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Analysis of the gene transcription patterns and DNA methylation characteristics of triploid sea cucumbers (Apostichopus japonicus)
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 a...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Nature Publishing Group UK
2021
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8027599/ https://www.ncbi.nlm.nih.gov/pubmed/33828212 http://dx.doi.org/10.1038/s41598-021-87278-9 |
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author | Han, Lingshu Sun, Yi Cao, Yue Gao, Pingping Quan, Zijiao Chang, Yaqing Ding, Jun |
author_facet | Han, Lingshu Sun, Yi Cao, Yue Gao, Pingping Quan, Zijiao Chang, Yaqing Ding, Jun |
author_sort | Han, Lingshu |
collection | PubMed |
description | 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 | Online Article Text |
id | pubmed-8027599 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-80275992021-04-08 Analysis of the gene transcription patterns and DNA methylation characteristics of triploid sea cucumbers (Apostichopus japonicus) Han, Lingshu Sun, Yi Cao, Yue Gao, Pingping Quan, Zijiao Chang, Yaqing Ding, Jun Sci Rep Article 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. Nature Publishing Group UK 2021-04-07 /pmc/articles/PMC8027599/ /pubmed/33828212 http://dx.doi.org/10.1038/s41598-021-87278-9 Text en © The Author(s) 2021 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Han, Lingshu Sun, Yi Cao, Yue Gao, Pingping Quan, Zijiao Chang, Yaqing Ding, Jun Analysis of the gene transcription patterns and DNA methylation characteristics of triploid sea cucumbers (Apostichopus japonicus) |
title | 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_short | 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) |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8027599/ https://www.ncbi.nlm.nih.gov/pubmed/33828212 http://dx.doi.org/10.1038/s41598-021-87278-9 |
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