Different transcriptomic architecture of the gill epithelia in Nile and Mozambique tilapia after salinity challenge

Campo, Aurora; Nitzan, Tali; Slosman, Tatiana; Doron‐Faigenboim, Adi; D'Cotta, Hélèna; Baroiller, Jean‐François; Cnaani, Avner

doi:10.1016/j.cbd.2021.100927

Cited by 5 publications

(2 citation statements)

References 72 publications

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“…Accordingly, excessive ions are secreted by specialised cells in the gill, ionocytes, containing ion pumps and transporters 57,58 . As a result, there are differential gill-specific transcriptional responses to salinity exposure in different tilapia species, triggering turnover of ionocytes as well as immune and cell stress response 59 . We therefore suggest that the interactions of both STAT1- prlr1 and SREBF2- cldnh are likely involved in salinity acclimation along the tilapia phylogeny.…”

Section: Discussionmentioning

confidence: 99%

Chromatin accessibility associated with aquaculture relevant traits in tilapia

Mehta

Man

Ciezarek

et al. 2023

Preprint

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The Nile tilapia (Oreochromis niloticus) accounts for ~9% of global freshwater finfish production however, extreme cold weather and decreasing freshwater resources has created the need to develop resilient strains. By determining the genetic bases of aquaculture relevant traits, we can genotype and breed desirable traits into farmed strains. We developed and optimised ATAC-seq from O. niloticus gill tissues to identify regulatory regions accounting for gene expression associated with gill adaptations. We find that SNPs from 27 tilapia species are enriched in noncoding regions, with 95% of accessible gene promoter regions being SNP-containing. Regulatory variants of TF binding sites are likely driving gene expression differences associated with tilapia gill adaptations, and differentially segregate in freshwater and euryhaline tilapia species. The generation of novel open chromatin data integrated with gene expression and genetic variants revealed candidate genes, genetic relationships, and loci associated with aquaculture relevant traits like salinity and osmotic stress acclimation.

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Section: Discussionmentioning

confidence: 99%

Chromatin accessibility associated with aquaculture relevant traits in tilapia

Mehta

Man

Ciezarek

et al. 2023

Preprint

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“…In light of these mechanisms, the gills exhibited ASE in genes associated with the ribonucleotide binding with and without adenyl group, upon salinity exposure (Supplementary 7). Earlier transcriptomic and proteomic analyses of these data indicated that there is a response in the gills to salinity by differential expression of genes related to epithelial turnover 42,43 . These previous results are consistent with our current analysis where ASE SNPs were associated to DEGs in the gills but not in the kidney (Table 1).…”

Section: Many Different Reasons Can Explain This Variable Expression ...mentioning

confidence: 99%

A pipeline for analysis of allele specific expression reveals salinity-dependent regulation in Nile tilapia

Campo,

Gershoni,

Doron-Faigenboim

et al. 2024

Preprint

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Species living in changing environments require the acclimatization of individual organisms, which may be significantly influenced by allele specific expression (ASE). Data from RNA-seq experiments can be used to identify and quantify the expressed alleles. However, conventional allele matching to the reference genome creates a mapping bias towards the reference allele that prevents a reliable estimation of the allele counts. We developed a pipeline that allows identification and unbiased quantification of the alleles corresponding to an RNA-seq dataset, without any previous knowledge of the haplotype. To achieve the unbiased mapping, we generate two pseudogenomes by substituting the alternative alleles on the reference genome. The SNPs are further called against each pseudogenome, providing two SNP data-sets that are averaged for calculation of the allele depth to be merged in a final SNP calling file. The pipeline presented here can calculate ASE in non-model organisms and can be applied to previous RNA-seq data-sets for expanding studies in gene expression regulation.

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Omics-driven insight into physiological responses of species in aquaculture

Martyniuk

2022

Comparative Biochemistry and Physiology Part D: Genomics and Pr

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Different transcriptomic architecture of the gill epithelia in Nile and Mozambique tilapia after salinity challenge

Cited by 5 publications

References 72 publications

Chromatin accessibility associated with aquaculture relevant traits in tilapia

Chromatin accessibility associated with aquaculture relevant traits in tilapia

A pipeline for analysis of allele specific expression reveals salinity-dependent regulation in Nile tilapia

Omics-driven insight into physiological responses of species in aquaculture

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