊论文 2018 ftchinacasciocas https://doi.org/10.1007/s10126-018-9838-0 2022-06-27T05:40:20Z Crassostrea gigas is a model mollusk, but its genetic features have not been studied comprehensively. In this study, we used whole-genome resequencing data to identify and characterize nucleotide diversity and population recombination rate in a diverse collection of 21 C. gigas samples. Our analyses revealed that C. gigas harbors both extremely high genetic diversity and recombination rates across the whole genome as compared with those of the other taxa. The noncoding regions, introns, intergenic spacers, and untranslated regions (UTRs) showed a lower level diversity than the synonymous sites. The larger introns tended to have lower diversity. Moreover, we found a negative association of the non-synonymous diversity with gene expression, which suggested that purifying selection played an important role in shaping genetic diversity. The nucleotide diversity at the 100- and 50-kb levels was positively correlated with population recombination rates, which was expected if the diversity was shaped by purifying selection or hitchhiking of advantageous mutants. Our work gives a general picture of the oyster's polymorphism pattern and its association with recombination rates. Report Crassostrea gigas Pacific oyster Institute of Oceanology, Chinese Academy of Sciences: IOCAS-IR Pacific Marine Biotechnology 20 5 676 684 |
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Open Polar |
collection |
Institute of Oceanology, Chinese Academy of Sciences: IOCAS-IR |
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ftchinacasciocas |
language |
English |
topic |
Single nucleotide polymorphism (SNP) Recombination rates Purifying selection Biotechnology & Applied Microbiology Marine & Freshwater Biology |
spellingShingle |
Single nucleotide polymorphism (SNP) Recombination rates Purifying selection Biotechnology & Applied Microbiology Marine & Freshwater Biology Song, Kai Li, Li Zhang, Guofan Relationship Among Intron Length, Gene Expression, and Nucleotide Diversity in the Pacific Oyster Crassostrea gigas |
topic_facet |
Single nucleotide polymorphism (SNP) Recombination rates Purifying selection Biotechnology & Applied Microbiology Marine & Freshwater Biology |
description |
Crassostrea gigas is a model mollusk, but its genetic features have not been studied comprehensively. In this study, we used whole-genome resequencing data to identify and characterize nucleotide diversity and population recombination rate in a diverse collection of 21 C. gigas samples. Our analyses revealed that C. gigas harbors both extremely high genetic diversity and recombination rates across the whole genome as compared with those of the other taxa. The noncoding regions, introns, intergenic spacers, and untranslated regions (UTRs) showed a lower level diversity than the synonymous sites. The larger introns tended to have lower diversity. Moreover, we found a negative association of the non-synonymous diversity with gene expression, which suggested that purifying selection played an important role in shaping genetic diversity. The nucleotide diversity at the 100- and 50-kb levels was positively correlated with population recombination rates, which was expected if the diversity was shaped by purifying selection or hitchhiking of advantageous mutants. Our work gives a general picture of the oyster's polymorphism pattern and its association with recombination rates. |
format |
Report |
author |
Song, Kai Li, Li Zhang, Guofan |
author_facet |
Song, Kai Li, Li Zhang, Guofan |
author_sort |
Song, Kai |
title |
Relationship Among Intron Length, Gene Expression, and Nucleotide Diversity in the Pacific Oyster Crassostrea gigas |
title_short |
Relationship Among Intron Length, Gene Expression, and Nucleotide Diversity in the Pacific Oyster Crassostrea gigas |
title_full |
Relationship Among Intron Length, Gene Expression, and Nucleotide Diversity in the Pacific Oyster Crassostrea gigas |
title_fullStr |
Relationship Among Intron Length, Gene Expression, and Nucleotide Diversity in the Pacific Oyster Crassostrea gigas |
title_full_unstemmed |
Relationship Among Intron Length, Gene Expression, and Nucleotide Diversity in the Pacific Oyster Crassostrea gigas |
title_sort |
relationship among intron length, gene expression, and nucleotide diversity in the pacific oyster crassostrea gigas |
publisher |
SPRINGER |
publishDate |
2018 |
url |
http://ir.qdio.ac.cn/handle/337002/160262 http://ir.qdio.ac.cn/handle/337002/160263 https://doi.org/10.1007/s10126-018-9838-0 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_relation |
MARINE BIOTECHNOLOGY http://ir.qdio.ac.cn/handle/337002/160262 http://ir.qdio.ac.cn/handle/337002/160263 doi:10.1007/s10126-018-9838-0 |
op_doi |
https://doi.org/10.1007/s10126-018-9838-0 |
container_title |
Marine Biotechnology |
container_volume |
20 |
container_issue |
5 |
container_start_page |
676 |
op_container_end_page |
684 |
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1766393701641224192 |