Comparative transcriptome analysis of male and female gonads reveals sex-biased genes in spotted scat (Scatophagus argus)

He, Fei-Xiang; Jiang, Dongneng; Huang, Yuanqing; Mustapha, Umar Farouk; Yang, Wei; Cui, Xuefan; Tian, Changxu; Chen, Huapu; Shi, Hongjuan; Deng, Si‐Ping; Li, Guangli; Zhu, Chunhua

doi:10.1007/s10695-019-00693-8

Cited by 48 publications

(30 citation statements)

References 92 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Our previous research indicated that Dmrt1 is linked to the Y chromosome, and the truncated homologue Dmrt1b, is X chromosome-linked [38]. The predicted Dmrt1 and Dmrt1b genes observed during S. argus transcriptome analysis were mapped to the draft genome using Localblast software (NCBI-blast-2.2.27) [22]. Sequence homology alignment of male and female fragments was performed using the MegAlign application of DNASTAR software (http://www.dnastar.com).…”

Section: Alignment Of the Male And Female Scaffolds On Dmrt1s Exonsmentioning

confidence: 99%

Genome Survey of Male and Female Spotted Scat (Scatophagus argus)

Huang

Jiang

et al. 2019

Animals

Self Cite

View full text Add to dashboard Cite

Simple Summary: The spotted scat, Scatophagus argus, is a marine aquaculture fish species that is economically important in Asia. As the spotted scat exhibits notable sexual dimorphism with respect to growth, aquaculture efficiency can be increased through the practice of sex control breeding. However, genomic data from S. argus is lacking. In the present study, a genomic survey was conducted using next-generation sequencing technologies. Data, including the size of the genome, sequence repeat ratio, heterozygosity ratio, whole genome sequence and gene annotation were obtained. This information will serve to support the breeding and aquaculture of S. argus. Abstract:The spotted scat, Scatophagus argus, is a species of fish that is widely propagated within the Chinese aquaculture industry and therefore has significant economic value. Despite this, studies of its genome are severely lacking. In the present study, a genomic survey of S. argus was conducted using next-generation sequencing (NGS). In total, 55.699 GB (female) and 51.047 GB (male) of high-quality sequence data were obtained. Genome sizes were estimated to be 598.73 (female) and 597.60 (male) Mbp. The sequence repeat ratios were calculated to be 27.06% (female) and 26.99% (male). Heterozygosity ratios were 0.37% for females and 0.38% for males. Reads were assembled into 444,961 (female) and 453,459 (male) contigs with N50 lengths of 5,747 and 5,745 bp for females and males, respectively. The average guanine-cytosine (GC) content of the female genome was 41.78%, and 41.82% for the male. A total of 42,869 (female) and 43,283 (male) genes were annotated to the non-redundant (NR) and SwissProt databases. The female and male genomes contained 66.6% and 67.8% BUSCO core genes, respectively. Dinucleotide repeats were the dominant form of simple sequence repeats (SSR) observed in females (68.69%) and males (68.56%). Additionally, gene fragments of Dmrt1 were only observed in the male genome. This is the first report of a genome-wide characterization of S. argus.

show abstract

Section: Alignment Of the Male And Female Scaffolds On Dmrt1s Exonsmentioning

confidence: 99%

Genome Survey of Male and Female Spotted Scat (Scatophagus argus)

Huang

Jiang

et al. 2019

Animals

Self Cite

View full text Add to dashboard Cite

show abstract

“…The third gene that lies in the cytoband 4p12-p11 is ZAR1 , a gene known for its maternal effect and responsible for the zygote–embryo transition and indicated as tumor suppressor in cancer cell lines by inhibiting the cell cycle progression [ 109 ]. It is described in literature its female sex-biased expression both in Scatophagus argus and eels [ 110 , 111 ], but also its a peak of expression in testis tissue [ 112 ]. Details and further discussion of “TRAM FGF” results will be the subject for our future investigations.…”

Section: Discussionmentioning

confidence: 99%

Sex-Specific Transcriptome Differences in Human Adipose Mesenchymal Stem Cells

Bianconi

Casadei

Frabetti

et al. 2020

Genes

View full text Add to dashboard Cite

In humans, sexual dimorphism can manifest in many ways and it is widely studied in several knowledge fields. It is increasing the evidence that also cells differ according to sex, a correlation still little studied and poorly considered when cells are used in scientific research. Specifically, our interest is on the sex-related dimorphism on the human mesenchymal stem cells (hMSCs) transcriptome. A systematic meta-analysis of hMSC microarrays was performed by using the Transcriptome Mapper (TRAM) software. This bioinformatic tool was used to integrate and normalize datasets from multiple sources and allowed us to highlight chromosomal segments and genes differently expressed in hMSCs derived from adipose tissue (hADSCs) of male and female donors. Chromosomal segments and differentially expressed genes in male and female hADSCs resulted to be related to several processes as inflammation, adipogenic and neurogenic differentiation and cell communication. Obtained results lead us to hypothesize that the donor sex of hADSCs is a variable influencing a wide range of stem cell biologic processes. We believe that it should be considered in biologic research and stem cell therapy.

show abstract

“…Genetic distance is an important measure of genetic variation among populations: greater genetic distances imply more distant relationships among groups (He et al., 2019; Jiang et al., 2019). Shaklee proposed three levels of fish classification based on genetic distance: population (≤0.05), species (>0.05 and ≤0.3), and genus (>0.3 and ≤0.9; Grant & Bowen, 1998).…”

Section: Discussionmentioning

confidence: 99%

“…Nucleotide mismatch distributions for the entireScatophagus arguspopulation, as well as the four genetically distinct lineages relationships among groups (He et al, 2019;Jiang et al, 2019).…”

Section: F I G U R Ementioning

confidence: 99%

Genetic diversity of mitochondrial D‐LOOP sequences in the spotted scat ( Scatophagus argus ) from different geographical populations along the northern coast of the South China Sea

et al. 2020

View full text Add to dashboard Cite

Summary The genetic diversity of 289 spotted scat (Scatophagus argus) from seven populations along the northern coast of the South China Sea was studied by analyzing the full‐length sequences of the mitochondrial control region (D‐LOOP). The S. argus D‐LOOP sequence was 1,004–1,010 bp long and contained 156 variant sites. The seven studied S. argus populations had a high degree of genetic diversity (haplotype diversity [Hd] = 0.99135; nucleotide diversity (π) = 0.01313). There was no obvious genetic differentiation among the seven geographical populations and gene exchange was frequent (Fst = −0.01867–0.01117, p > .05). Four distinct mitochondrial lineages were identified in the phylogenetic tree and the haplotype network. The between‐lineage Fst was 0.71690–0.84940 (p < .001), but these lineages showed no obvious phylogeographic pattern. Based on D‐LOOP mutation rates, we estimated that the four lineages diverged approximately 513,800–93,600 years ago, during the Eocene ice age, at which time falling sea levels may have led to population segregation. We estimated that S. argus population expansion occurred approximately 2.29–0.68 million years ago, during the late Pleistocene. During this period, sea levels rose again, allowing previously separated lineages to come into sympatry, which eventually gave rise to a highly genetically diverse population without pyhlogeographic structure. Here, we characterized the genetic structure and differentiation of seven S. argus populations from the northern coast of the South China Sea. Our results suggested that the seven S. argus populations from the northern coast of the South China Sea have a relatively low level of genetic variation and can be considered a single unit for the purposes of fishery development, utilization, and management.

show abstract

Comparative transcriptome analysis of male and female gonads reveals sex-biased genes in spotted scat (Scatophagus argus)

Cited by 48 publications

References 92 publications

Genome Survey of Male and Female Spotted Scat (Scatophagus argus)

Genome Survey of Male and Female Spotted Scat (Scatophagus argus)

Sex-Specific Transcriptome Differences in Human Adipose Mesenchymal Stem Cells

Genetic diversity of mitochondrial D‐LOOP sequences in the spotted scat ( Scatophagus argus ) from different geographical populations along the northern coast of the South China Sea

Contact Info

Product

Resources

About