Integrated application of Iso-seq and RNA-seq provides insights into unsynchronized growth in red swamp crayfish (Procambarus clarkii)

Abstract

Red swamp crayfish is one of the most important freshwater shrimps with high economic value in China. The crayfish shows obvious sexual dimorphism in growth and secondary sex characteristics, however, the mechanisms underlying the growth of muscle tissue in the crayfish still remain unclear. Both high-throughput RNA-Seq and Iso-seq strategies were applied to reveal the molecular basis of the growth difference between fast-growing and slow-growing crayfish. After splicing and assembling, 63,350 genes with an average length of 2151 bp and N50 of 2568 bp were obtained. A total of 122 growth-related differentially expressed genes (DEGs) were identified, of which 87 genes were significantly up-regulated and 35 were down-regulated. Using quantitative PCR it was confirmed that the expressions of tps, inpp5l, flna, flnc, tpnc3 and other genes was higher in the fast-growing individuals. Subsequently, 144 genes differentially expressed between males and females were identified. 130 of them, 84 up-regulated and 46 down-regulated, were identified in the fast-growing group, while only 14 genes, 3 up-regulated and 11 down-regulated, were identified in the slow-growing group. The KEGG pathway enrichment analysis indicated that the identified DEGs were mainly involved in metabolic pathways, including arachidonic acid metabolism, glutathione metabolism, alanine, aspartate and glutamate metabolism. This study provides a basis for understanding the molecular mechanism of the sexual growth dimorphism and its application for future genetic breeding in red swamp crayfish.