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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

The length distribution of contigs and coding sequences (CDSs) of C. hongkongensis.Contigs were generated from denovo assembly of Illumina sequencing reads. The minimum length of contigs was limited to 200 bp and that of CDSs was limited to 100 bp.
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pone-0111915-g001: The length distribution of contigs and coding sequences (CDSs) of C. hongkongensis.Contigs were generated from denovo assembly of Illumina sequencing reads. The minimum length of contigs was limited to 200 bp and that of CDSs was limited to 100 bp.

Mentions: The two cDNA libraries prepared used RNA from the two groups of C. hongkongensis, which included one group accumulated in filtered seawater with optimal salinity (HC group) and another group accumulated in that with low salinity (HT group). A total of 62,643,682 sequence reads from HC group, and 61,096,062 sequence reads from HT group were generated by Illumina sequencing, respectively. These reads have been deposited in the NCBI GEO database with the accession number of GSE51157. After trimming, a total of 54,032,237 and 53,044,352 clean reads were obtained, respectively (Table 1). Assembly of these reads generated 130,629 unique transcript sequences, with the lengths ranging from 201 to 21,597 bp and an average length of 645 bp (Figure 1). Similarly, we performed the denovo assembly with the transcriptomic data from C. gigas[27]. Apparently, the lower throughput sequencing in C. gigas resulted in the assembly of shorter contiguous sequences as compared to C. hongkongensis. The denovo assembly generated 300,382 unique transcript sequences for C. gigas, with the average length of 419 bp (Table 1).


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)

The length distribution of contigs and coding sequences (CDSs) of C. hongkongensis.Contigs were generated from denovo assembly of Illumina sequencing reads. The minimum length of contigs was limited to 200 bp and that of CDSs was limited to 100 bp.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0111915-g001: The length distribution of contigs and coding sequences (CDSs) of C. hongkongensis.Contigs were generated from denovo assembly of Illumina sequencing reads. The minimum length of contigs was limited to 200 bp and that of CDSs was limited to 100 bp.
Mentions: The two cDNA libraries prepared used RNA from the two groups of C. hongkongensis, which included one group accumulated in filtered seawater with optimal salinity (HC group) and another group accumulated in that with low salinity (HT group). A total of 62,643,682 sequence reads from HC group, and 61,096,062 sequence reads from HT group were generated by Illumina sequencing, respectively. These reads have been deposited in the NCBI GEO database with the accession number of GSE51157. After trimming, a total of 54,032,237 and 53,044,352 clean reads were obtained, respectively (Table 1). Assembly of these reads generated 130,629 unique transcript sequences, with the lengths ranging from 201 to 21,597 bp and an average length of 645 bp (Figure 1). Similarly, we performed the denovo assembly with the transcriptomic data from C. gigas[27]. Apparently, the lower throughput sequencing in C. gigas resulted in the assembly of shorter contiguous sequences as compared to C. hongkongensis. The denovo assembly generated 300,382 unique transcript sequences for C. gigas, with the average length of 419 bp (Table 1).

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