Transcriptome-seq provides insights into sex-preference pattern of gene expression between testis and ovary of the crucifix crab (Charybdis feriatus)

Abstract

The crucifix crab, Charybdis feriatus, which mainly inhabits Indo-Pacific region, is regarded as one of the most high-potential species for domestication and incorporation into the aquaculture sector. However, the regulatory mechanisms of sex determination and differentiation of this species remain unclear. To identify candidate genes involved in sex determination and differentiation, high throughput sequencing of transcriptome from the testis and ovary of C. feriatus was performed by the Illumina platform. After removing adaptor primers, low-quality sequences and very short (<50 nt) reads, we obtained 80.9 million and 66.2 million clean reads from testis and ovary, respectively. A total of 86,433 unigenes were assembled, and ~43% (37,500 unigenes) were successfully annotated to the NR, NT, Swiss-Prot, KEGG, COG, GO databases. By comparing the testis and ovary libraries, we obtained 27,636 differentially expressed genes. Some candidate genes involved in the sex determination and differentiation of C. feriatus were identified, such as vasa, pgds, vgr, hsp90, dsx-f, fem-1, and gpr. In addition, 88,608 simple sequence repeats were obtained, and 61,929 and 77,473 single nucleotide polymorphisms from testis and ovary were detected, respectively. The transcriptome profiling was validated by quantitative real-time PCR in 30 selected genes, which showed a good consistency. The present study is the first high-throughput transcriptome sequencing of C. feriatus. These findings will be useful for future functional analysis of sex-associated genes and molecular marker-assisted selections in C. feriatus.

Transcriptome Analysis of Male and Female Mature Gonads of Silver Sillago (Sillago sihama)

“…The total number of unigenes looks much higher than commonly imagined, which might be due to the high heterozygosity and high repetition rate of the genome of Sillaginidae fishes [22]. Using the same assembly method, large numbers of unigenes were also found in crab [7] and shrimp [23], species whose genomes also have high heterozygosity and high repetition rates. The sequence length distribution of the unigenes ranged from 201 bp to 20,589 bp, with a mean length of 1,004 bp (Table 2).…”

“…The MAPK signaling pathway plays an important role in the regulation of gonadotropin subunit gene expression and the transition of primary spermatocytes across the blood-testis barrier [52]. In the crucifix crab, the MAPK signaling pathway was identified as one of the enriched pathways related to the reproduction [7]. In fish, the GnRH signaling pathway plays an essential role in regulating the production of and activating signal transduction cascades that ultimately modulate gonadotropin biosynthesis [45].…”

“…Transcriptome sequencing provides a general representation of the genes that are expressed in specific tissues or organs [7] and has been widely applied to identifying sex-related genes and associated regulatory mechanisms, due to its advantages of high throughput and low cost. A set of sex-related genes or pathways has been identified by gonad transcriptomes in numerous aquaculture species, including the spotted knifejaw [6], Japanese scallop [8], olive flounder [9] and channel catfish [10].…”

Comparative transcriptome analysis of the ovary and testis of the lacustrine goby (Gobiopterus lacustris)

“…The N50 length is an important parameter for evaluating assembly quality, and the N50 length of our assembly (3082 bp) was higher than most published transcriptomes of aquatic animals, including Paralichthys olivaceus (809 bp) [9], Patinopecten yessonsis (565 bp) [31], Larimichthys crocea (1,934 bp) [32], Oratosquilla oratoria (1,502 bp) [33], Andrias davidianus (1,557 bp) [17] and Sillago sihama (2,190 bp) [14]. The annotation rate (76.53％ of 62,573) of G. lacustris gonad transcriptomes was higher than the gonad transcriptomes of C. feriatus (37,500, 43.4% of 86,433) [34], S. sihama (34,104 of 74,038) [14] and O. oratoria (19,404 of 37,906) [33]. However, 14,682 (23.47% of 62,573) unigenes did not have any BLAST hits.…”

Integrated mRNA and miRNA expression profile analyses reveal the potential roles of sex‐biased miRNA–mRNA pairs in gonad tissues of the Chinese concave‐eared torrent frog (Odorrana tormota)

“…Transcriptomics has also helped researchers to explore the molecular mechanisms underlying reproduction and sex differentiation. A set of differentially expressed genes were documented in the gonadal tissue of fish and other lower animals, such as Portunus trituberculatus (Wang et al, ), Oncorhynchus mykiss (Salem, Rexroad, Wang, Thorgaard, & Yao, ), Oreochromis niloticus (Tao et al, ), Pelteobagrus fulvidraco (Chen et al, ), Scophthalmus maximus (Ribas et al, ), Charybdis feriatus (Zhang et al, ), Bufo viridis (Gerchen et al, ), Paralichthys olivaceus (Zhang et al, ), and Pinctada margaritifera (Teaniniuraitemoana et al, ).…”