Transcriptomics analysis revealing candidate networks and genes for the body size sexual dimorphism of Chinese tongue sole (Cynoglossus semilaevis)

Wang, Na; Wang, Renkai; Wang, Ruoqing; Chen, Songlin

doi:10.1007/s10142-018-0595-y

Cited by 61 publications

(62 citation statements)

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“…Primers ( Table S1 ) were designed based on sequences from the National Center for Biotechnology Information (NCBI) database. β-actin gene was used as the internal control (Wang et al, 2018). One microgram total RNAs for high-throughput transcriptome sequencing was reverse transcribed into cDNA with the PrimeScript ™ RT reagent Kit with gDNA Eraser (Takara, Japan).…”

Section: Methodsmentioning

confidence: 99%

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Transcriptome of Gonads From High Temperature Induced Sex Reversal During Sex Determination and Differentiation in Chinese Tongue Sole, Cynoglossus semilaevis

et al. 2019

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The sex of Chinese tongue sole (Cynoglossus semilaevis) is determined by both genetic sex determination (GSD) and environmental sex determination (ESD), making it an ideal model to study the relationship between sex-determination and temperature. In the present study, transcriptomes of undifferentiated gonads from genetic females and males, as well as differentiated gonads from males, females, and pseudomales under high and normal temperature treatments were generated for comparative transcriptomic analysis. A mean of 68.24 M high-quality clean reads was obtained for each library. Differentially expressed genes (DEGs) between different sexes and environmental treatments were identified, revealing that the heat shock protein gene family was involved in the high temperature induced sex reversal. The Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways that were enriched in pseudomale and genetic female comparison included neuroactive ligand-receptor interaction, cortisol synthesis and secretion, and steroid hormone biosynthesis. Furthermore, weighted gene co-expression network analyses were conducted on all samples, and two modules were positive correlated with pseudomale under high temperature. An illustrated protein-protein interaction map of the module identified a hub gene, hsc70. These findings provide insights into the genetic network that is involved in sex determination and sexual differentiation, and improve our understanding of genes involved in sex reversal under high temperature.

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Section: Methodsmentioning

confidence: 99%

“…Previous studies identified genes related to sexual dimorphism through transcriptome analysis of adult C . semilaevis (Guo et al, 2016; Wang et al, 2018; Liu et al, 2019). Gene expression patterns in the gonads of C .…”

Section: Introductionmentioning

confidence: 99%

Transcriptome of Gonads From High Temperature Induced Sex Reversal During Sex Determination and Differentiation in Chinese Tongue Sole, Cynoglossus semilaevis

et al. 2019

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“…To gain insight into the molecular mechanisms underlying female-superior sexual dimorphism with respect to growth rate, WGCNA analysis of female banana shrimp ( Fenneropenaeus merguiensis ) digestive gland tissue samples was completed by Powell et al and revealed a gene module containing a large number of transcripts with homology to transcription factors and genes associated with growth regulation [13]. Wang et al found two gene modules (yellowgreen and salmon4) that were significantly positively correlated with female-biased sexual size dimorphism using WGCNA, and identified a series of hub genes by drawing an illustrated network map of these two modules in Chinese tongue sole ( Cynoglossus semilaevis ) [14].…”

Section: Introductionmentioning

confidence: 99%

Transcriptomics analysis revealing candidate genes and networks for sex differentiation of yesso scallop (Patinopecten yessoensis)

et al. 2019

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Background The Yesso scallop, Patinopecten ( Mizuhopecten ) yessoensis, is a commercially important bivalve in the coastal countries of Northeast Asia. It has complex modes of sex differentiation, but knowledge of the mechanisms underlying this sex determination and differentiation is limited. Results In this study, the gonad tissues from females and males at three developmental stages were used to investigate candidate genes and networks for sex differentiation via RNA-Req. A total of 901,980,606 high quality clean reads were obtained from 18 libraries, of which 417 expressed male-specific genes and 754 expressed female-specific genes. Totally, 10,074 genes differentially expressed in females and males were identified. Weighted gene co-expression network analysis (WGCNA) revealed that turquoise and green gene modules were significantly positively correlated with male gonads, while coral1 and black modules were significantly associated with female gonads. The most important gene for sex determination and differentiation was Pydmrt 1 , which was the only gene discovered that determined the male sex phenotype during early gonadal differentiation. Enrichment analyses of GO terms and KEGG pathways revealed that genes involved in metabolism, genetic and environmental information processes or pathways are sex-biased. Forty-nine genes in the five modules involved in sex differentiation or determination were identified and selected to construct a gene co-expression network and a hypothesized sex differentiation pathway. Conclusions The current study focused on screening genes of sex differentiation in Yesso scallop, highlighting the potential regulatory mechanisms of gonadal development in P. yessoensis . Our data suggested that WCGNA can facilitate identification of key genes for sex differentiation and determination. Using this method, a hypothesized P. yessoensis sex determination and differentiation pathway was constructed. In this pathway, Pydmrt 1 may have a leading function. Electronic supplementary material The online version of this article (10.1186/s12864-019-6021-6) contains supplementary material, which is available to authorized users.

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“…The normalized (screened for missing values) gene expression matrix was imported into WGCNA to construct co-expression modules. Gene expression matrix was searched for a suitable soft threshold for building gene networks using a scale-free topology model [56]. After a threshold lter, the nal selection is β = 22.…”

Section: Construction Of the Weighted Gene Co-expression Networkmentioning

confidence: 99%

Transcriptomics analysis and co-expression network revealing candidate genes for laccase activity of Lenzites gibbosa

Chen¹,

Chi²,

Zhao³

et al. 2020

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Background Lenzites gibbosa is a common white-rot fungus of Polyporaceae in the cold temperate zone which cause spongy white decay of wood. Results In this study, the lignin degradation pathway of L. gibbosa at 5-time points under wood treatment was studied by RNA-Req technology. A total of 5232 DEGs were identified from 15 libraries. In 0–3 days, the mycelia are in the adaptive stage, and the mycelia began to proliferate within 3–5 days. After 5 days, the number of DGEs decreased significantly, the mycelium growth entered the platform stage, and the life activity was basically stable. In the secondary metabolism, oxidoreductase such as laccase, 2-oxoglutarate-Fe (II) type oxidoreductase, peroxisomal hydratase-dehydrogenase, dual-functional monooxygenase dominated and increased steadily, and manganese peroxidase appeared in the middle stage. With the accumulation of lignin intermediate products, P450 and ABC transporters were from the inhibition to the activation. Weighted gene co-expression network analysis (WGCNA) showed that among the 24 modules 6 modules were significantly correlated with laccase activity and the most correlated were turquoise and blue module. The central hub genes were also identified, including gene_7458, gene_61, gene_7458, gene_1741, gene_11087 which were consistent with the DGEs. These genes have high connectivity, module membership, and gene significance in the module. The enrichment analysis of GO and KEGG pathway indicated that the genes involved in cell cycle, citrate cycle (TCA cycle), nicotinate and nicotinamide metabolism, mitochondrial outer membrane, succinate dehydrogenase, carboxypeptidase and exopeptidase activity, flavin adenine dinucleotide binding, oxidoreductase activity, acting on the CH-CH group of donors, quinone or related compound as acceptor pathway were highly related to laccase synthesis pathway. Construction of gene co-expression network and hypothetical L. gibbosa laccase synthesis pathway. Conclusion This study focused on the screening of L. gibbosa degradation of lignin-related genes. And, this is the first study reporting co-expression patterns of a gene network in L. gibbosa laccase activity after wood treatment which is helpful to understand the synthesis pathway of laccase and improve the activity of laccase, which can be used to increase the rate of lignin degradation by L. gibbosa in the further.

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Transcriptomics analysis revealing candidate networks and genes for the body size sexual dimorphism of Chinese tongue sole (Cynoglossus semilaevis)

Cited by 61 publications

References 62 publications

Transcriptome of Gonads From High Temperature Induced Sex Reversal During Sex Determination and Differentiation in Chinese Tongue Sole, Cynoglossus semilaevis

Transcriptome of Gonads From High Temperature Induced Sex Reversal During Sex Determination and Differentiation in Chinese Tongue Sole, Cynoglossus semilaevis

Transcriptomics analysis revealing candidate genes and networks for sex differentiation of yesso scallop (Patinopecten yessoensis)

Transcriptomics analysis and co-expression network revealing candidate genes for laccase activity of Lenzites gibbosa

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