Comparative Transcriptome and DNA methylation analyses of the molecular mechanisms underlying skin color variations in Crucian carp (Carassius carassius L.)
Abstract 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 (...
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| Format: | Article |
| Language: | English |
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BMC
2017-11-01
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| Series: | BMC Genetics |
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| Online Access: | http://link.springer.com/article/10.1186/s12863-017-0564-9 |
| _version_ | 1811252584665579520 |
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| author | Yongqin Zhang Jinhui Liu Wen Fu Wenting Xu Huiqin Zhang Shujuan Chen Wenbin Liu Liangyue Peng Yamei Xiao |
| author_facet | Yongqin Zhang Jinhui Liu Wen Fu Wenting Xu Huiqin Zhang Shujuan Chen Wenbin Liu Liangyue Peng Yamei Xiao |
| author_sort | Yongqin Zhang |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-04-12T16:37:53Z |
| format | Article |
| id | doaj.art-b8808bb41b614470837c6c148fd486c3 |
| institution | Directory Open Access Journal |
| issn | 1471-2156 |
| language | English |
| last_indexed | 2024-04-12T16:37:53Z |
| publishDate | 2017-11-01 |
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| series | BMC Genetics |
| spelling | doaj.art-b8808bb41b614470837c6c148fd486c32022-12-22T03:24:56ZengBMCBMC Genetics1471-21562017-11-0118111210.1186/s12863-017-0564-9Comparative Transcriptome and DNA methylation analyses of the molecular mechanisms underlying skin color variations in Crucian carp (Carassius carassius L.)Yongqin Zhang0Jinhui Liu1Wen Fu2Wenting Xu3Huiqin Zhang4Shujuan Chen5Wenbin Liu6Liangyue Peng7Yamei Xiao8State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal UniversityState Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal UniversityState Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal UniversityState Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal UniversityState Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal UniversityState Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal UniversityState Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal UniversityState Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal UniversityState Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal UniversityAbstract 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.http://link.springer.com/article/10.1186/s12863-017-0564-9Body colorPigment cellTranscriptomeDNA methylationCrucian carp |
| spellingShingle | Yongqin Zhang Jinhui Liu Wen Fu Wenting Xu Huiqin Zhang Shujuan Chen Wenbin Liu Liangyue Peng Yamei Xiao Comparative Transcriptome and DNA methylation analyses of the molecular mechanisms underlying skin color variations in Crucian carp (Carassius carassius L.) BMC Genetics Body color Pigment cell Transcriptome DNA methylation Crucian carp |
| 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 | Body color Pigment cell Transcriptome DNA methylation Crucian carp |
| url | http://link.springer.com/article/10.1186/s12863-017-0564-9 |
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