Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar)

نویسندگان

چکیده

Abstract Background The flesh pigmentation of farmed Atlantic salmon is formed by accumulation carotenoids derived from commercial diets. In the gastrointestinal system, hindgut considered critical in processes uptake and metabolism. Tasmania, color depletion can noticeably affect at different levels severity following extremely hot summers. this study, RNA sequencing (RNA-Seq) was performed to investigate reduction pigmentation. Library preparation a key step that significantly impacts effectiveness experiments. Besides commonly used whole transcript RNA-Seq method, 3’ mRNA-Seq method being applied widely, owing its reduced cost, enabling more repeats be sequenced expense lower resolution. Therefore, output Illumina TruSeq kit (whole RNA-Seq) Lexogen QuantSeq (3’ mRNA-Seq) analyzed identify genes are differentially expressed (DEGs) between two phenotypes. Results both methods, DEGs phenotypes were associated with metal ion transport, oxidation-reduction processes, immune responses. We also found related lipid metabolism method. missense mutation detected traits. number libraries much higher than QuantSeq; however, trend library methods similar validated qPCR. Conclusions Flesh coloration which apolipoproteins, serum albumin fatty acid-binding protein hypothesized linked absorption, transport deposition carotenoids. Our findings suggest Grp could inhibit feeding behavior low color-banded fish, resulting dietary carotenoid shortage. Several SNPs involving carotenoid-binding cholesterol oxidative stress Regarding choice selection criteria depend on research design purpose. ideal for targeted identification highly genes, while recommended unknown splice variants trait-associated SNPs, as we have duox2 duoxa1 .

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ژورنال

عنوان ژورنال: BMC Genomics

سال: 2021

ISSN: ['1471-2164']

DOI: https://doi.org/10.1186/s12864-021-07884-9