Gill Transcriptome Analysis Revealed the Difference in Gene Expression Between Freshwater and Seawater Acclimated Guppy (Poecilia reticulata)

Chen, Xiuxia; Gong, Hui; Chi, Hongshu; Xu, Baohua; Zheng, Zaiyu; Bai, Yulin

doi:10.1007/s10126-021-10053-4

Cited by 17 publications

(12 citation statements)

References 52 publications

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“…Malik and Kim (2021) identified that about 40% (162/405) of the DEGs were classified as belonging to the transportome in a meta-analysis of four different salinity challenge studies in Chinese mitten crab. In a study with the Guppy Poecilia reticulata it was also shown that a large number of DEGs were involved in ion transport and transmembrane transport [ 26 ]. Similarly, when hybrid tilapia underwent various laboratory salinity stress treatments, numerous ion transport enzymes and ion transporters associated with osmoregulation were identified [ 32 ].…”

Section: Discussionmentioning

confidence: 99%

Field application of de novo transcriptomic analysis to evaluate the effects of sublethal freshwater salinization on Gasterosteus aculeatus in urban streams

Escobar-Sierra,

Lampert

2024

PLoS ONE

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Freshwater salinization poses global challenges for aquatic organisms inhabiting urban streams, impacting their physiology and ecology. However, current salinization research predominantly focuses on mortality endpoints in limited model species, overlooking the sublethal effects on a broader spectrum of organisms and the exploration of adaptive mechanisms and pathways under natural field conditions. To address these gaps, we conducted high-throughput sequencing transcriptomic analysis on the gill tissue of the euryhaline fish Gasterosteus aculeatus, investigating its molecular response to salinity stress in the highly urbanized river Boye, Germany. We found that in stream sections with sublethal concentrations of chloride costly osmoregulatory systems were activated, evidenced by the differential expression of genes related to osmoregulation. Our enrichment analysis revealed differentially expressed genes (DEGs) related to transmembrane transport and regulation of transport and other osmoregulation pathways, which aligns with the crucial role of these pathways in maintaining biological homeostasis. Notably, we identified candidate genes involved in increased osmoregulatory activity under salinity stress, including those responsible for moving ions across membranes: ion channels, ion pumps, and ion transporters. Particularly, genes from the solute carrier family SLC, aquaporin AQP1, chloride channel CLC7, ATP-binding cassette transporter ABCE1, and ATPases member ATAD2 exhibited prominent differential expression. These findings provide insights into the potential molecular mechanisms underlying the adaptive response of euryhaline fish to salinity stress and have implications for their conservation and management in the face of freshwater salinization.

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Section: Discussionmentioning

confidence: 99%

Field application of de novo transcriptomic analysis to evaluate the effects of sublethal freshwater salinization on Gasterosteus aculeatus in urban streams

Escobar-Sierra,

Lampert

2024

PLoS ONE

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“…Studies on the gills of various fish species in varying saline habitats have shown a significant number of differentially expressed genes (DEGs) involved in ion transport and transmembrane transport (X. Chen et al, 2021; Escobar-Sierra & Lampert, 2023; Gibbons et al, 2017; Guo et al, 2018b; Su et al, 2020a). Specifically, for gill tissue, we found enrichment of osmoregulation-related pathways like “chloride channel inhibitor activity”.…”

Section: Discussionmentioning

confidence: 99%

“…The gill, as a primary organ for osmotic homeostasis, has been the focus of osmotic stress transcriptomic research, revealing differential expression of genes associated with immune system, membrane transport, and regulation pathways in diverse fish species exposed to varying salinities (X. Chen et al, 2021; Cui et al, 2019; Escobar-Sierra & Lampert, 2023; Guo et al, 2018a; Lee et al, 2020; Su et al, 2020a). Recent studies have also identified differential gene expression in the brain and liver of certain fish species under osmotic stress, emphasizing pathways related to immunity, reproduction, growth, osmoregulation, energy metabolism, oxidative stress, and ion transporters (Lin et al, 2020; Liu et al, 2018; K. Zhou et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Unravelling the molecular mechanisms of fish salinity adaptation in the face of multiple stressors: A comparative multi-tissue transcriptomic study in the Llobregat River, Barcelona, Spain

Escobar-Sierra,

Cañedo-Argüelles,

Vinyoles

et al. 2023

Preprint

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Freshwater salinization poses a growing global environmental concern, introducing complex chemical cocktails and jeopardizing freshwater biodiversity, particularly fish populations. This research aimed to elucidate the molecular foundations of salinity adaptation in a non-native minnow species (Phoxinus septimaniaexP. dragarum) exposed to saline effluents from potash mines in the Llobregat River, Barcelona, Spain. Employing high-throughput mRNA sequencing and differential gene expression analyses, we examined brain, gills, and liver tissues collected from fish at two stations (upstream and downstream of saline effluent discharge). Salinization markedly influenced global gene expression profiles, with the brain exhibiting the most differentially expressed genes, emphasizing its unique sensitivity to salinity fluctuations. Pathway analyses revealed the expected enrichment of ion transport and osmoregulation pathways across all tissues. Furthermore, tissue-specific pathways associated with stress, reproduction, growth, immune responses, methylation, and neurological development were identified in the context of salinization. Rigorous validation of RNA-seq data through quantitative PCR (qPCR) underscored the robustness and consistency of our findings across platforms. This investigation unveils intricate molecular mechanisms steering salinity adaptation in non-native minnows confronting diverse environmental stressors. Advancing our comprehension of genomic responses to salinity changes, our study provides crucial insights into the adaptive strategies of aquatic organisms grappling with freshwater salinization. This comprehensive analysis sheds light on the underlying genetic and physiological mechanisms governing fish adaptation in salinity-stressed environments, offering essential knowledge for the conservation and management of freshwater ecosystems facing escalating salinization pressures.

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“…Simultaneously, we employed KEGG enrichment analyses on the same modules, and the results indicated that proteasome pathway, protein kinases were the significantly enriched pathways (KEGG enrichment.xlsx 47 ). After taking the intersection of hub genes set and DEGs set, 80 genes were defined as candidate salinity-associated hub genes, and six genes (NDUFV1 75 , EMSY 76 , RBBP6 77 , ATF2 78 , Map3k7 79 and PSMC2 80 ) had been certified to be related to salinity stress. For example, RBBP6 was one of the identified candidate genes for freshwater vs. marine adaptation in threespine stickleback 77 .…”

Section: Methodsmentioning

confidence: 99%

Identification of stress-related genes by co-expression network analysis based on the improved turbot genome

Zheng

Meng

et al. 2022

Sci Data

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Turbot (Scophthalmus maximus), commercially important flatfish species, is widely cultivated in Europe and China. With the continuous expansion of the intensive breeding scale, turbot is exposed to various stresses, which greatly impedes the healthy development of turbot industry. Here, we present an improved high-quality chromosome-scale genome assembly of turbot using a combination of PacBio long-read and Illumina short-read sequencing technologies. The genome assembly spans 538.22 Mb comprising 27 contigs with a contig N50 size of 25.76 Mb. Annotation of the genome assembly identified 104.45 Mb repetitive sequences, 22,442 protein-coding genes and 3,345 ncRNAs. Moreover, a total of 345 stress responsive candidate genes were identified by gene co-expression network analysis based on 14 published stress-related RNA-seq datasets consisting of 165 samples. Significantly improved genome assembly and stress-related candidate gene pool will provide valuable resources for further research on turbot functional genome and stress response mechanism, as well as theoretical support for the development of molecular breeding technology for resistant turbot varieties.

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Gill Transcriptome Analysis Revealed the Difference in Gene Expression Between Freshwater and Seawater Acclimated Guppy (Poecilia reticulata)

Cited by 17 publications

References 52 publications

Field application of de novo transcriptomic analysis to evaluate the effects of sublethal freshwater salinization on Gasterosteus aculeatus in urban streams

Field application of de novo transcriptomic analysis to evaluate the effects of sublethal freshwater salinization on Gasterosteus aculeatus in urban streams

Unravelling the molecular mechanisms of fish salinity adaptation in the face of multiple stressors: A comparative multi-tissue transcriptomic study in the Llobregat River, Barcelona, Spain

Identification of stress-related genes by co-expression network analysis based on the improved turbot genome

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