RNA-seq analysis of compensatory growth in the skeletal muscle of fine flounder (Paralichthys adspersus)

Abstract

The fine flounder (Paralichthys adspersus) is a highly quoted flatfish species in the international and Chilean aquaculture markets. Despite presenting extraordinary nutritional value and quality white flesh, P. adspersus farming is limited by slow growth rates. This limitation can be offset with fast-refeed protocols, which result in a phenomenon termed compensatory growth. The aim of the present study was to assess the responses of the P. adspersus skeletal muscle transcriptome to a compensatory growth trial. Skeletal muscle sequence reads were obtained using Illumina Mi-Seq RNA technology for fine flounder under Control, Fasting, and Refeeding conditions. A total of 48,020,133 paired-ends reads were generated. Quality-controlled reads were de novo assembled, resulting in a reference transcriptome of 75,037 transcripts with an N50 of 2033 base pairs and average read coverage of 48X. Reads mapped onto the assembled reference transcriptome revealed 109 and 177 differentially expressed transcripts under the Fasting and Refeeding conditions, respectively. The up-regulated transcripts under Fasting were related to organic substance catabolic process, whereas down-regulated transcripts were associated with organic substance biosynthetic process. For Refeeding, significant up-and down-regulations were respectively recorded for mitotic nuclear division and muscle system processes. These results were validated by real-time qPCR analysis of 16 candidate transcripts. The obtained dataset will serve as an important transcriptomic resource for the fine flounder, with this study providing the first global gene expression analysis of a flatfish during compensatory growth.

The fine flounder (Paralichthys adspersus) is a highly quoted flatfish species in the international and Chilean aquaculture markets. Despite presenting extraordinary nutritional value and quality white flesh, P. adspersus farming is limited by slow growth rates. This limitation can be offset with fast-refeed protocols, which result in a phenomenon termed compensatory growth. The aim of the present study was to assess the responses of the P. adspersus skeletal muscle transcriptome to a compensatory growth trial. Skeletal muscle sequence reads were obtained using Illumina Mi-Seq RNA technology for fine flounder under Control, Fasting, and Refeeding conditions. A total of 48,020,133 paired-ends reads were generated. Quality-controlled reads were de novo assembled, resulting in a reference transcriptome of 75,037 transcripts with an N50 of 2033 base pairs and average read coverage of 48X. Reads mapped onto the assembled reference transcriptome revealed 109 and 177 differentially expressed transcripts under the Fasting and Refeeding conditions, respectively. The up-regulated transcripts under Fasting were related to organic substance catabolic process, whereas down-regulated transcripts were associated with organic substance biosynthetic process. For Refeeding, significant up-and down-regulations were respectively recorded for mitotic nuclear division and muscle system processes. These results were validated by real-time qPCR analysis of 16 candidate transcripts. The obtained dataset will serve as an important transcriptomic resource for the fine flounder, with this study providing the first global gene expression analysis of a flatfish during compensatory growth.