Comparative transcriptome analysis of two oysters, Crassostrea gigas and Crassostrea hongkongensis provides insights into adaptation to hypo-osmotic conditions.
Environmental salinity creates a key barrier to limit the distribution of most aquatic organisms. Adaptation to osmotic fluctuation is believed to be a factor facilitating species diversification. Adaptive evolution often involves beneficial mutations at more than one locus. Bivalves hold great inte...
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ftdoajarticles:oai:doaj.org/article:40c04711d84d4f19bdb05c3c1e375419 2023-05-15T15:59:03+02:00 Comparative transcriptome analysis of two oysters, Crassostrea gigas and Crassostrea hongkongensis provides insights into adaptation to hypo-osmotic conditions. Xuelin Zhao Hong Yu Lingfeng Kong Shikai Liu Qi Li 2014-01-01T00:00:00Z https://doi.org/10.1371/journal.pone.0111915 https://doaj.org/article/40c04711d84d4f19bdb05c3c1e375419 EN eng Public Library of Science (PLoS) https://doi.org/10.1371/journal.pone.0111915 https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0111915 https://doaj.org/article/40c04711d84d4f19bdb05c3c1e375419 PLoS ONE, Vol 9, Iss 11, p e111915 (2014) Medicine R Science Q article 2014 ftdoajarticles https://doi.org/10.1371/journal.pone.0111915 2022-12-31T12:48:35Z Environmental salinity creates a key barrier to limit the distribution of most aquatic organisms. Adaptation to osmotic fluctuation is believed to be a factor facilitating species diversification. Adaptive evolution often involves beneficial mutations at more than one locus. Bivalves hold great interest, with numerous species living in waters, as osmoconformers, who maintain the osmotic pressure balance mostly by free amino acids. In this study, 107,076,589 reads from two groups of Crassostrea hongkongensis were produced and the assembled into 130,629 contigs. Transcripts putatively involved in stress-response, innate immunity and cell processes were identified according to Gene ontology and KEGG pathway analyses. Comparing with the transcriptome of C. gigas to characterize the diversity of transcripts between species with osmotic divergence, we identified 182,806 high-quality single nucleotide polymorphisms (SNPs) for C. hongkongensis, and 196,779 SNPs for C. gigas. Comparison of 11,602 pairs of putative orthologs allowed for identification of 14 protein-coding genes that experienced strong positive selection (Ka/Ks>1). In addition, 45 genes that may show signs of moderate positive selection (1 ≥ Ka/Ks>0.5) were also identified. Based on Ks ratios and divergence time between the two species published previously, we estimated a neutral transcriptome-wide substitution mutation rate of 1.39 × 10(-9) per site per year. Several genes were differentially expressed across the control and treated groups of each species. This is the first time to sequence the transcriptome of C. hongkongensis and provide the most comprehensive transcriptomic resource available for it. The increasing amount of transcriptome data on Crassostrea provides an excellent resource for phylogenetic analysis. A large number of SNPs identified in this work are expected to provide valuable resources for future marker and genotyping assay development. The analysis of natural selection provides an innovative view on the adaptation within ... Article in Journal/Newspaper Crassostrea gigas Directory of Open Access Journals: DOAJ Articles PLoS ONE 9 11 e111915 |
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Medicine R Science Q Xuelin Zhao Hong Yu Lingfeng Kong Shikai Liu Qi Li Comparative transcriptome analysis of two oysters, Crassostrea gigas and Crassostrea hongkongensis provides insights into adaptation to hypo-osmotic conditions. |
topic_facet |
Medicine R Science Q |
description |
Environmental salinity creates a key barrier to limit the distribution of most aquatic organisms. Adaptation to osmotic fluctuation is believed to be a factor facilitating species diversification. Adaptive evolution often involves beneficial mutations at more than one locus. Bivalves hold great interest, with numerous species living in waters, as osmoconformers, who maintain the osmotic pressure balance mostly by free amino acids. In this study, 107,076,589 reads from two groups of Crassostrea hongkongensis were produced and the assembled into 130,629 contigs. Transcripts putatively involved in stress-response, innate immunity and cell processes were identified according to Gene ontology and KEGG pathway analyses. Comparing with the transcriptome of C. gigas to characterize the diversity of transcripts between species with osmotic divergence, we identified 182,806 high-quality single nucleotide polymorphisms (SNPs) for C. hongkongensis, and 196,779 SNPs for C. gigas. Comparison of 11,602 pairs of putative orthologs allowed for identification of 14 protein-coding genes that experienced strong positive selection (Ka/Ks>1). In addition, 45 genes that may show signs of moderate positive selection (1 ≥ Ka/Ks>0.5) were also identified. Based on Ks ratios and divergence time between the two species published previously, we estimated a neutral transcriptome-wide substitution mutation rate of 1.39 × 10(-9) per site per year. Several genes were differentially expressed across the control and treated groups of each species. This is the first time to sequence the transcriptome of C. hongkongensis and provide the most comprehensive transcriptomic resource available for it. The increasing amount of transcriptome data on Crassostrea provides an excellent resource for phylogenetic analysis. A large number of SNPs identified in this work are expected to provide valuable resources for future marker and genotyping assay development. The analysis of natural selection provides an innovative view on the adaptation within ... |
format |
Article in Journal/Newspaper |
author |
Xuelin Zhao Hong Yu Lingfeng Kong Shikai Liu Qi Li |
author_facet |
Xuelin Zhao Hong Yu Lingfeng Kong Shikai Liu Qi Li |
author_sort |
Xuelin Zhao |
title |
Comparative transcriptome analysis of two oysters, Crassostrea gigas and Crassostrea hongkongensis provides insights into adaptation to hypo-osmotic conditions. |
title_short |
Comparative transcriptome analysis of two oysters, Crassostrea gigas and Crassostrea hongkongensis provides insights into adaptation to hypo-osmotic conditions. |
title_full |
Comparative transcriptome analysis of two oysters, Crassostrea gigas and Crassostrea hongkongensis provides insights into adaptation to hypo-osmotic conditions. |
title_fullStr |
Comparative transcriptome analysis of two oysters, Crassostrea gigas and Crassostrea hongkongensis provides insights into adaptation to hypo-osmotic conditions. |
title_full_unstemmed |
Comparative transcriptome analysis of two oysters, Crassostrea gigas and Crassostrea hongkongensis provides insights into adaptation to hypo-osmotic conditions. |
title_sort |
comparative transcriptome analysis of two oysters, crassostrea gigas and crassostrea hongkongensis provides insights into adaptation to hypo-osmotic conditions. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2014 |
url |
https://doi.org/10.1371/journal.pone.0111915 https://doaj.org/article/40c04711d84d4f19bdb05c3c1e375419 |
genre |
Crassostrea gigas |
genre_facet |
Crassostrea gigas |
op_source |
PLoS ONE, Vol 9, Iss 11, p e111915 (2014) |
op_relation |
https://doi.org/10.1371/journal.pone.0111915 https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0111915 https://doaj.org/article/40c04711d84d4f19bdb05c3c1e375419 |
op_doi |
https://doi.org/10.1371/journal.pone.0111915 |
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PLoS ONE |
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9 |
container_issue |
11 |
container_start_page |
e111915 |
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1766394835203260416 |