Analysis of the gene transcription patterns and DNA methylation characteristics of triploid sea cucumbers (Apostichopus japonicus)

Abstract Breeding of polyploid aquatic animals is still an important approach and research hotspot for realizing the economic benefits afforded by the improvement of aquatic animal germplasm. To better understand the molecular mechanisms of the growth of triploid sea cucumbers, we performed gene exp...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Lingshu Han, Yi Sun, Yue Cao, Pingping Gao, Zijiao Quan, Yaqing Chang, Jun Ding
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9c693d520be34e81b87612e22a548be3
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:9c693d520be34e81b87612e22a548be3
record_format	dspace
spelling	oai:doaj.org-article:9c693d520be34e81b87612e22a548be32021-12-02T14:26:07ZAnalysis of the gene transcription patterns and DNA methylation characteristics of triploid sea cucumbers (Apostichopus japonicus)10.1038/s41598-021-87278-92045-2322https://doaj.org/article/9c693d520be34e81b87612e22a548be32021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-87278-9https://doaj.org/toc/2045-2322Abstract Breeding of polyploid aquatic animals is still an important approach and research hotspot for realizing the economic benefits afforded by the improvement of aquatic animal germplasm. To better understand the molecular mechanisms of the growth of triploid sea cucumbers, we performed gene expression and genome-wide comparisons of DNA methylation using the body wall tissue of triploid sea cucumbers using RNA-seq and MethylRAD-seq technologies. We clarified the expression pattern of triploid sea cucumbers and found no dosage effect. DEGs were significantly enriched in the pathways of nucleic acid and protein synthesis, cell growth, cell division, and other pathways. Moreover, we characterized the methylation pattern changes and found 615 differentially methylated genes at CCGG sites and 447 differentially methylated genes at CCWGG sites. Integrative analysis identified 23 genes (such as Guf1 , SGT , Col5a1 , HAL , HPS1, etc.) that exhibited correlations between promoter methylation and expression. Altered DNA methylation and expression of various genes suggested their roles and potential functional interactions in the growth of triploid sea cucumbers. Our data provide new insights into the epigenetic and transcriptomic alterations of the body wall tissue of triploid sea cucumbers and preliminarily elucidate the molecular mechanism of their growth, which is of great significance for the breeding of fine varieties of sea cucumbers.Lingshu HanYi SunYue CaoPingping GaoZijiao QuanYaqing ChangJun DingNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Lingshu Han Yi Sun Yue Cao Pingping Gao Zijiao Quan Yaqing Chang Jun Ding Analysis of the gene transcription patterns and DNA methylation characteristics of triploid sea cucumbers (Apostichopus japonicus)
description	Abstract Breeding of polyploid aquatic animals is still an important approach and research hotspot for realizing the economic benefits afforded by the improvement of aquatic animal germplasm. To better understand the molecular mechanisms of the growth of triploid sea cucumbers, we performed gene expression and genome-wide comparisons of DNA methylation using the body wall tissue of triploid sea cucumbers using RNA-seq and MethylRAD-seq technologies. We clarified the expression pattern of triploid sea cucumbers and found no dosage effect. DEGs were significantly enriched in the pathways of nucleic acid and protein synthesis, cell growth, cell division, and other pathways. Moreover, we characterized the methylation pattern changes and found 615 differentially methylated genes at CCGG sites and 447 differentially methylated genes at CCWGG sites. Integrative analysis identified 23 genes (such as Guf1 , SGT , Col5a1 , HAL , HPS1, etc.) that exhibited correlations between promoter methylation and expression. Altered DNA methylation and expression of various genes suggested their roles and potential functional interactions in the growth of triploid sea cucumbers. Our data provide new insights into the epigenetic and transcriptomic alterations of the body wall tissue of triploid sea cucumbers and preliminarily elucidate the molecular mechanism of their growth, which is of great significance for the breeding of fine varieties of sea cucumbers.
format	article
author	Lingshu Han Yi Sun Yue Cao Pingping Gao Zijiao Quan Yaqing Chang Jun Ding
author_facet	Lingshu Han Yi Sun Yue Cao Pingping Gao Zijiao Quan Yaqing Chang Jun Ding
author_sort	Lingshu Han
title	Analysis of the gene transcription patterns and DNA methylation characteristics of triploid sea cucumbers (Apostichopus japonicus)
title_short	Analysis of the gene transcription patterns and DNA methylation characteristics of triploid sea cucumbers (Apostichopus japonicus)
title_full	Analysis of the gene transcription patterns and DNA methylation characteristics of triploid sea cucumbers (Apostichopus japonicus)
title_fullStr	Analysis of the gene transcription patterns and DNA methylation characteristics of triploid sea cucumbers (Apostichopus japonicus)
title_full_unstemmed	Analysis of the gene transcription patterns and DNA methylation characteristics of triploid sea cucumbers (Apostichopus japonicus)
title_sort	analysis of the gene transcription patterns and dna methylation characteristics of triploid sea cucumbers (apostichopus japonicus)
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/9c693d520be34e81b87612e22a548be3
work_keys_str_mv	AT lingshuhan analysisofthegenetranscriptionpatternsanddnamethylationcharacteristicsoftriploidseacucumbersapostichopusjaponicus AT yisun analysisofthegenetranscriptionpatternsanddnamethylationcharacteristicsoftriploidseacucumbersapostichopusjaponicus AT yuecao analysisofthegenetranscriptionpatternsanddnamethylationcharacteristicsoftriploidseacucumbersapostichopusjaponicus AT pingpinggao analysisofthegenetranscriptionpatternsanddnamethylationcharacteristicsoftriploidseacucumbersapostichopusjaponicus AT zijiaoquan analysisofthegenetranscriptionpatternsanddnamethylationcharacteristicsoftriploidseacucumbersapostichopusjaponicus AT yaqingchang analysisofthegenetranscriptionpatternsanddnamethylationcharacteristicsoftriploidseacucumbersapostichopusjaponicus AT junding analysisofthegenetranscriptionpatternsanddnamethylationcharacteristicsoftriploidseacucumbersapostichopusjaponicus
_version_	1718391384155619328

Analysis of the gene transcription patterns and DNA methylation characteristics of triploid sea cucumbers (Apostichopus japonicus)

Ejemplares similares