The giant river prawn Macrobrachium rosenbergii is an important aquaculture prawn, showing sexual dimorphism in growth, with males growing much faster than females. However, the mechanisms controlling these complex traits are not yet well understood. The nervous system plays an important role in regulating life functions. This study aimed to obtain and characterize the full-length transcriptomes of brain and ganglion in female and male prawns by PacBio RNA sequencing. Based on the result of PacBio sequencing, transcript’s functional annotation, transcript factors, and simple sequence repeat analysis, long non-coding RNAs (LncRNAs) and transposable element predictions were accomplished. Total 159.1-Gb subreads were obtained and average length was 2,175 bp, with 93.2% completeness. After clustering and polishing, 84,627 high quality unigene sequences were produced and annotated by functional databases. 6,367 transcript factors and 6,287 LncRNAs were predicted. Illumina sequencing of brains and ganglia extracted from female and male prawns was carried out. A significant number of differentially expressed genes (DEGs) were found and confirmed by qRT-PCR analysis. Of the related 435 genes in protein processing pathways in the endoplasmic reticula, compared to females, 42 DEGs were detected, and 21/26 DEGs with up-regulated expression in male prawn brain/ganglion. DEGs in this pathway are likely to be regulated by multiple LncRNAs in polypeptide folding and misfolded protein degradation in the different organs and sexes of the prawn. Our study lays a foundation for understanding the growth dimorphism controlled by nervous system, and is a valuable resource for sex-controlled breeding of prawns in the future.

Hook snout carp Opsariichthys bidens is an important farmed fish in East Asia that shows sexual dimorphism in growth, with males growing faster and larger than females. To understand these complex traits and improve molecular breeding, chromosome-level genome assembly of male O. bidens was performed using Illumina, Nanopore, and Hi-C sequencing. The 992.9 Mb genome sequences with a contig N50 of 5.2 Mb were anchored to 38 chromosomes corresponding to male karyotypes. Of 30,922 functionally annotated genes, 97.5% of BUSCO genes were completely detected. Genome evolution analysis showed that the expanded and contracted gene families in male o.bedins genome were enriched in 76 KEGG pathways, and 78 expanded genes were involved in the GnRH signaling pathway that regulates the synthesis and secretion of luteinizing hormone and glycoprotein hormones, further acting on male growth by inducing growth hormone. Compared to the released female O. bidens genome, the number of annotated genes in males was much higher than in females (23,992). The male chromosome LG06 exhibited over 97% of identity with the female’s GH14/GH38. Male-specific genes were identified for LG06, where structural variety, including deletions and insertions, occurred at a lower rate, suggesting a centric fusion of acrocentric chromosomes GH14 and GH38. The genome-synteny analysis uncovered significant inter-chromosome conservation between male O. bidens and grass carp, and the former originating from ancestral chromosome breakage to increase the chromosome number. Our results provide a valuable genetic resource for studying the regulation of sexual dimorphism, sex-determining mechanisms and molecular-guided breeding of O. bidens.