Limits...
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.

Show MeSH

Related in: MedlinePlus

Venn diagram of DEGs among three tissues.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3852516&req=5

Figure 4: Venn diagram of DEGs among three tissues.

Mentions: We found 477, 2,761 and 3,376 DEGs in the gill, kidney, and liver, respectively, of AW population compared to FW population with FDR ≤ 0.01 and fold-change ≥ 2 (Figure 2). M-A plots were drafted using “eps” format files as shown in Figure 3. Of these differentially expressed genes, 154, 1,087, 1,949 genes showed higher expression in gill, kidney, and liver of the AW population, respectively; and 323, 1,674, 1,427 genes showed higher expression in gill, kidney, and liver of the FW population, respectively. Of these, 127, 64, 314 genes were exclusively expressed in gill, kidney, and liver of the AW population, and 85, 335, 125 genes were exclusively expressed in in gill, kidney, and liver of the FW population (Additional file 1: Table S1). Venn diagram of the DEGs illustrated that majority of these genes were not shared in three tissues, suggesting that the mechanism and pathways in response to alkaline stress are significant different in gill, kidney, and liver (Figure 4).


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)

Venn diagram of DEGs among three tissues.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Venn diagram of DEGs among three tissues.
Mentions: We found 477, 2,761 and 3,376 DEGs in the gill, kidney, and liver, respectively, of AW population compared to FW population with FDR ≤ 0.01 and fold-change ≥ 2 (Figure 2). M-A plots were drafted using “eps” format files as shown in Figure 3. Of these differentially expressed genes, 154, 1,087, 1,949 genes showed higher expression in gill, kidney, and liver of the AW population, respectively; and 323, 1,674, 1,427 genes showed higher expression in gill, kidney, and liver of the FW population, respectively. Of these, 127, 64, 314 genes were exclusively expressed in gill, kidney, and liver of the AW population, and 85, 335, 125 genes were exclusively expressed in in gill, kidney, and liver of the FW population (Additional file 1: Table S1). Venn diagram of the DEGs illustrated that majority of these genes were not shared in three tissues, suggesting that the mechanism and pathways in response to alkaline stress are significant different in gill, kidney, and liver (Figure 4).

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