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Liu Y, Wang L, Li Z, Li L, Ding T, Chen S, Duan P, Wang X, Qiu Y, Ding X, Tian Y. DNA Methylation and Transcriptome Profiling Reveal the Role of the Antioxidant Pathway and Lipid Metabolism in Plectropomus leopardus Skin Color Formation. Antioxidants (Basel) 2025; 14:93. [PMID: 39857428 PMCID: PMC11763275 DOI: 10.3390/antiox14010093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Revised: 01/06/2025] [Accepted: 01/07/2025] [Indexed: 01/27/2025] Open
Abstract
Leopard coral grouper (Plectropomus leopardus), possessing a distinct red body color, is an important species in commercial markets; however, the high ratio of black individuals under intensive cultivation has limited the commercial value of the species. To dissect the regulatory mechanisms underlying the red skin trait in P. leopardus, gene expression and DNA methylation modifications were compared between red and black skin tissues after astaxanthin treatment. Astaxanthin effectively increased the redness value a* and body weight. Multi-omics analyses revealed the crucial roles of pathways related to antioxidants and lipid metabolism, particularly "Tyrosine metabolism", "Melanogenesis", "Fatty acid metabolism", "Fatty acid elongation", and "Biosynthesis of unsaturated acids", in red skin coloration. A molecular network for the regulation of red skin coloration in P. leopardus was constructed, and pmel, tyr, tyrp1a, tyrp1b, dct, slc24a5, wnt1, acsl4, elovl1, elovl6l.1, elovl6l.2, and elovl7 were identified as key genes. Notably, pmel, acsl4, and elovl7 were negatively regulated by differential DNA methylation. Our results provide new insight into the molecular and epigenetic mechanisms of body color variation, representing a significant step towards breeding for the red skin trait in P. leopardus.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Y.L.); (L.W.); (Z.L.); (L.L.); (T.D.); (S.C.); (P.D.); (X.W.); (Y.Q.); (X.D.)
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Qingdao 266071, China
- Hainan Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya 572025, China
| | - Linna Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Y.L.); (L.W.); (Z.L.); (L.L.); (T.D.); (S.C.); (P.D.); (X.W.); (Y.Q.); (X.D.)
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Qingdao 266071, China
- Hainan Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya 572025, China
| | - Zhentong Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Y.L.); (L.W.); (Z.L.); (L.L.); (T.D.); (S.C.); (P.D.); (X.W.); (Y.Q.); (X.D.)
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Qingdao 266071, China
- Hainan Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya 572025, China
| | - Linlin Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Y.L.); (L.W.); (Z.L.); (L.L.); (T.D.); (S.C.); (P.D.); (X.W.); (Y.Q.); (X.D.)
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Qingdao 266071, China
- Hainan Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya 572025, China
| | - Tangtang Ding
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Y.L.); (L.W.); (Z.L.); (L.L.); (T.D.); (S.C.); (P.D.); (X.W.); (Y.Q.); (X.D.)
- College of Fisheries, Tianjin Agricultural University, Tianjin 300392, China
| | - Shuai Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Y.L.); (L.W.); (Z.L.); (L.L.); (T.D.); (S.C.); (P.D.); (X.W.); (Y.Q.); (X.D.)
| | - Pengfei Duan
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Y.L.); (L.W.); (Z.L.); (L.L.); (T.D.); (S.C.); (P.D.); (X.W.); (Y.Q.); (X.D.)
| | - Xinyi Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Y.L.); (L.W.); (Z.L.); (L.L.); (T.D.); (S.C.); (P.D.); (X.W.); (Y.Q.); (X.D.)
| | - Yishu Qiu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Y.L.); (L.W.); (Z.L.); (L.L.); (T.D.); (S.C.); (P.D.); (X.W.); (Y.Q.); (X.D.)
| | - Xiaoyu Ding
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Y.L.); (L.W.); (Z.L.); (L.L.); (T.D.); (S.C.); (P.D.); (X.W.); (Y.Q.); (X.D.)
| | - Yongsheng Tian
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (Y.L.); (L.W.); (Z.L.); (L.L.); (T.D.); (S.C.); (P.D.); (X.W.); (Y.Q.); (X.D.)
- Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Qingdao 266071, China
- Hainan Innovation Research Institute, Chinese Academy of Fishery Sciences, Sanya 572025, China
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Zhang X, Chen Y, Yang H, Ding H, Cai P, Ge Y, Zheng H, Sun X, Yang Y, Li X, Lin T. Plasma Metabolomics Indicates Potential Biomarkers and Abnormal Metabolic Pathways in Female Melasma Patients. Ann Dermatol 2024; 36:300-309. [PMID: 39343757 PMCID: PMC11439978 DOI: 10.5021/ad.23.141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/18/2024] [Accepted: 02/18/2024] [Indexed: 10/01/2024] Open
Abstract
BACKGROUND Melasma is a common and chronic pigmentary disorder with complex pathogenesis, and the relationship between melasma and metabolic syndrome remains elusive. Thus, metabolomics might contribute to the early detection of potential metabolic abnormalities in individuals with melasma. OBJECTIVE The present study aims to analyze changes in plasma metabolites of female melasma patients and identify disease markers as well as explore potential therapeutic targets. METHODS Plasma samples from 20 female patients with melasma and 21 healthy female controls that were comparable in terms of age and body mass index were collected for untargeted metabolomics investigations. Ultra-high performance liquid chromatography-mass spectrometry was used to analyze metabolites in the plasma. Metabolic pathway analyses were employed to identify significantly differentially expressed metabolites in melasma patients. Receiver operating characteristic curves were constructed, and correlation analyses were performed using the modified Melasma Area and Severity Index and oxidative stress levels. RESULTS In contrast to healthy subjects, melasma patients showed significant alterations in 125 plasma metabolites, including amino acids, lipids, and carbohydrate-related metabolites. KEGG pathway analysis suggested that primary pathways associated with the development of melasma include tryptophan metabolism, as well as the biosynthesis of phenylalanine, tyrosine, and tryptophan. Importantly, based on receiver operating characteristic curves and correlation analyses, several metabolites were identified as robust biomarkers for melasma. CONCLUSION Collectively, this study identified significant changes in plasma metabolites in melasma patients, providing new insights into the pathogenesis of melasma and opening novel therapeutic avenues.
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Affiliation(s)
- Xiaoli Zhang
- Department of Cosmetic Laser Surgery, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, China
| | - Yi Chen
- Pharmacal Research Laboratory, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, China
| | - Hedan Yang
- Department of Cosmetic Laser Surgery, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, China
| | - Hui Ding
- Department of Cosmetic Laser Surgery, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, China
| | - Pingping Cai
- Department of Cosmetic Laser Surgery, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, China
| | - Yiping Ge
- Department of Cosmetic Laser Surgery, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, China
| | - Huiying Zheng
- Department of Cosmetic Laser Surgery, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, China
| | - Xiaojie Sun
- Department of Cosmetic Laser Surgery, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, China
| | - Yin Yang
- Department of Cosmetic Laser Surgery, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, China.
| | - Xinyu Li
- Pharmacal Research Laboratory, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, China.
| | - Tong Lin
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, China.
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Li X, Wang X, Yu X, Yang C, Lin L, Huang Y. The draft genome of the Temminck's tragopan (Tragopan temminckii) with evolutionary implications. BMC Genomics 2023; 24:751. [PMID: 38062370 PMCID: PMC10702090 DOI: 10.1186/s12864-023-09857-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND High-quality genome data of birds play a significant role in the systematic study of their origin and adaptive evolution. The Temminck's tragopan (Tragopan temminckii) (Galliformes, Phasianidae), a larger pheasant, is one of the most abundant and widely distributed species of the genus Tragopan, and was defined as class II of the list of national key protected wild animals in China. The absence of a sequenced genome has restricted previous evolutionary trait studies of this taxa. RESULTS The whole genome of the Temminck's tragopan was sequenced using Illumina and PacBio platform, and then de novo assembled and annotated. The genome size was 1.06 Gb, with a contig N50 of 4.17 Mb. A total of 117.22 Mb (11.00%) repeat sequences were identified. 16,414 genes were predicted using three methods, with 16,099 (98.08%) annotated as functional genes based on five databases. In addition, comparative genome analyses were conducted across 12 Galliformes species. The results indicated that T. temminckii was the first species to branch off from the clade containing Lophura nycthemera, Phasianus colchicus, Chrysolophus pictus, Syrmaticus mikado, Perdix hodgsoniae, and Meleagris gallopavo, with a corresponding divergence time of 31.43 million years ago (MYA). Expanded gene families associated with immune response and energy metabolism were identified. Genes and pathways associated with plumage color and feather development, immune response, and energy metabolism were found in the list of positively selected genes (PSGs). CONCLUSIONS A genome draft of the Temminck's tragopan was reported, genome feature and comparative genome analysis were described, and genes and pathways related to plumage color and feather development, immune response, and energy metabolism were identified. The genomic data of the Temminck's tragopan considerably contribute to the genome evolution and phylogeny of the genus Tragopan and the whole Galliformes species underlying ecological adaptation strategies.
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Affiliation(s)
- Xuejuan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xiaoyang Wang
- School of Biological and Environmental Engineering, Xi'an University, Xi'an, China
| | - Xiaoping Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Chao Yang
- Shaanxi Institute of Zoology, Xi'an, China
| | - Liliang Lin
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
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Lu H, Chen W, Peng K, Huang M, Zhao J, Chen X, Sun Y, Ruan Z, Li C, Liu D, Liu Z, Li H, Zhang Y, Huang W. Rapid adaptive and acute stimulatory responses to low salinity stress in Pacific white shrimp (Litopenaeus vannamei): Insights from integrative transcriptomic and proteomic analysis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 48:101149. [PMID: 37883838 DOI: 10.1016/j.cbd.2023.101149] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/28/2023] [Accepted: 10/15/2023] [Indexed: 10/28/2023]
Abstract
The Pacific white shrimp (Litopenaeus vannamei) is a euryhaline crustacean capable of tolerating a wide range of ambient salinity, but the strategies of hepatopancreas to rapid adaptive or acute stimulatory responses to extremely low salinity fluctuations remains unclear. In this study, we integrated transcriptomic and proteomic analyses on the hepatopancreas derived from rapid adaptative (RA) and acute stimulatory (AS) responses to extremely low salinity stress (0.3 ppt) to unveil specific regulatory mechanisms. The RA group displayed normal epithelial cells and tubule structures, while the AS group showed histological changes and lesions. A total of 754 and 649 differentially expressed genes (DEGs) were identified in RA and AS treatments, respectively. For proteome, a total of 206 and 66 differentially expressed proteins (DEPs) were obtained in the RA/CT and AS/CT comparison groups, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were conducted among the DEGs and DEPs, revealing that metabolic related pathways were significantly enriched pathways in both comparison groups. In addition, correlation analysis of transcriptomic and proteomic results showed that 20 and 3 pairs of DEGs/DEPs were identified in RA vs. CT and AS vs. CT comparison groups, respectively. This study is the first report on the rapid adaptive and acute stimulatory transcriptomic and proteomic responses of L. vannamei to extremely low salinity, shedding light on the mechanisms underlying osmoregulation in euryhaline crustaceans.
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Affiliation(s)
- Huijie Lu
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Wenchun Chen
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Kai Peng
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Minwei Huang
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jichen Zhao
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xiaoying Chen
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yuping Sun
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Zhuohao Ruan
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Chaozheng Li
- Maoming Branch Center of Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Maoming 525099, China; State Key Laboratory of Biocontrol and School of Life Sciences, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou 510275, China
| | - Ding Liu
- Guangdong Provincial Engineering Research Center of Prawn Culture, Guangdong Havwii Agricultural Group Co., Ltd., Zhanjiang 524000, China
| | - Zhenxing Liu
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Huo Li
- Guangdong Provincial Engineering and Technology Research Center, Guangdong Jinyang Biotechnology Co., Ltd., Maoming 525027, China
| | - Yong Zhang
- State Key Laboratory of Biocontrol and School of Life Sciences, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wen Huang
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; Maoming Branch Center of Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Maoming 525099, China; Guangdong Provincial Engineering Research Center of Prawn Culture, Guangdong Havwii Agricultural Group Co., Ltd., Zhanjiang 524000, China; Guangdong Provincial Engineering and Technology Research Center, Guangdong Jinyang Biotechnology Co., Ltd., Maoming 525027, China.
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