Comparative transcriptome analysis of Triplophysa yarkandensis in response to salinity and alkalinity stress

Chen, Sheng-Ao; Hou, Jilun; Yao, Na; Xie, Congxin; Li, Dapeng

doi:10.1016/j.cbd.2019.100629

Cited by 15 publications

(18 citation statements)

References 35 publications

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“…In recent years, climate change and human activities resulted in the water curtailment and river desiccation of the Tarim River basin [ 1 ]. As a result, due to the gradual depletion of water resources, together with alien invasion and agricultural cultivation in the Tarim River, the population size of T. yarkandensis has been diminishing and it is critically endangered [ 2 ]. Changing this trajectory will require coordinated research and conservation strategies to provide a better understanding of population genetics at large spatial scales.…”

Section: Introductionmentioning

confidence: 99%

“…T. yarkandensis plays an important role in the fragile local ecosystem of the Tarim River basin, and previous studies have shown that the origin and evolution of the genus of Triplophysa may be associated with uplifts of the Tibetan Plateau [ 3 , 4 , 5 ]. Previously, many studies have reported the distribution, morphological [ 6 ] and reproductive characteristics [ 7 ], mitochondrial genome [ 8 , 9 ] and transcriptome [ 2 ] of T. yarkandensis . However, information on population structure and historical population dynamics of T. yarkandensis populations in the Tarim River basin is still lacking.…”

Section: Introductionmentioning

confidence: 99%

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Genetic Diversity and Population Differentiation of Kashgarian Loach (Triplophysa yarkandensis) in Xinjiang Tarim River Basin

Zhou

Zhao

et al. 2021

Biology

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The distribution of Triplophysa yarkandensis is restricted to Xinjiang’s Tarim River basin. We collected 119 T. yarkandensis samples from nine geographic populations in the Tarim River basin and utilized the RAD-seq method for SNP genotyping. In this study, a total of 164.81 Gb bases were generated with the Illumina platform, and 129,873 candidate SNPs were obtained with the Stacks pipeline for population genetic analyses. High levels of genetic diversity were detected among nine populations. The AMOVA results showed that the majority of genetic variations originated from among populations (FST = 0.67), and the pairwise FST values ranged from 0.4579 to 0.8736, indicating high levels of genetic differentiation among these populations. The discriminate analysis of principal components (DAPCs) and neighbor joining (NJ) tree revealed that the nine populations could be separated into two clusters (i.e., south and north populations), and modest genetic differentiation between south and north populations was observed, while the individuals from several populations were not clustered together by geographical location. The evidence of two genetic boundaries between south and north populations (except TTM) was supported by barrier analysis. The Bayesian skyline plotting indicated that T. yarkandensis populations in the Tarim River basin had not experienced genetic bottlenecks, and the effective population size remained stable. This study first clarified the genetic diversity and differentiation of T. yarkandensis populations in the Tarim River basin, and it provided valuable molecular data for conservation and management of natural populations.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Population Differentiation of Kashgarian Loach (Triplophysa yarkandensis) in Xinjiang Tarim River Basin

Zhou

Zhao

et al. 2021

Biology

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“…The harsh environment, characterized by high altitude, cold habitat and poor nutrition in the Qinghai-Tibet Plateau, has brought severe challenges to local species ( Yang et al, 2015 ). Nevertheless, as the representative indigenous species in the Qinghai-Tibet Plateau, Triplophysa fishes can well adapt to these severe natural conditions ( Chen et al, 2020 ). Given their taxonomic status, evolutionary process, geographical distribution and biological characteristics, Triplophysa genus offers an attractive study model for the fish phylogeny, geological change, life evolution, and extreme environmental adaptation ( Chen et al, 2020 ; Wu et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Population Structure, Genetic Diversity and Differentiation of Triplophysa tenuis in Xinjiang Tarim River

Huo

Chen

et al. 2022

Front. Genet.

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Triplophysa tenuis is an important indigenous fish in the Xinjiang Tarim River. In this study, we collected 120 T. tenuis individuals from 8 T. tenuis populations in the Tarim River. Through genotyping-by-sequencing (GBS), a total of 582,678,756 clean reads were generated for all the genotypes, and after quality filtering, 595,379 SNPs were obtained for the population genetic analyses. Multiple genetic parameters showed that the 8 T. tenuis populations had high genetic diversity. Phylogenetic tree analysis indicated that all T. tenuis individuals were divided into five branches, the individuals from the north of Tarim River were grouped into cluster 1 (SF and WS) and cluster 3 (DWQ, TKX, and KZE), while the AETS, WLWT and LF individuals from the south of Tarim River were clustered into cluster 2. The result was consistent with the admixture analysis, which supported that the 8 T. tenuis populations were clustered into three subgroups. Furthermore, the pairwise FST values and genetic distance indicated that there was a large genetic differentiation between WS and other T. tenuis populations. Collectively, this study provides valuable genome-wide data for the conservation of natural T. tenuis populations in the Tarim River.

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“…In recent years, exploring the growth and development (Sun et al 2017;Xing et al 2021), immune function Shi et al 2020), and phylogeny (Zhao et al 2020;Carmona et al 2017) of aquaculture animals using various omic techniques have gradually become a research hotspot (Chen et al 2020). The combined analysis of transcriptome and metabolome is widely used to reveal the molecular mechanism in organisms (Wang et al 2020;Liu et al 2019;Kong et al 2020).…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic and Metabolomic Analyses Provide Insights into the Growth and Development Advantages of Triploid Apostichopus japonicus

et al. 2022

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Polyploid breeding is widely used in aquaculture as an important area of new research. We have previously grown Apostichopus japonicus triploids with a growth advantage. The body length, body weight, and aestivation time of triploid and diploid A. japonicus were measured in this study, and the transcriptome and metabolome were used to examine the growth advantage of triploids A. japonicus. The results showed that the proportion of triploid A. japonicus with a body length of 6–12 cm and 12–18 cm was significantly higher than that of diploid A. japonicus, and triploid A. japonicus had a shorter aestivation time (39 days) than diploid (63 days). We discovered 3296 differentially expressed genes (DEGs); 13 DEGs (for example, cyclin-dependent kinase 2) related to growth advantage, immune regulation, and energy storage were screened as potential candidates. According to Gene Ontology (GO) enrichment analysis, DEGs were significantly enriched in the cytoplasm (cellular component), ATP binding process (molecular function), oxidation–reduction process (biological process), and other pathways. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment data, DEGs were significantly enriched in ribosome production and other areas. We discovered 414 significant differential metabolites (SDMs), with 11 important SDMs (for example, nocodazole) linked to a growth advantage. SDMs are significantly enriched in metabolic pathways, as well as other pathways, according to the KEGG enrichment results. According to a combined transcriptome and metabolome analysis, 6 DEGs have regulatory relationships with 11 SDMs, which act on 11 metabolic pathways together. Our results further enrich the biological data of triploid A. japonicus and provide useful resources for genetic improvement of this species.

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Comparative transcriptome analysis of Triplophysa yarkandensis in response to salinity and alkalinity stress

Cited by 15 publications

References 35 publications

Genetic Diversity and Population Differentiation of Kashgarian Loach (Triplophysa yarkandensis) in Xinjiang Tarim River Basin

Genetic Diversity and Population Differentiation of Kashgarian Loach (Triplophysa yarkandensis) in Xinjiang Tarim River Basin

Population Structure, Genetic Diversity and Differentiation of Triplophysa tenuis in Xinjiang Tarim River

Transcriptomic and Metabolomic Analyses Provide Insights into the Growth and Development Advantages of Triploid Apostichopus japonicus

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