RNA sequencing and LncRNA identification in muscle of the Pacific white shrimp Litopenaeus vannamei at different growth rates

As a typical crustacean species, the growth of the Pacific white shrimp Litopenaeus vannamei has important economic and scientific value. Muscle growth in L. vannamei is regulated by a complex network of transcriptional and post-transcriptional processes. Although many genes have been found to be involved in shrimp muscle growth, their regulatory mechanisms remain largely unexplored. In this study, we compared gene expression differences in L. vannamei muscle with different growth rates, and identified a total of 2419 differentially expressed genes (DEGs). These DEGs were found to be associated with muscle growth, molting, epidermal structure, and immune and stress response. Furthermore, we discovered 9673 candidate lncRNAs in muscle, which showed distinct transcript characteristics compared to mRNAs. Among these, 1324 differentially expressed lncRNAs may affect muscle growth by regulating gene expression in cis- or trans-mode at the transcriptional level. For example, the lncRNA MSTRG.15718.1 was found to potentially affect muscle growth by regulating nearby genes. Our analyses enabled the discovery of novel genes and lncRNA regulatory networks that affect shrimp growth. These results not only provide new insights into the mechanism of shrimp muscle growth but also offer valuable clues for molecular breeding of shrimp growth traits.