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Gene expression changes leading extreme alkaline tolerance in Amur ide (Leuciscus waleckii) inhabiting soda lake.

Xu J, Li Q, Xu L, Wang S, Jiang Y, Zhao Z, Zhang Y, Li J, Dong C, Xu P, Sun X - BMC Genomics (2013)

Bottom Line: Our results showed that out of assembled 64,603 transcript contigs, 28,391 contigs had been assigned with a known function, corresponding to 20,371 unique protein accessions.We found 477, 2,761 and 3,376 differentially expressed genes (DEGs) in the gill, kidney, and liver, respectively, of Dali Nor population compared to Ganggeng Nor population with FDR ≤ 0.01 and fold-change ≥ 2.The results set a foundation for further analyses on alkaline-responsive candidate genes, which help us understand teleost adaptation under extreme environmental stress and ultimately benefit future breeding for alkaline-tolerant fish strains.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China. xupeng@cafs.ac.cn.

ABSTRACT

Background: Amur ide (Leuciscus waleckii) is an economically and ecologically important cyprinid species in Northern Asia. The Dali Nor population living in the soda lake Dali Nor can adapt the extremely high alkalinity, providing us a valuable material to understand the adaptation mechanism against extreme environmental stress in teleost.

Results: In this study, we generated high-throughput RNA-Seq data from three tissues gill, liver and kidney of L. waleckii living in the soda lake Dali Nor and the fresh water lake Ganggeng Nor, then performed parallel comparisons of three tissues. Our results showed that out of assembled 64,603 transcript contigs, 28,391 contigs had been assigned with a known function, corresponding to 20,371 unique protein accessions. We found 477, 2,761 and 3,376 differentially expressed genes (DEGs) in the gill, kidney, and liver, respectively, of Dali Nor population compared to Ganggeng Nor population with FDR ≤ 0.01 and fold-change ≥ 2. Further analysis revealed that well-known functional categories of genes and signaling pathway, which are associated with stress response and extreme environment adaptation, have been significantly enriched, including the functional categories of "response to stimulus", "transferase activity", "transporter activity" and "oxidoreductase activity", and signaling pathways of "mTOR signaling", "EIF2 signaling", "superpathway of cholesterol biosynthesis". We also identified significantly DEGs encoding important modulators on stress adaptation and tolerance, including carbonic anhydrases, heat shock proteins, superoxide dismutase, glutathione S-transferases, aminopeptidase N, and aminotransferases.

Conclusions: Overall, this study demonstrated that transcriptome changes in L. waleckii played a role in adaptation to complicated environmental stress in the highly alkalized Dali Nor lake. The results set a foundation for further analyses on alkaline-responsive candidate genes, which help us understand teleost adaptation under extreme environmental stress and ultimately benefit future breeding for alkaline-tolerant fish strains.

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Differentially expressed genes validated by qRT-PCR. Comparison between RNA-Seq results and qRT-PCR validation results. X-axis shows genes in three tissues validated in this study; Y-axis shows Log2Ratio of expression of AW (alkaline water) versus FW (fresh water).
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Figure 5: Differentially expressed genes validated by qRT-PCR. Comparison between RNA-Seq results and qRT-PCR validation results. X-axis shows genes in three tissues validated in this study; Y-axis shows Log2Ratio of expression of AW (alkaline water) versus FW (fresh water).

Mentions: To validate RNA-Seq results, 35 genes with high level of significance or important stress-responding functions were selected for qRT-PCR analysis with beta-actin as reference gene. Primers for all genes are listed in Additional file 2: Table S2. Overall, the expression patterns of 30 genes were in agreement across the RNA-Seq and qRT-PCR analyses with minor differences in the expression level (Figure 5). There were only 5 genes that not showed the consistency of expression in the two assays. Thus, these genes showed similar patterns of mRNA abundance in RNA-Seq analysis and qRT-PCR, validated the genome-wide expressed profiling in gill, kidney, and liver in response to AW stress.


Gene expression changes leading extreme alkaline tolerance in Amur ide (Leuciscus waleckii) inhabiting soda lake.

Xu J, Li Q, Xu L, Wang S, Jiang Y, Zhao Z, Zhang Y, Li J, Dong C, Xu P, Sun X - BMC Genomics (2013)

Differentially expressed genes validated by qRT-PCR. Comparison between RNA-Seq results and qRT-PCR validation results. X-axis shows genes in three tissues validated in this study; Y-axis shows Log2Ratio of expression of AW (alkaline water) versus FW (fresh water).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3852516&req=5

Figure 5: Differentially expressed genes validated by qRT-PCR. Comparison between RNA-Seq results and qRT-PCR validation results. X-axis shows genes in three tissues validated in this study; Y-axis shows Log2Ratio of expression of AW (alkaline water) versus FW (fresh water).
Mentions: To validate RNA-Seq results, 35 genes with high level of significance or important stress-responding functions were selected for qRT-PCR analysis with beta-actin as reference gene. Primers for all genes are listed in Additional file 2: Table S2. Overall, the expression patterns of 30 genes were in agreement across the RNA-Seq and qRT-PCR analyses with minor differences in the expression level (Figure 5). There were only 5 genes that not showed the consistency of expression in the two assays. Thus, these genes showed similar patterns of mRNA abundance in RNA-Seq analysis and qRT-PCR, validated the genome-wide expressed profiling in gill, kidney, and liver in response to AW stress.

Bottom Line: Our results showed that out of assembled 64,603 transcript contigs, 28,391 contigs had been assigned with a known function, corresponding to 20,371 unique protein accessions.We found 477, 2,761 and 3,376 differentially expressed genes (DEGs) in the gill, kidney, and liver, respectively, of Dali Nor population compared to Ganggeng Nor population with FDR ≤ 0.01 and fold-change ≥ 2.The results set a foundation for further analyses on alkaline-responsive candidate genes, which help us understand teleost adaptation under extreme environmental stress and ultimately benefit future breeding for alkaline-tolerant fish strains.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China. xupeng@cafs.ac.cn.

ABSTRACT

Background: Amur ide (Leuciscus waleckii) is an economically and ecologically important cyprinid species in Northern Asia. The Dali Nor population living in the soda lake Dali Nor can adapt the extremely high alkalinity, providing us a valuable material to understand the adaptation mechanism against extreme environmental stress in teleost.

Results: In this study, we generated high-throughput RNA-Seq data from three tissues gill, liver and kidney of L. waleckii living in the soda lake Dali Nor and the fresh water lake Ganggeng Nor, then performed parallel comparisons of three tissues. Our results showed that out of assembled 64,603 transcript contigs, 28,391 contigs had been assigned with a known function, corresponding to 20,371 unique protein accessions. We found 477, 2,761 and 3,376 differentially expressed genes (DEGs) in the gill, kidney, and liver, respectively, of Dali Nor population compared to Ganggeng Nor population with FDR ≤ 0.01 and fold-change ≥ 2. Further analysis revealed that well-known functional categories of genes and signaling pathway, which are associated with stress response and extreme environment adaptation, have been significantly enriched, including the functional categories of "response to stimulus", "transferase activity", "transporter activity" and "oxidoreductase activity", and signaling pathways of "mTOR signaling", "EIF2 signaling", "superpathway of cholesterol biosynthesis". We also identified significantly DEGs encoding important modulators on stress adaptation and tolerance, including carbonic anhydrases, heat shock proteins, superoxide dismutase, glutathione S-transferases, aminopeptidase N, and aminotransferases.

Conclusions: Overall, this study demonstrated that transcriptome changes in L. waleckii played a role in adaptation to complicated environmental stress in the highly alkalized Dali Nor lake. The results set a foundation for further analyses on alkaline-responsive candidate genes, which help us understand teleost adaptation under extreme environmental stress and ultimately benefit future breeding for alkaline-tolerant fish strains.

Show MeSH
Related in: MedlinePlus