De novo transcriptome assembly of four organs of Collichthys lucidus and identification of genes involved in sex determination and reproduction

Abstract

The spinyhead croaker (Collichthys lucidus) is a commercially important fish species, which is mainly distributed in the coastal regions of China. However, little is known about the molecular regulatory mechanism underlying reproduction in C. lucidus. A de novo transcriptome assembly in brain, liver, ovary and testis tissues of C. lucidus was performed. Illumina sequencing generated 60,322,004, 57,044,284, 60,867,978 and 57,087,688 clean reads from brain, liver, ovary and testis tissues of C. lucidus, respectively. Totally, 131,168 unigenes with an average length of 644 bp and an N50 value of 1033 bp were assembled. In addition, 1288 genes were differentially expressed between ovary and testis, including 442 up-regulated and 846 down-regulated in ovary. Functional analysis revealed that the differentially expressed genes between ovary and testis were mainly involved in the function of sexual reproduction, sex differentiation, development of primary male sexual characteristics, female gamete generation, and male sex differentiation. A number of genes which might be involved in the regulation of reproduction and sex determination were found, including HYAL and SYCP3 and BMP15. Furthermore, 35,476 simple sequence repeats (SSRs) were identified in this transcriptome dataset, which would contribute to further genetic and mechanism researches. De novo transcriptome sequencing analysis of four organs of C. lucidus provides rich resources for understanding the mechanism of reproductive development of C. lucidus and further investigation of the molecular regulation of sex determination and reproduction of C. lucidus.

Small RNA sequencing reveals sex-related miRNAs in Collichthys lucidus

“…To understand the expression patterns of DE-miRNAs, hierarchical clustering of DE-miRNAs was performed using Cluster 3.0. The target genes of each DE-miRNA were predicted via the analysis of differentially expressed genes between the ovaries and testes from the results of previous de novo transcriptome sequencing (Song et al, 2020). In brief, the 3′-UTR sequences of C. lucidus mRNAs were determined by the results of the de novo transcriptomes.…”

“…As a result, to ensure a stable C. lucidus population, it is essential to elucidate the molecular mechanisms underlying reproduction and sex differentiation in this species. A previous study revealed that 333 and 556 unigenes were specifically expressed in the ovaries and testes, respectively, via de novo transcriptome sequencing of C. lucidus, and hyal, sycp3, and bmp15 might play an important role in reproduction and sex determination (Song et al, 2020). Furthermore, Li et al (2019) illustrated that vasa was highly conserved in C. lucidus and may take part in germ cell development.…”

“…In this study, we investigated the sex-related molecular mechanism using small RNA sequencing of ovaries and testes in C. lucidus. In addition, we identified differentially expressed miRNAs (DE-miRNAs) between the ovaries and testes, and analyzed their target genes based on differentially expressed mRNAs (DE-mRNAs) between the ovaries and testes from the de novo transcriptome findings of our previous research (Song et al, 2020). Furthermore, we identified the signaling pathways connected with sex.…”

Spinyhead Croaker Germ Cells Gene dnd Visualizes Primordial Germ Cells in Medaka

“…Therefore, large-scale artificial reproduction is imperative to compensate for the limited natural reproductive rate. Nevertheless, research on C. lucidus is mainly limited to morphology, immune-related gene identification, population genetics, genome assembly, and transcriptome assembly with few reports on sex determination [ 29 , 31 , 32 , 33 , 34 , 35 , 36 ]. In the previous study, C. lucidus germ cells marker gene vasa was isolated by us [ 37 ].…”

Whole-Genome Sequencing and Genome-Wide Studies of Spiny Head Croaker (Collichthys lucidus) Reveals Potential Insights for Well-Developed Otoliths in the Family Sciaenidae

“…Mitochondrial genome maps of spiny head croaker and candidate genes related to its sex determination have been examined by mitochondrial genome sequencing ( Cheng et al, 2012b ), chromosome assembly ( Cai et al, 2019 ), and RNA sequencing ( Song et al, 2020 ). However, the genetic basis of well-developed otoliths in Sciaenidae species is still unknown.…”