Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp
Abstract Background Long non-coding RNAs (lncRNAs) perform crucial roles in biological process involving complex mechanisms. However, information regarding their abundance, characteristics and potential functions linked to fish skin color is limited. Herein, Illumina sequencing and bioinformatics we...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-06-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-019-5894-8 |
| _version_ | 1818522386508546048 |
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| author | Mingkun Luo Lanmei Wang Haoran Yin Wenbin Zhu Jianjun Fu Zaijie Dong |
| author_facet | Mingkun Luo Lanmei Wang Haoran Yin Wenbin Zhu Jianjun Fu Zaijie Dong |
| author_sort | Mingkun Luo |
| collection | DOAJ |
| description | Abstract Background Long non-coding RNAs (lncRNAs) perform crucial roles in biological process involving complex mechanisms. However, information regarding their abundance, characteristics and potential functions linked to fish skin color is limited. Herein, Illumina sequencing and bioinformatics were conducted on black, white, and red skin of Koi carp (Cyprinus carpio L.). Results A total of 590,415,050 clean reads, 446,614 putative transcripts, 4252 known and 72,907 novel lncRNAs were simultaneously obtained, including 92 significant differentially expressed lncRNAs and 722 mRNAs. Ccr_lnc5622441 and Ccr_lnc765201 were up-regulated in black and red skin, Ccr_lnc14074601 and Ccr_lnc2382951 were up-regulated in white skin, and premelanosome protein a (Pmela), Pmelb and tyrosinase (Tyr) were up-regulated in black skin. The expression patterns of 18 randomly selected differentially expressed genes were validated using the quantitative real-time PCR method. Moreover, 70 lncRNAs acting on 107 target mRNAs in cis and 79 lncRNAs acting on 41,625 target mRNAs in trans were investigated. The resulting co-expression networks revealed that a single lncRNA can connect with numerous mRNAs, and vice versa. To further reveal their potential functions, Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed, and membrane, pigment cell development, cAMP signaling, melanogenesis and tyrosine metabolism appear to affect skin pigmentation. Additionally, three lncRNAs (Ccr_lnc142711, Ccr_lnc17214525 and Ccr_lnc14830101) and three mRNAs (Asip, Mitf and Tyr) involved in the melanogenesis pathway were investigated in terms of potential functions in embryogenesis and different tissues. Conclusions The findings broaden our understanding of lncRNAs and skin color genetics, and provide new insight into the mechanisms underlying lncRNA-mediated pigmentation and differentiation in Koi carp. |
| first_indexed | 2024-12-11T05:32:35Z |
| format | Article |
| id | doaj.art-65ce365154e2426e87375b26a2636cdc |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-11T05:32:35Z |
| publishDate | 2019-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-65ce365154e2426e87375b26a2636cdc2022-12-22T01:19:23ZengBMCBMC Genomics1471-21642019-06-0120111410.1186/s12864-019-5894-8Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carpMingkun Luo0Lanmei Wang1Haoran Yin2Wenbin Zhu3Jianjun Fu4Zaijie Dong5Wuxi Fisheries College, Nanjing Agricultural UniversityFreshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural AffairsWuxi Fisheries College, Nanjing Agricultural UniversityFreshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural AffairsFreshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural AffairsWuxi Fisheries College, Nanjing Agricultural UniversityAbstract Background Long non-coding RNAs (lncRNAs) perform crucial roles in biological process involving complex mechanisms. However, information regarding their abundance, characteristics and potential functions linked to fish skin color is limited. Herein, Illumina sequencing and bioinformatics were conducted on black, white, and red skin of Koi carp (Cyprinus carpio L.). Results A total of 590,415,050 clean reads, 446,614 putative transcripts, 4252 known and 72,907 novel lncRNAs were simultaneously obtained, including 92 significant differentially expressed lncRNAs and 722 mRNAs. Ccr_lnc5622441 and Ccr_lnc765201 were up-regulated in black and red skin, Ccr_lnc14074601 and Ccr_lnc2382951 were up-regulated in white skin, and premelanosome protein a (Pmela), Pmelb and tyrosinase (Tyr) were up-regulated in black skin. The expression patterns of 18 randomly selected differentially expressed genes were validated using the quantitative real-time PCR method. Moreover, 70 lncRNAs acting on 107 target mRNAs in cis and 79 lncRNAs acting on 41,625 target mRNAs in trans were investigated. The resulting co-expression networks revealed that a single lncRNA can connect with numerous mRNAs, and vice versa. To further reveal their potential functions, Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed, and membrane, pigment cell development, cAMP signaling, melanogenesis and tyrosine metabolism appear to affect skin pigmentation. Additionally, three lncRNAs (Ccr_lnc142711, Ccr_lnc17214525 and Ccr_lnc14830101) and three mRNAs (Asip, Mitf and Tyr) involved in the melanogenesis pathway were investigated in terms of potential functions in embryogenesis and different tissues. Conclusions The findings broaden our understanding of lncRNAs and skin color genetics, and provide new insight into the mechanisms underlying lncRNA-mediated pigmentation and differentiation in Koi carp.http://link.springer.com/article/10.1186/s12864-019-5894-8LncRNAmRNASkin colorFunction annotationKoi carpIllumina sequencing |
| spellingShingle | Mingkun Luo Lanmei Wang Haoran Yin Wenbin Zhu Jianjun Fu Zaijie Dong Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp BMC Genomics LncRNA mRNA Skin color Function annotation Koi carp Illumina sequencing |
| title | Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp |
| title_full | Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp |
| title_fullStr | Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp |
| title_full_unstemmed | Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp |
| title_short | Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp |
| title_sort | integrated analysis of long non coding rna and mrna expression in different colored skin of koi carp |
| topic | LncRNA mRNA Skin color Function annotation Koi carp Illumina sequencing |
| url | http://link.springer.com/article/10.1186/s12864-019-5894-8 |
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