Whole genome-wide chromosome fusion and new gene birth in the Monopterus albus genome

Cheng, Yang; Shang, Dantong; Luo, Majing; Huang, Chunhua; Lai, Fengling; Wang, Xin; Xu, Xu; Ying, Ruhong; Wang, Lingling; Zhao, Yu; Zhang, Li; Long, Manyuan; Cheng, Hanhua; Zhou, Rongjia

doi:10.1186/s13578-020-00432-0

Cited by 18 publications

(9 citation statements)

References 72 publications

(92 reference statements)

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“…There were multiple members of Dnmt3 in both mammals [ 32 ] and teleosts [ 33 ]. Two dnmt3a members ( dnmt3aa and dnmt3ab ) have been detected in the genome of Monopterus albus [ 34 ], which would be duplicated through whole-genome duplication event [ 35 ]. To further explore association of de novo DNA methylation with gonadal differentiation, we characterized transcription regulation of dnmt3aa and found that the transcription factor Foxa1 was responsible for transcriptional activation of dnmt3a gene.…”

Section: Discussionmentioning

confidence: 99%

DNA methylation modification is associated with gonadal differentiation in Monopterus albus

et al. 2020

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Background Both testis and ovary can be produced sequentially in an individual with the same genome when sex reversal occurs in the teleost Monopterus albus, and epigenetic modification is supposed to be involved in gonadal differentiation. However, DNA methylation regulation mechanism underlying the gonadal differentiation remains unclear. Results Here, we used liquid chromatography-electrospray ionization tandem mass spectrometry (LC–ESI–MS/MS) to simultaneously determine endogenous levels of both 5-methyl-2′-deoxycytidine (m5dC) and 5-hydroxymethyl-2′-deoxycytidine (hm5dC) during gonadal differentiation. Overall DNA methylation level was upregulated from ovary to testis via ovotestis. As a de novo methylase, dnmt3aa expression was also upregulated in the process. Notably, we determined transcription factor Foxa1 for dnmt3aa gene expression. Site-specific mutations and chromatin immunoprecipitation showed that Foxa1 can bind to and activate the dnmt3aa promoter. Furthermore, DNA methylation levels of key genes foxl2 (forkhead box L2) and cyp19a1a (cytochrome P450, family 19, subfamily A, polypeptide 1a) in regulation of female hormone synthesis were consistently upregulated during gonadal differentiation. Conclusions These data suggested that dynamic change of DNA methylation modification is associated with gonadal differentiation.

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Section: Discussionmentioning

confidence: 99%

DNA methylation modification is associated with gonadal differentiation in Monopterus albus

et al. 2020

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“…Otherwise, in the absence of SRY, ovary development will start via several female pathways. RSPO1/WNT signaling is a major pathway for ovary development, which includes RSPO1, WNT4B, CTNNB1 and GSK3A/B 7,8 . Mutations in these sex-determining genes and the dysregulation of relevant pathways will lead to DSDs, including 46,XY complete or partial gonadal dysgenesis, 46,XX testicular DSD, and 46,XX ovotesticular DSD.…”

Section: Introductionmentioning

confidence: 99%

Cellular fate of intersex differentiation

et al. 2021

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Infertile ovotestis (mixture of ovary and testis) often occurs in intersex individuals under certain pathological and physiological conditions. However, how ovotestis is formed remains largely unknown. Here, we report the first comprehensive single-cell developmental atlas of the model ovotestis. We provide an overview of cell identities and a roadmap of germline, niche, and stem cell development in ovotestis by cell lineage reconstruction and a uniform manifold approximation and projection. We identify common progenitors of germline stem cells with two states, which reveal their bipotential nature to differentiate into both spermatogonial stem cells and female germline stem cells. Moreover, we found that ovotestis infertility was caused by degradation of female germline cells via liquid–liquid phase separation of the proteasomes in the nucleus, and impaired histone-to-protamine replacement in spermatid differentiation. Notably, signaling pathways in gonadal niche cells and their interaction with germlines synergistically determined distinct cell fate of both male and female germlines. Overall, we reveal a cellular fate map of germline and niche cell development that shapes cell differentiation direction of ovotestis, and provide novel insights into ovotestis development.

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“…So far, many studies on new genes have focused on the model organisms including primates, rodents and Drosophila [1,[10][11][12][13]. However, there are few researches on new genes in non-model vertebrates, and no study using phylogenomic data has been conducted to investigate new genes in a lineage of teleosts [14]. In addition, teleosts usually have an additional genome-wide duplication event, compared to other vertebrates, which may result in more duplicate genes and some of them may have functions in these fishes [15,16].…”

Section: Introductionmentioning

confidence: 99%

Pattern of New Gene Origination in a Special Fish Lineage, the Flatfishes

Chen

Wang

et al. 2021

Genes

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Origination of new genes are of inherent interest of evolutionary geneticists for decades, but few studies have addressed the general pattern in a fish lineage. Using our recent released whole genome data of flatfishes, which evolved one of the most specialized body plans in vertebrates, we identified 1541 (6.9% of the starry flounder genes) flatfish-lineage-specific genes. The origination pattern of these flatfish new genes is largely similar to those observed in other vertebrates, as shown by the proportion of DNA-mediated duplication (1317; 85.5%), RNA-mediated duplication (retrogenes; 96; 6.2%), and de novo–origination (128; 8.3%). The emergence rate of species-specific genes is 32.1 per Mya and the whole average level rate for the flatfish-lineage-specific genes is 20.9 per Mya. A large proportion (31.4%) of these new genes have been subjected to selection, in contrast to the 4.0% in primates, while the old genes remain quite similar (66.4% vs. 65.0%). In addition, most of these new genes (70.8%) are found to be expressed, indicating their functionality. This study not only presents one example of systematic new gene identification in a teleost taxon based on comprehensive phylogenomic data, but also shows that new genes may play roles in body planning.

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Whole genome-wide chromosome fusion and new gene birth in the Monopterus albus genome

Cited by 18 publications

References 72 publications

DNA methylation modification is associated with gonadal differentiation in Monopterus albus

DNA methylation modification is associated with gonadal differentiation in Monopterus albus

Cellular fate of intersex differentiation

Pattern of New Gene Origination in a Special Fish Lineage, the Flatfishes

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