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Comparative Transcriptome and DNA methylation analyses of the molecular mechanisms underlying skin color variations in Crucian carp (Carassius carassius L.)

BACKGROUND: Crucian carp is a popular ornamental strain in Asia with variants in body color. To further explore the genetic mechanisms underlying gray and red body color formation in crucian carp, the skin transcriptomes and partial DNA methylation sites were obtained from red crucian carp (RCC) and...

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Autores principales: Zhang, Yongqin, Liu, Jinhui, Fu, Wen, Xu, Wenting, Zhang, Huiqin, Chen, Shujuan, Liu, Wenbin, Peng, Liangyue, Xiao, Yamei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5680753/
https://www.ncbi.nlm.nih.gov/pubmed/29121864
http://dx.doi.org/10.1186/s12863-017-0564-9
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author Zhang, Yongqin
Liu, Jinhui
Fu, Wen
Xu, Wenting
Zhang, Huiqin
Chen, Shujuan
Liu, Wenbin
Peng, Liangyue
Xiao, Yamei
author_facet Zhang, Yongqin
Liu, Jinhui
Fu, Wen
Xu, Wenting
Zhang, Huiqin
Chen, Shujuan
Liu, Wenbin
Peng, Liangyue
Xiao, Yamei
author_sort Zhang, Yongqin
collection PubMed
description BACKGROUND: Crucian carp is a popular ornamental strain in Asia with variants in body color. To further explore the genetic mechanisms underlying gray and red body color formation in crucian carp, the skin transcriptomes and partial DNA methylation sites were obtained from red crucian carp (RCC) and white crucian carp (WCC). Here, we show significant differences in mRNA expression and DNA methylation sites between skin tissues of RCC and WCC. RESULTS: Totals of 3434 and 3683 unigenes had significantly lower and higher expression in WCC, respectively, compared with unigenes expressed in RCC. Some potential genes for body color development were further identified by quantitative polymerase chain reaction, such as mitfa, tyr, tyrp1, and dct, which were down-regulated, and foxd3, hpda, ptps, and gch1, which were up-regulated. A KEGG pathway analysis indicated that the differentially expressed genes were mainly related to mitogen activated protein kinase (MAPK), Wnt, cell cycle, and endocytosis signaling pathways, as well as variations in melanogenesis in crucian carp. In addition, some differentially expressed DNA methylation site genes were related to pigmentation, including mitfa, tyr, dct, foxd3, and hpda. The differentially expressed DNA methylation sites were mainly involved in signaling pathways, including MAPK, cAMP, endocytosis, melanogenesis, and Hippo. CONCLUSIONS: Our study provides the results of comparative transcriptome and DNA methylation analyses between RCC and WCC skin tissues and reveals that the molecular mechanism of body color variation in crucian carp is strongly related to disruptions in gene expression and DNA methylation during pigmentation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12863-017-0564-9) contains supplementary material, which is available to authorized users.
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spelling pubmed-56807532017-11-17 Comparative Transcriptome and DNA methylation analyses of the molecular mechanisms underlying skin color variations in Crucian carp (Carassius carassius L.) Zhang, Yongqin Liu, Jinhui Fu, Wen Xu, Wenting Zhang, Huiqin Chen, Shujuan Liu, Wenbin Peng, Liangyue Xiao, Yamei BMC Genet Research Article BACKGROUND: Crucian carp is a popular ornamental strain in Asia with variants in body color. To further explore the genetic mechanisms underlying gray and red body color formation in crucian carp, the skin transcriptomes and partial DNA methylation sites were obtained from red crucian carp (RCC) and white crucian carp (WCC). Here, we show significant differences in mRNA expression and DNA methylation sites between skin tissues of RCC and WCC. RESULTS: Totals of 3434 and 3683 unigenes had significantly lower and higher expression in WCC, respectively, compared with unigenes expressed in RCC. Some potential genes for body color development were further identified by quantitative polymerase chain reaction, such as mitfa, tyr, tyrp1, and dct, which were down-regulated, and foxd3, hpda, ptps, and gch1, which were up-regulated. A KEGG pathway analysis indicated that the differentially expressed genes were mainly related to mitogen activated protein kinase (MAPK), Wnt, cell cycle, and endocytosis signaling pathways, as well as variations in melanogenesis in crucian carp. In addition, some differentially expressed DNA methylation site genes were related to pigmentation, including mitfa, tyr, dct, foxd3, and hpda. The differentially expressed DNA methylation sites were mainly involved in signaling pathways, including MAPK, cAMP, endocytosis, melanogenesis, and Hippo. CONCLUSIONS: Our study provides the results of comparative transcriptome and DNA methylation analyses between RCC and WCC skin tissues and reveals that the molecular mechanism of body color variation in crucian carp is strongly related to disruptions in gene expression and DNA methylation during pigmentation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12863-017-0564-9) contains supplementary material, which is available to authorized users. BioMed Central 2017-11-09 /pmc/articles/PMC5680753/ /pubmed/29121864 http://dx.doi.org/10.1186/s12863-017-0564-9 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Zhang, Yongqin
Liu, Jinhui
Fu, Wen
Xu, Wenting
Zhang, Huiqin
Chen, Shujuan
Liu, Wenbin
Peng, Liangyue
Xiao, Yamei
Comparative Transcriptome and DNA methylation analyses of the molecular mechanisms underlying skin color variations in Crucian carp (Carassius carassius L.)
title Comparative Transcriptome and DNA methylation analyses of the molecular mechanisms underlying skin color variations in Crucian carp (Carassius carassius L.)
title_full Comparative Transcriptome and DNA methylation analyses of the molecular mechanisms underlying skin color variations in Crucian carp (Carassius carassius L.)
title_fullStr Comparative Transcriptome and DNA methylation analyses of the molecular mechanisms underlying skin color variations in Crucian carp (Carassius carassius L.)
title_full_unstemmed Comparative Transcriptome and DNA methylation analyses of the molecular mechanisms underlying skin color variations in Crucian carp (Carassius carassius L.)
title_short Comparative Transcriptome and DNA methylation analyses of the molecular mechanisms underlying skin color variations in Crucian carp (Carassius carassius L.)
title_sort comparative transcriptome and dna methylation analyses of the molecular mechanisms underlying skin color variations in crucian carp (carassius carassius l.)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5680753/
https://www.ncbi.nlm.nih.gov/pubmed/29121864
http://dx.doi.org/10.1186/s12863-017-0564-9
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