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Comparative transcriptome analysis of two oysters, Crassostrea gigas and Crassostrea hongkongensis provides insights into adaptation to hypo-osmotic conditions.

Zhao X, Yu H, Kong L, Liu S, Li Q - PLoS ONE (2014)

Bottom Line: 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 species and sets the basis for future genetic and evolutionary studies.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.

ABSTRACT
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 species and sets the basis for future genetic and evolutionary studies.

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Related in: MedlinePlus

GO comparison between the C. hongkongensis and C. gigas transcriptome.The C. gigas data was from a previous study by Zhao et al. (2012).
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pone-0111915-g002: GO comparison between the C. hongkongensis and C. gigas transcriptome.The C. gigas data was from a previous study by Zhao et al. (2012).

Mentions: Gene Ontology (GO) analysis was widely used to classify gene functions in terms of biological process, molecular function and cellular component [38]. As shown in Figure 2, a total of 9,724 transcripts were assigned with at least one GO term for a total of 57,185 GO assignments. The distribution of assignments of proteins to more specialized GO terms further indicated that C. hongkongensis transcripts represent proteins from a diverse range of functional classes (Figure 2). Transport and response to stimulus in biological process may be related to osmotic stress directly. Overall, equal percentages of the transcripts for C. gigas and C. hongkongensis had GO assignments relating to the three major categories (Figure 2). However, there were some categories that were different between the two species, such as metabolic process and macromolecule metabolic process. This implies that a difference in regulation of metabolic mechanism may exist between the two species in response to low salinity.


Comparative transcriptome analysis of two oysters, Crassostrea gigas and Crassostrea hongkongensis provides insights into adaptation to hypo-osmotic conditions.

Zhao X, Yu H, Kong L, Liu S, Li Q - PLoS ONE (2014)

GO comparison between the C. hongkongensis and C. gigas transcriptome.The C. gigas data was from a previous study by Zhao et al. (2012).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4219811&req=5

pone-0111915-g002: GO comparison between the C. hongkongensis and C. gigas transcriptome.The C. gigas data was from a previous study by Zhao et al. (2012).
Mentions: Gene Ontology (GO) analysis was widely used to classify gene functions in terms of biological process, molecular function and cellular component [38]. As shown in Figure 2, a total of 9,724 transcripts were assigned with at least one GO term for a total of 57,185 GO assignments. The distribution of assignments of proteins to more specialized GO terms further indicated that C. hongkongensis transcripts represent proteins from a diverse range of functional classes (Figure 2). Transport and response to stimulus in biological process may be related to osmotic stress directly. Overall, equal percentages of the transcripts for C. gigas and C. hongkongensis had GO assignments relating to the three major categories (Figure 2). However, there were some categories that were different between the two species, such as metabolic process and macromolecule metabolic process. This implies that a difference in regulation of metabolic mechanism may exist between the two species in response to low salinity.

Bottom Line: 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 species and sets the basis for future genetic and evolutionary studies.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.

ABSTRACT
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 species and sets the basis for future genetic and evolutionary studies.

Show MeSH
Related in: MedlinePlus