The Atlantic salmon whole blood transcriptome and how it relates to major locus maturation genotypes and other tissues

Andrew, Samuel C.; Primmer, Craig R.; Debes, Paul V.; Erkinaro, Jaakko; Verta, Jukka‐Pekka

doi:10.1016/j.margen.2020.100809

Cited by 10 publications

(8 citation statements)

References 18 publications

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Section: Introductionmentioning

confidence: 99%

“…Atlantic salmon ( Salmo salar ), one of the most economically important fish utilized for aquaculture, is a key species in marine and freshwater ecosystems and has a high economic value to ecotourism and fisheries (Andrew et al 2021 ; Wang et al 2019 ). The economic importance of this species as well as other factors have led to it becoming a model species for biological research (Andrew et al 2021 ). Atlantic salmon is by quantity the largest species of salmonids produced worldwide (FAO, 2018 ), and they are mainly farmed in cold waters in Northern Europe, North America, Chile, and Tasmania (Gjessing et al 2020 ), and were introduced into China using recirculating aquaculture system (RAS) in 2010 due to their high nutritional and economic value (Wang et al 2019 ).…”

Section: Introductionmentioning

confidence: 99%

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Comparative Transcriptome Analysis of Spleen Reveals Potential Regulation of Genes and Immune Pathways Following Administration of Aeromonas salmonicida subsp. masoucida Vaccine in Atlantic Salmon (Salmo salar)

Zhang

et al. 2022

Mar Biotechnol

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Aeromonas salmonicida is a global fish pathogen. Aeromonas salmonicida subsp. masoucida (ASM) is classified as atypical A. salmonicida and caused huge losses to salmonid industry in China. Hence, it is of great significance to develop ASM vaccine and explore its protection mechanism in salmonids. In this regard, we conducted RNA-seq analysis with spleen tissue of Atlantic salmon after ASM vaccination to reveal genes, their expression patterns, and pathways involved in immune protections. In our results, a total of 441.63 million clean reads were obtained, and 389.37 million reads were mapped onto the Atlantic salmon reference genome. In addition, 1125, 2126, 1098, 820, and 1351 genes were significantly up-regulated, and 747, 2626, 818, 254, and 908 genes were significantly down-regulated post-ASM vaccination at 12 h, 24 h, 1 month, 2 months, and 3 months, respectively. Subsequent pathway analysis revealed that many differentially expressed genes (DEGs) following ASM vaccination were involved in cytokine-cytokine receptor interaction ( TNFRSF11b , IL-17RA , CCR9 , and CXCL11 ), HTLV-I infection ( MR1 and HTLV-1 ), MAPK signaling pathway ( MAPK , IL8 , and TNF-α-1 ), PI3K-Akt signaling pathway ( PIK3R3 , THBS4 , and COL2A1 ), and TNF signaling pathway ( PTGS2 , TNFRSF21-l , and CXCL10 ). Finally, the results of qRT-PCR showed a significant correlation with RNA-seq results, suggesting the reliability of RNA-seq for gene expression analysis. This study provided insights into regulation of gene expression and their involved pathways in Atlantic salmon spleen in responses to vaccine, and set the foundation for further study on the vaccine protective mechanism in Atlantic salmon as well as other teleost species. Supplementary Information The online version contains supplementary material available at 10.1007/s10126-021-10089-6.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Comparative Transcriptome Analysis of Spleen Reveals Potential Regulation of Genes and Immune Pathways Following Administration of Aeromonas salmonicida subsp. masoucida Vaccine in Atlantic Salmon (Salmo salar)

Zhang

et al. 2022

Mar Biotechnol

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“…Dicentrarchus labrax (Magnanou et al 2014), and Salmo salar (Glencross et al 2015;Andrew et al 2021). De novo transcriptome assembly can be used in several different contexts, like genomics/gene expression analyses and may be applied in many key areas of study, such as conservation genetics, selective breeding, reproductive biology, and nutrition (Leaver et al 2008;Calduch-Giner et al 2013;Fox et al 2014).…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic Profiling and Microsatellite Identification in Cobia (Rachycentron canadum), Using High-Throughput RNA Sequencing

et al. 2021

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Cobia (Rachycentron canadum) is a marine teleost species with great productive potential worldwide. However, the genomic information currently available for this species in public databases is limited. Such lack of information hinders gene expression assessments that might bring forward novel insights into the physiology, ecology, evolution, and genetics of this potential aquaculture species. In this study, we report the first de novo transcriptome assembly of R. canadum liver, improving the availability of novel gene sequences for this species. Illumina sequencing of liver transcripts generated 1,761,965,794 raw reads, which were filtered into 1,652,319,304 high-quality reads. De novo assembly resulted in 101,789 unigenes and 163,096 isoforms, with an average length of 950.61 and 1,617.34 nt, respectively. Moreover, we found that 126,013 of these transcripts bear potentially coding sequences, and 125,993 of these elements (77.3%) correspond to functionally annotated genes found in six different databases. We also identified 701 putative ncRNA and 35,414 putative lncRNA. Interestingly, homologues for 410 of these putative lncRNAs have already been observed in previous analyses with Danio rerio, Lates calcarifer, Seriola lalandi dorsalis, Seriola dumerili, or Echeneis naucrates. Finally, we identified 7894 microsatellites related to cobia's putative lncRNAs. Thus, the information derived from the transcriptome assembly described herein will likely assist future nutrigenomics and breeding programs involving this important fish farming species.

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“…Recent advances in DNA sequencing technologies and computational resources have made it possible to study the functional content of the genome in a way that was previously impossible. Massively parallel sequencing of the transcriptome from different tissue types has been used to address the biological questions of species from diverse terrestrial and marine environments [ 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 ].…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic Diversity in the Livers of South African Sardines Participating in the Annual Sardine Run

Emami‐Khoyi

Roux

Adair

et al. 2021

Genes

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During austral winter, the southern and eastern coastlines of South Africa witness one of the largest animal migrations on the planet, the KwaZulu-Natal sardine run. Hundreds of millions of temperate sardines, Sardinops sagax, form large shoals that migrate north-east towards the subtropical Indian Ocean. Recent studies have highlighted the role that genetic and environmental factors play in sardine run formation. In the present study, we used massively parallel sequencing to assemble and annotate the first reference transcriptome from the liver cells of South African sardines, and to investigate the functional content and transcriptomic diversity. A total of 1,310,530 transcripts with an N50 of 1578 bp were assembled de novo. Several genes and core biochemical pathways that modulate energy production, energy storage, digestion, secretory processes, immune responses, signaling, regulatory processes, and detoxification were identified. The functional content of the liver transcriptome from six individuals that participated in the 2019 sardine run demonstrated heterogeneous levels of variation. Data presented in the current study provide new insights into the complex function of the liver transcriptome in South African sardines.

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The Atlantic salmon whole blood transcriptome and how it relates to major locus maturation genotypes and other tissues

Cited by 10 publications

References 18 publications

Comparative Transcriptome Analysis of Spleen Reveals Potential Regulation of Genes and Immune Pathways Following Administration of Aeromonas salmonicida subsp. masoucida Vaccine in Atlantic Salmon (Salmo salar)

Comparative Transcriptome Analysis of Spleen Reveals Potential Regulation of Genes and Immune Pathways Following Administration of Aeromonas salmonicida subsp. masoucida Vaccine in Atlantic Salmon (Salmo salar)

Transcriptomic Profiling and Microsatellite Identification in Cobia (Rachycentron canadum), Using High-Throughput RNA Sequencing

Transcriptomic Diversity in the Livers of South African Sardines Participating in the Annual Sardine Run

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