Dataset Information

Transcriptional Profiling Reveals Differential Gene Expression of Amur Ide (Leuciscus waleckii) during Spawning Migration.

ABSTRACT: Amur ide (Leuciscus waleckii), an important aquaculture species, inhabits neutral freshwater but can tolerate high salinity or alkalinity. As an extreme example, the population in Dali Nor lake inhabits alkalized soda water permanently, and migrates from alkaline water to neutral freshwater to spawn. In this study, we performed comparative transcriptome profiling study on the livers of Amur ide to interrogate the expression differences between the population that permanently inhabit freshwater in Ganggeng Nor lake (FW) and the spawning population that recently migrated from alkaline water into freshwater (SM). A total of 637,234,880 reads were generated, resulting in 53,440 assembled contigs that were used as reference sequences. Comparisons of these transcriptome files revealed 444 unigenes with significant differential expression (p-value ? 0.01, fold-change ? 2), including 246 genes that were up-regulated in SM and 198 genes that were up-regulated in FW. The gene ontology (GO) enrichment analysis and KEGG pathway analysis indicated that the mTOR signaling pathway, Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling pathway, and oxidative phosphorylation were highly likely to affect physiological changes during spawning migration. Overall, this study demonstrates that transcriptome changes played a role in Amur ide spawning migration. These results provide a foundation for further analyses on the physiological and molecular mechanisms underlying Amur ide spawning migration.

SUBMITTER: Cui J

PROVIDER: S-EPMC4490533 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Transcriptional Profiling Reveals Differential Gene Expression of Amur Ide (Leuciscus waleckii) during Spawning Migration.

Cui Jun J Xu Jian J Zhang Songhao S Wang Kai K Jiang Yanliang Y Mahboob Shahid S Al-Ghanim Khalid A KA Xu Peng P

International journal of molecular sciences 20150618 6

Amur ide (Leuciscus waleckii), an important aquaculture species, inhabits neutral freshwater but can tolerate high salinity or alkalinity. As an extreme example, the population in Dali Nor lake inhabits alkalized soda water permanently, and migrates from alkaline water to neutral freshwater to spawn. In this study, we performed comparative transcriptome profiling study on the livers of Amur ide to interrogate the expression differences between the population that permanently inhabit freshwater i ...[more]

PMID: 26096003

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Project description: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.

Project description:BackgroundAmur ide (Leuciscus waleckii) is an economically and ecologically important species in Northern Asia. The Dali Nor population inhabiting Dali Nor Lake, a typical saline-alkaline lake in Inner Mongolia, is well-known for its adaptation to extremely high alkalinity. Genome information is needed for conservation and aquaculture purposes, as well as to gain further understanding into the genetics of stress tolerance. The objective of the study is to sequence the transcriptome and obtain a well-assembled transcriptome of Amur ide.ResultsThe transcriptome of Amur ide was sequenced using the Illumina platform and assembled into 53,632 cDNA contigs, with an average length of 647 bp and a N50 length of 1,094 bp. A total of 19,338 unique proteins were identified, and gene ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses classified all contigs into functional categories. Open Reading Frames (ORFs) were detected from 34,888 (65.1%) of contigs with an average length of 577 bp, while 9,638 full-length cDNAs were identified. Comparative analyses revealed that 31,790 (59.3%) contigs have a significant similarity to zebrafish proteins, and 27,096 (50.5%), 27,524 (51.3%) and 27,996 (52.2%) to teraodon, medaka and three-spined stickleback proteins, respectively. A total of 10,395 microsatellites and 34,299 SNPs were identified and classified. A dN/dS analysis on unigenes was performed, which identified that 61 of the genes were under strong positive selection. Most of the genes are associated with stress adaptation and immunity, suggesting that the extreme alkaline-saline environment resulted in fast evolution of certain genes.ConclusionsThe transcriptome of Amur ide had been deeply sequenced, assembled and characterized, providing a valuable resource for a better understanding of the Amur ide genome. The transcriptome data will facilitate future functional studies on the Amur ide genome, as well as provide insight into potential mechanisms for adaptation to an extreme alkaline-saline environment.

Project description:The Amur ide (Leuciscus waleckii) is a fish in the Cyprinidae family. Compared with other Amur ide living in freshwater ecosystems, the Amur ide population in Lake Dali Nor of China is famous for its high tolerance to the alkaline conditions of 54 mM (pH 9.6). Yet, surprisingly, the ionoregulatory mechanism responsible for this remarkable alkaline adaptation remains unclear. Therefore, this study sought to investigate how bicarbonate affects the acid-base balancing and ionoregulatory responses of this animal. Here, using a comparative approach, the alkali form of Amur ide and its ancestral freshwater form living in other freshwater basins were each exposed to 50 mM (pH 9.59 ± 0.09), a level close to the alkalinity of Lake Dali Nor, and their physiological (AE1) adjustment of ions and acid-base regulation were investigated. This study highlighted differences in blood pH and serum ions (e.g., Na+, K+, Cl-, and Ca2+), Na+/K+ ATPase (NKA) activity and its mRNA level, and mRNA expression of gill transporters (Na+/H+ exchanger member 2 and/or 3, Na+/ HCO3- cotransporter (NBC1), Cl-/ HCO3- exchanger, Na+/Cl- cotransporter (NCC), Na+/K+/2Cl- (NKCC1), SLC26A5, and SLC26A6) for alkalinity adaptation between the two forms of Amur ide differing in alkalinity tolerance. Specifically, close relationships among the serum Na+ and mRNA levels of NCC, NKCC1, and NHE, and also NKA and NBC1, in addition to serum Cl- and bicarbonate transporters (e.g., SLC26A5 and SLC26A6), characterized the alkali form of Amur ide. We propose that this ecotype can ensure its transepithelial Cl- and Na+ uptake/base secretions are highly functional, by its basolateral NKA with NBC1 and apical ionic transporters, and especially NCC incorporated with other transporters (e.g., SLC26). This suggests an evolved strong ability to maintain an ion osmotic and acid-base balance for more effectively facilitating its adaptability to the high alkaline environment. This study provides new insights into the physiological responses of the alkaline form of the Amur ide fish for adapting to extreme alkaline conditions. This information could be used as a reference to cultivating alkaline-tolerant fish species in abandoned alkaline waters.

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Transcriptional Profiling Reveals Differential Gene Expression of Amur Ide (Leuciscus waleckii) during Spawning Migration.

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Transcriptional Profiling Reveals Differential Gene Expression of Amur Ide (Leuciscus waleckii) during Spawning Migration.

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