Identification and comparative analysis of the ovary and testis microRNAome of mud crab Scylla paramamosain

Abstract

The role of microRNA (miRNA) in reproductive regulation is attracting increasingly more attention. In this study, we obtained 9,643,114 and 15,498,999 raw reads from the ovary and testis library of important farmed mud crab Scylla paramamosain, respectively. After data mining, a total of 4,096,464 and 11,737,973 mappable small RNA sequences remained for analysis. By mapping to the reference genome and expressed sequence tag (EST) of Daphnia pulex and other crabs, a total of 1,417 miRNAs were identified. On the basis of 1,417 miRNAs, 514 (36.3%) unique miRNAs coexpressed in the gonad of female and male libraries, and 336 (23.7%) and 567 (40%) expressed preferentially in female and male libraries, respectively. Analysis of library sequencing data resulted in the identification of 108 miRNAs (out of 1,417; 7.6%) that showed significant differential expression between the two samples. Of these, 13 miRNAs were expressed only in the testis, two miRNAs were expressed only in the ovary, and 93 miRNAs were coexpressed: 57 (61.3%) were upregulated (ovary/testis) and 36 (38.7%) were downregulated (ovary/testis). To confirm the expression patterns of the predicted miRNAs, we randomly selected 14 candidate miRNAs from 108 differentially expressed miRNAs and performed stem-loop real time quantitative PCR (RT-qPCR) assays in five ovary developing stages. Five miRNAs showed similar expression patterns in almost every stage as those revealed by identification of differentially expressed genes (IDEG6) analysis. The above five miRNAs were predicted to match the 3'-untranslated region of the published S. paramamosain gene. Four out of five miRNA had a regulation effect on many genes, especially the genes related to gonadal development.

miR‐34 regulates reproduction by inhibiting the expression of MIH, CHH, EcR, and FAMeT genes in mud crab Scylla paramamosain

“…Liu, Wu, and Hua () proved that miR‐34c performed some particular functions during the development of mammalian germ cells. Moreover, our miRNA transcriptome data and qRT‐PCR results confirmed that miR‐34 was differentially expressed between ovary and testis (Jia et al, ). In this study, the target genes of miR‐34 that are related to the gonadal development were predicted and validated in eyestalk.…”

“…Even in invertebrates, miRNAs are required for oocyte maturation and ovulation because worms are sterile and fail to ovulate with reduced miRNA biogenesis due to loss of Drosha or Pasha/DGCR8 activity (Kadener et al, ). MiR‐9, miR‐9c, miR‐263a, and miR263b may have effects on many genes in mud crab, especially the genes related to gonadal development (Jia et al, ). All of these research works suggest that miRNAs are involved in the regulation of reproduction, especially in gonadal development.…”

Identification and Comparison of microRNAs in the Gonad of the Yellowfin Seabream (Acanthopagrus Latus)

“…Additionally, some miRNAs, including miR-34c-5p, miR-153-5p, and miR-749, were expressed exclusively in Nile tilapia XX gonads at five days post-hatching, whereas miR-1306-5p, miR-132b, and miR-18c were expressed exclusively in the XY gonads [ 21 ]. MiRNA expression patterns have also been studied in the gonads of Oplegnathus punctatus [ 22 ], Scylla paramamosain [ 23 , 24 ], Acipenser schrenckii [ 25 ], Trachinotus ovatus [ 26 ], and Odontobutis potamophila [ 27 ]. These studies help to clarify the roles of miRNAs in sexual differentiation and gonadal development.…”

Identification and profiling of microRNAs responsive to cadmium toxicity in hepatopancreas of the freshwater crab Sinopotamon henanense

“…With the developments of high-throughput sequencing technologies, a large number of miRNA transcriptome profiles have been obtained and characterized in various crustaceans, such as P. trituberculatus [21, 22, 27], E. sinensis [20, 23, 25], and S. paramamosain [24, 26, 28, 29]. Furthermore, miRNAs have been demonstrated to be vital for regulating gene expression and several biological functions, such as growth regulation [21], metabolism processes [22], and responses to viral infection [24].…”