Comparative transcriptome analysis of Nile tilapia (Oreochromis niloticus) in response to alkalinity stress

Zhao, Yan; Wang, J; Thammaratsuntorn, J. Jeerawat; Jw, Wu; Jh, Wei; Wang, Y; Jw, Xu; Jl, Zhao

doi:10.4238/2015.december.22.16

Cited by 25 publications

(14 citation statements)

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“…In tilapia, much attention has been paid to stress responses. The gene expression changes in response to different stressors including cold stress [ 35 ], alkalinity stress [ 36 ], salinity adaptation [ 37 ], hypoxia stress [ 31 , 32 , 38 ] have been investigated by RNA-seq. The QTL intervals for hypoxia and salt tolerance traits were mapped recently [ 39 , 40 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification and differentially expression analysis of lncRNAs in tilapia

Jiang

Meng

et al. 2018

BMC Genomics

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BackgroundLong noncoding RNAs (LncRNAs) play important roles in fundamental biological processes. However, knowledge about the genome-wide distribution and stress-related expression of lncRNAs in tilapia is still limited.ResultsGenome-wide identification of lncRNAs in the tilapia genome was carried out in this study using bioinformatics tools. 103 RNAseq datasets that generated in our laboratory or collected from NCBI database were analyzed. In total, 72,276 high-confidence lncRNAs were identified. The averaged positive correlation coefficient (r_mean = 0.286) between overlapped lncRNA and mRNA pairs showed significant differences with the values for all lncRNA-mRNA pairs (r_mean = 0.176, z statistics = − 2.45, p value = 0.00071) and mRNA-mRNA pairs (r_mean = 0.186, z statistics = − 2.23, p value = 0.0129). Weighted correlation network analysis of the lncRNA and mRNA datasets from 12 tissues identified 21 modules and many interesting mRNA genes that clustered with lncRNAs. Overrepresentation test indicated that these mRNAs enriched in many biological processes, such as meiosis (p = 0.00164), DNA replication (p = 0.00246), metabolic process (p = 0.000838) and in molecular function, e.g., helicase activity (p = 0.000102) and catalytic activity (p = 0.0000612). Differential expression (DE) analysis identified 99 stress-related lncRNA genes and 1955 tissue-specific DE lncRNA genes. MiRNA-lncRNA interaction analysis detected 72,267 lncRNAs containing motifs with sequence complementary to 458 miRNAs.ConclusionsThis study provides an invaluable resource for further studies on molecular bases of lncRNAs in tilapia genomes. Further function analysis of the lncRNAs will help to elucidate their roles in regulating stress-related adaptation in tilapia.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5115-x) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Genome-wide identification and differentially expression analysis of lncRNAs in tilapia

Jiang

Meng

et al. 2018

BMC Genomics

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“…Comparative transcriptomic analyses have also been performed between zebrafish, blue tilapia and Nile tilapia, suggesting positive selection of immune-related genes, such as notch2 and nfatc3b, in tilapia species (Xiao et al, 2015). The transcriptomic response of tilapia has also been evaluated against different abiotic stressors and stimulus including alkalinity (Zhao et al, 2015), hypoxia , salinity (Xu et al, 2015), different concentrations of resveratrol in diet (Zheng et al, 2018) and dietary protein to starch ratio (Xiong et al, 2014).…”

Section: Rna-seqmentioning

confidence: 99%

Genomics to accelerate genetic improvement in tilapia

2020

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Summary Selective breeding of tilapia populations started in the early 1990s and over the past three decades tilapia has become one of the most important farmed freshwater species, being produced in more than 125 countries around the globe. Although genome assemblies have been available since 2011, most of the tilapia industry still depends on classical selection techniques using mass spawning or pedigree information to select for growth traits with reported genetic gains of up to 20% per generation. The involvement of international breeding companies and research institutions has resulted in the rapid development and application of genomic resources in the last few years. GWAS and genomic selection are expected to contribute to uncovering the genetic variants involved in economically relevant traits and increasing the genetic gain in selective breeding programs, respectively. Developments over the next few years will probably focus on achieving a deep understanding of genetic architecture of complex traits, as well as accelerating genetic progress in the selection for growth‐, quality‐ and robustness‐related traits. Novel phenotyping technologies (i.e. phenomics), lower‐cost whole‐genome sequencing approaches, functional genomics and gene editing tools will be crucial in future developments for the improvement of tilapia aquaculture.

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“…Transcriptome profiling of Tilapia was also carried out in response to alkalinity stress (Zhao et al . ), and also the molecular pathways of genes were analysed in association with salinity adaptation (Xu et al . ).…”

Section: Current Status Of Transcriptomics In Aquaculturementioning

confidence: 99%

Transcriptomics in aquaculture: current status and applications

Chandhini

Kumar

2018

Reviews in Aquaculture

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Transcriptomics is the analysis of total RNA transcript in a cell, which gives a broad idea of cellular processes that are active and dormant. Recent advancement in next-generation sequencing technologies like high-throughput mRNA sequencing (RNA-seq) facilitates in deciphering the functional complexity of the whole transcriptome of an organism. In the recent past, transcriptome profiling has been widely used in aquaculture for effective identification and expression analysis of candidate genes involved in growth, reproduction, development, immunity, disease, stress and toxicology. On the paucity of a comprehensive genome sequence, transcriptomics enables the detection of molecular markers such as simple sequence repeats and single-nucleotide polymorphism associated with the trait of interest. This review summarizes the process of transcriptome analysis and the current state of transcriptomics in aquaculture related to diseases and immunity, reproduction and development, growth and nutrition, toxicology and stress. Further, this review highlights the application of transcriptomics, including generation of genetic resources, differential gene expression, analysis of molecular pathways and development of molecular markers.

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Comparative transcriptome analysis of Nile tilapia (Oreochromis niloticus) in response to alkalinity stress

Cited by 25 publications

References 36 publications

Genome-wide identification and differentially expression analysis of lncRNAs in tilapia

Genome-wide identification and differentially expression analysis of lncRNAs in tilapia

Genomics to accelerate genetic improvement in tilapia

Transcriptomics in aquaculture: current status and applications

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