Screening and characterisation of sex differentiation-related long non-coding RNAs in Chinese soft-shell turtle (Pelodiscus sinensis)

Zhang, Jun; Yu, Peng; Zhou, Qinyan; Li, Xilei; Ding, Shuquan; Su, Shiping; Zhang, Xiaohua; Yang, Xiaoli; Zhou, Weicheng; Wan, Qing; Gui, Jian‐Fang

doi:10.1038/s41598-018-26841-3

Cited by 27 publications

(29 citation statements)

References 59 publications

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“…However, their exact functions in the soft-shelled turtle remain poorly understood. Despite limited studies that have identi ed lncRNAs in the turtle [3], the miRNAs and lncRNAs in the database are still insu cient. In the present study, to understand the molecular mechanism involved in the reproduction of P. sinensis, we analysed the genome-wide expression of miRNAs, lncRNAs, and mRNAs in the mature ovaries and testes during the reproductive season.…”

Section: Discussionmentioning

confidence: 99%

“…In a previous study, Huang et al [32] identi ed only 10 miRNAs in P. sinensis based on EST and GSS information using a bioinformatics approach. Zhang et al [3] identi ed 5 994 lncRNAs by high-throughput sequencing in juvenile turtle gonads. MiRNAs and lncRNAs have been shown to have stage-speci c expression in animals [16,33].…”

Section: Discussionmentioning

confidence: 99%

“…The Chinese soft-shelled turtle (Pelodiscus sinensis) is an important freshwater aquaculture species in China. The turtle has a sex-dependent growth pattern, with males showing a signi cantly larger weight and size, thicker and wider calipash, and lower levels of fat than females [3]. Similar to other reptiles and mammals, the soft-shelled turtle has the ability to store sperm in the ovary [4].…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide identification and comparison of differentially expressed profiles of miRNAs and lncRNAs with associated ceRNA networks in the gonads of Chinese soft-shelled turtle, Pelodiscus sinensis

Cen

Wang

et al. 2020

Preprint

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Abstract Background: The gonad is the major factor affecting animal reproduction. The regulatory mechanism of the expression of protein-coding genes involved in reproduction still remains to be elucidated. Increasing evidence has shown that ncRNAs play key regulatory roles in gene expression in many life processes. The roles of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in reproduction have been investigated in some species. However, the regulatory patterns of miRNA and lncRNA in the sex biased expression of protein coding genes remains to be elucidated. In this study, we performed an integrated analysis of miRNA, messenger RNA (mRNA), and lncRNA expression profiles to explore their regulatory patterns in the female ovary and male testis of Pelodiscus sinensis.Results: We identified 10 446 mature miRNAs, 20 414 mRNAs and 28 500 lncRNAs in the ovaries and testes, and 633 miRNAs, 11 319 mRNAs, and 10 495 lncRNAs showed differential expression. A total of 2 814 target genes were identified for miRNAs. The predicted target genes of these differentially expressed (DE) miRNAs and lncRNAs included abundant genes related to reproductive regulation. Furthermore, we found that 189 DEmiRNAs and 5 408 DElncRNAs showed sex-specific expression. Of these, 3 DEmiRNAs and 917 DElncRNAs were testis-specific, and 186 DEmiRNAs and 4 491 DElncRNAs were ovary-specific. We further constructed complete endogenous lncRNA-miRNA-mRNA networks using bioinformatics, including 103 DEmiRNAs, 636 DEmRNAs, and 1 622 DElncRNAs. The target genes for the differentially expressed miRNAs and lncRNAs included abundant genes involved in gonadal development, including Wt1, Creb3l2, Gata4, Wnt2, Nr5a1, Hsd17, Igf2r, H2afz, Lin52, Trim71, Zar1, and Jazf1.Conclusions: In animals, miRNA and lncRNA as master regulators regulate reproductive processes by controlling the expression of mRNAs. Considering their importance, the identified miRNAs, lncRNAs, and their targets in P. sinensis might be useful for studying the molecular processes involved in sexual reproduction and genome editing to produce higher quality aquaculture animals. A thorough understanding of ncRNA-based cellular regulatory networks will aid in the improvement of P. sinensis reproductive traits for aquaculture.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Genome-wide identification and comparison of differentially expressed profiles of miRNAs and lncRNAs with associated ceRNA networks in the gonads of Chinese soft-shelled turtle, Pelodiscus sinensis

Cen

Wang

et al. 2020

Preprint

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“…Multiple studies have shown that lncRNA participate in many biological processes, such as sexual reproduction (Zhang et al, 2014), gonadal development (Taylor et al, 2015), and gametogenesis (Herrera et al, 2005;Laiho et al, 2013). Bioinformatic analysis of Amur sturgeon (Zhang et al, 2019) and Chinese softshell turtle (Zhang et al, 2018) gonads have shown that the expression of the majority of lncRNAs is signi cantly different between males and females. Target genes prediction has shown lncRNAs could regulate many genes responsible for sex determination and gametogenesis (Wen et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Analysis of miRNA-mRNA/lncRNA During Gonadal Development of Triploid Rainbow Trout (Oncorhynchus mykiss)

Huang

Liu

Shi

et al. 2020

Preprint

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Background: Polyploidy is an important force to improve biological evolution. Chromosomal ploidy manipulation is one of the means to create excellent germplasm. It has an important significance to understand the effect of genome duplication on fertility in polyploidy breeding. In this study, coding and non-coding RNAs involved in gonadal development were characterized, and their relationships were explored. Results: By high-throughput sequencing, we compared the expression profiles of gonadal mRNA, long non-coding RNA (lncRNA), and microRNA (miRNA) at different developmental stages [65 days post fertilisation (dpf), 180 dpf, and 600 dpf] between the diploid (XX) and triploid (XXX) rainbow trout. A majority of differentially expressed (DE) RNAs was screened. The overlapped DE mRNAs of three stages were functionally annotated by Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis. According to the overlapped miRNAs, the predicted miRNA-mRNA/lncRNA network was constructed based on the target pairs of lncRNA-miRNA and mRNA-miRNA. Also, RT-qPCR was performed to validate the credibility of the network. Conclusions: Lots of lncRNAs involved in fertility were characterised by this network, which provided a reference sequence for further research. In summary, this study explored the potential interplay between coding and noncoding RNAs during the gonadal development of polyploid fish and elaborated the effect of triploidization on fertility.

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“…However, their exact functions in the soft-shelled turtle remain poorly understood. Despite limited studies that have identified lncRNAs in the turtle[3], the miRNAs and lncRNAs in the database are still insufficient. In the present study, to understand the molecular mechanism involved in the reproduction of P. sinensis, we analyzed a genome-wide expression of miRNAs, lncRNAs, and mRNAs in the mature ovaries and testes during the reproduction season.…”

mentioning

confidence: 99%

Genome-wide identification and comparison of differentially expressed profiles of miRNAs and lncRNAs with associated ceRNA networks in the gonads of Chinese soft-shelled turtle, Pelodiscus sinensis

Cen

Wang

et al. 2019

Preprint

View full text Add to dashboard Cite

Abstract Background: Gonad is the major factor affecting the animal reproduction. The regulation mechanism of protein coding genes expression involved in reproduction still remains to be elucidated. Increasing evidence has shown that ncRNAs play key regulatory roles in gene expression in many life processes. The roles of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in reproduction have been investigated in some species. However, the regulation patterns of miRNA and lncRNA in sex biased expression of protein coding genes remains to be elucidated. In this study, we performed an integrated analysis of miRNA, messenger RNA (mRNA), and lncRNA expression profiles to explore their regulatory patterns in the female ovary and male testis of the soft-shelled turtle, Pelodiscus sinensis. Results: We identified 10 446 mature miRNAs, 20 414 mRNAs and 28 500 lncRNAs in the ovaries and testes, and 633 miRNAs, 11 319 mRNAs, and 10 495 lncRNAs showed different expression. A total of 2 814 target genes were identified for miRNAs. The predicted target genes of these differential expression (DE) miRNAs and lncRNAs included abundant genes related to reproductive regulation. Furthermore, we found that 189 DE miRNAs and 5 408 DElncRNAs showed sex-specific expression. Of these, 3 DEmiRNAs and 917 DElncRNAs were testis specific and 186 DEmiRNAs and 4 491 DElncRNAs were ovary specific. We further constructed compete endogenous lncRNA-miRNA-mRNA networks using bioinformatics, including 103 DEmiRNAs, 636 DEmRNAs, and 1 622 DElncRNAs. The target genes for the different expressed of miRNAs and lncRNAs contained abundant genes invloved gonadal development, including Wt1, Creb3l2, Gata4, Wnt2, Nr5a1, Hsd17, Igf2r, H2afz, Lin52, Trim71, Zar1, and Jazf1, etc. Conclusions: In animals, miRNA and lncRNA as master regulators regulate the reproduction processes by controlling the expression of mRNAs. Considering their importance, the identified miRNAs, lncRNAs, and their targets in P. sinensis might be useful for studying the molecular processes involved in sexual reproduction and genome editing to produce higher quality aquaculture animals. A thorough understanding of ncRNA-based cellular regulatory networks will aid in the improvement of P. sinensis reproduction traits for aquaculture.

show abstract

Screening and characterisation of sex differentiation-related long non-coding RNAs in Chinese soft-shell turtle (Pelodiscus sinensis)

Cited by 27 publications

References 59 publications

Genome-wide identification and comparison of differentially expressed profiles of miRNAs and lncRNAs with associated ceRNA networks in the gonads of Chinese soft-shelled turtle, Pelodiscus sinensis

Genome-wide identification and comparison of differentially expressed profiles of miRNAs and lncRNAs with associated ceRNA networks in the gonads of Chinese soft-shelled turtle, Pelodiscus sinensis

Comprehensive Analysis of miRNA-mRNA/lncRNA During Gonadal Development of Triploid Rainbow Trout (Oncorhynchus mykiss)

Genome-wide identification and comparison of differentially expressed profiles of miRNAs and lncRNAs with associated ceRNA networks in the gonads of Chinese soft-shelled turtle, Pelodiscus sinensis

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