Phenotypic sorting of individual male and female intersex Cherax quadricarinatus and analysis of molecular differences in the gonadal transcriptome

Cherax quadricarinatus exhibit sexual dimorphism, with males outpacing females in size specification and growth rate. However, there is limited understanding of the molecular mechanisms underlying sex determination and sex differentiation in crustaceans. To study the differences between intersex individuals and normal individuals, this study counted the proportion of intersex individuals in the natural population, collected the proportion of 7 different phenotypes in 200 intersex individuals, and observed the differences in tissue sections. RNA-seq was used to study the different changes in the transcriptome of normal and intersex gonads. The results showed that: the percentage of intersex in the natural population was 1.5 %, and the percentage of different types of intersex ranged from 0.5 % to 22.5 %; the sections revealed that the development of normal ovaries was stagnant at the primary oocyte stage when intersex individuals with ovaries were present; We screened for pathways and genes that may be associated with gonadal development and sex, including ovarian steroid synthesis, estrogen signaling pathway, oocyte meiosis, progesterone-mediated oocyte maturation, etc. Relevant genes including tra2a, dmrta2, ccnb2, foxl2, and smad4. This study provides an important molecular basis for sex determination, sex-controlled breeding, and unisex breeding in red crayfish. The Cherax quadricarinatus is one of the world's most valuable freshwater economic shrimps and is sexually dimorphic. In this study, we investigated the percentage of red crayfish intersexed between males and females in natural populations, and screened for genes and pathways that may be associated with sex regulation. These findings complement our understanding of molecular differences in sex determination and gonadal differentiation in intersex individuals of the red crayfish. [Display omitted] •The proportion of intersex individuals in red crayfish is about 1.5 %, with seven different intersex phenotypes.•Ovarian development in intersex individuals with ovaries stalled at the primary oocyte cell stage.•Gonadal transcriptome analyses of red crayfish and intersex individuals screened for sexually differentially expressed genes.•The intersexed individuals functioned more differently from normal females and more closely to normal males.