Transcriptome analysis reveals the effects of sand substrate removal and body colour change of kuruma shrimp,Marsupenaeus japonicus

Kuruma shrimp,Marsupenaeus japonicus,is an important economic species widely cultured in the world. Kuruma shrimp usually are cultured in the ponds with sand substrates, which could cause multiple pollutions to the environment. In this study, we investigated a new kuruma shrimp culture pattern by removing the sand substrates at the pond bottom and replacing with plastic membranes. The result showed that kuruma shrimp survived in the pond without sand substrates. The body colour of adult kuruma shrimp in the experimental group was dark blue, obviously different from the brown body colour in shrimps cultured under normal conditions. A comprehensive study of gene profiling by transcriptome analysis provided a new perspective to understand the impact of removing sand substrates on kuruma shrimp. A total of 60,780 genes were obtained in the transcriptome sequencing. 1,005 DEGs were identified in gills with 427 genes were up-regulated and 578 genes were down-regulated. Meanwhile, only 115 DEGs were identified in hepatopancreas with 41 genes were up-regulated and 74 genes were down-regulated. Multiple essential genes were inhibited, such as actin. The expression levels of crustacyanin subunit A and C were significantly higher in the shrimp cultured without sand substrates than that shrimp cultured in normal conditions. The body colour change may be a self-protection strategy for kuruma shrimp to deal with environmental challenges.