Integrated analysis of long non-coding RNA and mRNA expression in different colored skin of koi carp
文献类型： 外文期刊
作者： Luo, Mingkun 1 ; Wang, Lanmei 2 ; Yin, Haoran 1 ; Zhu, Wenbin 2 ; Fu, Jianjun 2 ; Dong, Zaijie 1 ;
作者机构： 1.Nanjing Agr Univ, Wuxi Fisheries Coll, Wuxi 214081, Jiangsu, Peoples R China
2.Chinese Acad Fishery Sci, Freshwater Fisheries Res Ctr, Minist Agr & Rural Affairs, Key Lab Freshwater Fisheries & Germplasm Resource, Wuxi 214081, Jiangsu, Peoples R China
关键词： LncRNA; mRNA; Skin color; Function annotation; Koi carp; Illumina sequencing
期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）
ISSN： 1471-2164
年卷期： 2019 年 20 卷
页码：
收录情况： SCI
摘要： BackgroundLong 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.).ResultsA 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.ConclusionsThe 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.
- 相关文献
作者其他论文 更多>>
-
Genome-wide methylation and transcriptome analysis in koi carp (Cyprinus carpio var. koi): Uncovering novel molecular mechanisms in skin color differentiation and pigmentation
作者：Shi, Xiulan;Chen, Xiaoyu;Dong, Zaijie;Zhu, Wenbin;Fu, Jianjun;Wang, Lanmei;Luo, Mingkun;Dong, Zaijie;Guo, Jun;Lin, Kai
关键词：Koi carp; Skin color; DNA methylation; RNA-sequencing
-
Unraveling the stress response: How low temperature and nanoparticles impact the chinese mitten crab (Eriocheir sinensis)
作者：Zhou, Zihan;Wang, Lanmei;Zhou, Zihan;Tian, Jian;Jiang, Qichen;Zhou, Zihan;Tay, Yi Juin;Han, Mingming;Si, Qin
关键词：Eriocheir sinensis; Nanoplastics; PI3K-Akt-FoxO; Multi-omics
-
Artificial Induction of Meiotic Gynogenesis in Koi Carp Using Blunt Snout Bream Sperm and Identification of Gynogenetic Offspring
作者：Chen, Xiaoyu;Shi, Xiulan;Dong, Zaijie;Guo, Jun;Lin, Kai;Luo, Mingkun;Dong, Zaijie
关键词：gynogenesis;
koi carp; microsatellite; chromosome; 5S rDNA -
Knockout of the fih gene by CRISPR/Cas9 enhances the hypoxia tolerance in grass carp (Ctenopharyngodon idella)
作者：Zhang, Huimei;Yang, Ziquan;Yuan, Ziming;Chen, Jie;Zheng, Guodong;Zou, Shuming;Zhang, Huimei;Yang, Ziquan;Yuan, Ziming;Chen, Jie;Zheng, Guodong;Zou, Shuming;Zhang, Huimei;Yang, Ziquan;Yuan, Ziming;Chen, Jie;Zheng, Guodong;Zou, Shuming;Fu, Jianjun;Dong, Zaijie;Shen, Rengao
关键词：Grass carp; Fih; Hypoxia tolerance; Apoptosis; hif1 alpha
-
Rice-fish co-culture improves carp (Cyprinus carpio) quality by modulating the gut microbiota and metabolites
作者：Nie, Zhijuan;Xu, Xiaotong;Ji, Yanhan;Gao, Ping;Zhou, Sihan;He, Jian;Liu, Xu;Wang, Baozhan;Nie, Zhijuan;Sun, Yi;Wang, Lanmei;Shao, Nailing;Xu, Pao;Shi, Yu
关键词：Rice-fish co-culture; Gut microbiome; Community assembly; Network analysis
-
Evaluation of muscle quality and movement-related traits in two common carp strains under a rice-fish farming system
作者：Gong, Yating;Zhu, Wenbin;Wang, Lanmei;Dong, Zaijie;Luo, Mingkun;Zhu, Wenbin;Wang, Lanmei;Fu, Jianjun;Dong, Zaijie;Zhang, Xianbo;Qin, Ning
关键词：Cyprinus carpio; Muscle characteristics; Nutrition; Movement; Rice-fish symbiosis system
-
Single nucleotide polymorphism SNP19140160 A > C is a potential breeding locus for fast-growth largemouth bass (Micropterus salmoides)
作者：Hua, Jixiang;Zhong, Chunyi;Wang, Qingchun;Qiang, Jun;Hua, Jixiang;Zhong, Chunyi;Fu, Jianjun;Li, Yan;Tao, Yifan;Dong, Yalun;Lu, Siqi;Liu, Wenting;Qiang, Jun;Chen, Wenhua;Zhu, Geyan;Zhang, Maoyou;Wang, Jian
关键词：Largemouth bass; RAD-seq; SNP; Growth traits; Dominant genotypes
