Searching And Identifying Pigmentation Genes From Neocaridina Denticulata Sinensis

Neocaridina denticulata sinensis is widely distributed in Asian freshwater waters.Because of its rich and varied body color,since 2003 this species has become an important ornamental shrimp.However,the pigmentation molecular genetics of N.denticulata sinensis is almost not reported.The genetic traits of red,yellow and transparent strains are very stable.In this study,many pigmentation genes were gotten by comparingthe skins transcriptomes of the three strains.The expression levels of candidate genes were detected by qPCR in red,yellow,transparent and glass strains.The main conclusion as follows:1.There were 268,629,208 clean reads from skin transcriptomes.Then,these clean reads were assembled into 45,434 unigenes with mean length of 837 bp and N50 length of 1,551 bp by TRINITY.19,992 unigenes were annotationed by aligned with the NR,Swiss-Prot,KEGG,COQ database2.14,915 unigenes with significantly different expressions were found by comparing three strains skin transcriptomes.Ribosomal protein genes,actin,calmodulin,EF1? and AK may play roles in the cytological process of pigment migration and chromatophore maintenance.The two cytological process may result in the different pigmentation of the three strains.The genes of guanine synthesis pathway had high level expressions,which suggested the red pigment of N.denticulata sinensis was mainly pteridine.There was no any high expressing pigment synthesis pathway in yellow strain.The result suggested the yellow pigment of N.denticulata sinensis was closely to carotenoid.3.Numerious color genes associated with multiple pathways including melanin,ommochrome and pteridines pathways were identified.The expression patterns of 25 candidate genes were gotten by qPCR in red,yellow,transparent and glass strains.The qPCR results in red,yellow and transparent were consistent with the level of RPKM values in the transcriptomes.4.The results of in situ hybridization showed that ebony,GCH-I,SPR and XDH genes were expressed in the zoea larva and post larvae.The four genes of N.denticulata sinensis may play similar roles with their homologous genes of insects.The above results will advance our knowledge of skin color varieties in N.denticulata sinensis and help the genetic selection of crustaceans with consumer-favored colors.Futhermore,it can also provide some candidate pigmentation genes to investigate the correlation between coloration and sympatric speciation in crustaceans.