Transcriptomic analysis to elucidate the effects of high stocking density on grass carp (Ctenopharyngodon idella)

Yan He,Yubang Shen,Qingjing Zhang,Anqi Wang,Jiale Li,Hongyan Yu,Honggang Zhao,Xiaoyan Xu,Hua Zhu

doi:10.1186/s12864-021-07924-4

Abstract

BackgroundGrass carp (Ctenopharyngodon idella) is one of the most widely cultivated fishes in China. High stocking density can reportedly affect fish growth and immunity. Herein we performed PacBio long-read single-molecule real-time (SMRT) sequencing and Illumina RNA sequencing to evaluate the effects of high stocking density on grass carp transcriptome.ResultsSMRT sequencing led to the identification of 33,773 genes (14,946 known and 18,827 new genes). From the structure analysis, 8,009 genes were detected with alternative splicing events, 10,219 genes showed alternative polyadenylation sites and 15,521 long noncoding RNAs. Further, 1,235, 962, and 213 differentially expressed genes (DEGs) were identified in the intestine, muscle, and brain tissues, respectively. We performed functional enrichment analyses of DEGs, and they were identified to be significantly enriched in nutrient metabolism and immune function. The expression levels of several genes encoding apolipoproteins and activities of enzymes involved in carbohydrate enzymolysis were found to be upregulated in the high stocking density group, indicating that lipid metabolism and carbohydrate decomposition were accelerated. Besides, four isoforms of grass carp major histocompatibility complex class II antigen alpha and beta chains in the aforementioned three tissue was showed at least a 4-fold decrease.ConclusionsThe results suggesting that fish farmed at high stocking densities face issues associated with the metabolism and immune system. To conclude, our results emphasize the importance of maintaining reasonable density in grass carp aquaculture.

Highlights

Grass carp (Ctenopharyngodon idella) is a fish species with the largest reported production (> 6 million tons per year) in aquaculture globally [1]
It plays a key role in translation efficiency, stability, and localization of mRNA and alters protein-coding sequences [9]. long noncoding RNAs (lncRNAs) can participate in a variety of biological functions, including cis or trans transcription regulation, nuclear domain organization, and protein or RNA molecule regulation [10]
2,495 fusion genes were identified in the PacBio library and were validated using transcriptome datasets (Table S1)

Summary

Introduction

Grass carp (Ctenopharyngodon idella) is a fish species with the largest reported production (> 6 million tons per year) in aquaculture globally [1]. To maximize the efficiency of aquaculture systems, He et al BMC Genomics (2021) 22:620 associated with alterations in fish behavior, metabolism, and immune function [5]. The combination of long- and short-read sequencing has been applied to detect low-expression isoforms and elucidate functional gene dynamics [6]. PacBio SMRT sequencing can provide information on transcript diversity, including alternative splicing (AS), alternative polyadenylation (APA), and long noncoding RNAs (lncRNAs) [7]. APA acts in association with AS to regulate gene expression. It plays a key role in translation efficiency, stability, and localization of mRNA and alters protein-coding sequences [9]. We performed PacBio long-read singlemolecule real-time (SMRT) sequencing and Illumina RNA sequencing to evaluate the effects of high stocking density on grass carp transcriptome

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