SNP mining in Crassostrea gigas EST data: transferability to four other Crassostrea species, phylogenetic inferences and outlier SNPs under selection.
Oysters, with high levels of phenotypic plasticity and wide geographic distribution, are a challenging group for taxonomists and phylogenetics. Our study is intended to generate new EST-SNP markers and to evaluate their potential for cross-species utilization in phylogenetic study of the genus Crass...
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ftdoajarticles:oai:doaj.org/article:51c64f567ad94ee68d3026c597ef3460 2023-05-15T15:58:51+02:00 SNP mining in Crassostrea gigas EST data: transferability to four other Crassostrea species, phylogenetic inferences and outlier SNPs under selection. Xiaoxiao Zhong Qi Li Hong Yu Lingfeng Kong 2014-01-01T00:00:00Z https://doi.org/10.1371/journal.pone.0108256 https://doaj.org/article/51c64f567ad94ee68d3026c597ef3460 EN eng Public Library of Science (PLoS) https://doi.org/10.1371/journal.pone.0108256 https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0108256 https://doaj.org/article/51c64f567ad94ee68d3026c597ef3460 PLoS ONE, Vol 9, Iss 9, p e108256 (2014) Medicine R Science Q article 2014 ftdoajarticles https://doi.org/10.1371/journal.pone.0108256 2022-12-31T16:19:59Z Oysters, with high levels of phenotypic plasticity and wide geographic distribution, are a challenging group for taxonomists and phylogenetics. Our study is intended to generate new EST-SNP markers and to evaluate their potential for cross-species utilization in phylogenetic study of the genus Crassostrea. In the study, 57 novel SNPs were developed from an EST database of C. gigas by the HRM (high-resolution melting) method. Transferability of 377 SNPs developed for C. gigas was examined on four other Crassostrea species: C. sikamea, C. angulata, C. hongkongensis and C. ariakensis. Among the 377 primer pairs tested, 311 (82.5%) primers showed amplification in C. sikamea, 353 (93.6%) in C. angulata, 254 (67.4%) in C. hongkongensis and 253 (67.1%) in C. ariakensis. A total of 214 SNPs were found to be transferable to all four species. Phylogenetic analyses showed that C. hongkongensis was a sister species of C. ariakensis and that this clade was sister to the clade containing C. sikamea, C. angulata and C. gigas. Within this clade, C. gigas and C. angulata had the closest relationship, with C. sikamea being the sister group. In addition, we detected eight SNPs as potentially being under selection by two outlier tests (fdist and hierarchical methods). The SNPs studied here should be useful for genetic diversity, comparative mapping and phylogenetic studies across species in Crassostrea and the candidate outlier SNPs are worth exploring in more detail regarding association genetics and functional studies. Article in Journal/Newspaper Crassostrea gigas Directory of Open Access Journals: DOAJ Articles PLoS ONE 9 9 e108256 |
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Medicine R Science Q |
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Medicine R Science Q Xiaoxiao Zhong Qi Li Hong Yu Lingfeng Kong SNP mining in Crassostrea gigas EST data: transferability to four other Crassostrea species, phylogenetic inferences and outlier SNPs under selection. |
topic_facet |
Medicine R Science Q |
description |
Oysters, with high levels of phenotypic plasticity and wide geographic distribution, are a challenging group for taxonomists and phylogenetics. Our study is intended to generate new EST-SNP markers and to evaluate their potential for cross-species utilization in phylogenetic study of the genus Crassostrea. In the study, 57 novel SNPs were developed from an EST database of C. gigas by the HRM (high-resolution melting) method. Transferability of 377 SNPs developed for C. gigas was examined on four other Crassostrea species: C. sikamea, C. angulata, C. hongkongensis and C. ariakensis. Among the 377 primer pairs tested, 311 (82.5%) primers showed amplification in C. sikamea, 353 (93.6%) in C. angulata, 254 (67.4%) in C. hongkongensis and 253 (67.1%) in C. ariakensis. A total of 214 SNPs were found to be transferable to all four species. Phylogenetic analyses showed that C. hongkongensis was a sister species of C. ariakensis and that this clade was sister to the clade containing C. sikamea, C. angulata and C. gigas. Within this clade, C. gigas and C. angulata had the closest relationship, with C. sikamea being the sister group. In addition, we detected eight SNPs as potentially being under selection by two outlier tests (fdist and hierarchical methods). The SNPs studied here should be useful for genetic diversity, comparative mapping and phylogenetic studies across species in Crassostrea and the candidate outlier SNPs are worth exploring in more detail regarding association genetics and functional studies. |
format |
Article in Journal/Newspaper |
author |
Xiaoxiao Zhong Qi Li Hong Yu Lingfeng Kong |
author_facet |
Xiaoxiao Zhong Qi Li Hong Yu Lingfeng Kong |
author_sort |
Xiaoxiao Zhong |
title |
SNP mining in Crassostrea gigas EST data: transferability to four other Crassostrea species, phylogenetic inferences and outlier SNPs under selection. |
title_short |
SNP mining in Crassostrea gigas EST data: transferability to four other Crassostrea species, phylogenetic inferences and outlier SNPs under selection. |
title_full |
SNP mining in Crassostrea gigas EST data: transferability to four other Crassostrea species, phylogenetic inferences and outlier SNPs under selection. |
title_fullStr |
SNP mining in Crassostrea gigas EST data: transferability to four other Crassostrea species, phylogenetic inferences and outlier SNPs under selection. |
title_full_unstemmed |
SNP mining in Crassostrea gigas EST data: transferability to four other Crassostrea species, phylogenetic inferences and outlier SNPs under selection. |
title_sort |
snp mining in crassostrea gigas est data: transferability to four other crassostrea species, phylogenetic inferences and outlier snps under selection. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2014 |
url |
https://doi.org/10.1371/journal.pone.0108256 https://doaj.org/article/51c64f567ad94ee68d3026c597ef3460 |
genre |
Crassostrea gigas |
genre_facet |
Crassostrea gigas |
op_source |
PLoS ONE, Vol 9, Iss 9, p e108256 (2014) |
op_relation |
https://doi.org/10.1371/journal.pone.0108256 https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0108256 https://doaj.org/article/51c64f567ad94ee68d3026c597ef3460 |
op_doi |
https://doi.org/10.1371/journal.pone.0108256 |
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PLoS ONE |
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9 |
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9 |
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e108256 |
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