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Tian Y, Lin Y, Ma Y, Li J, Sahu SK, Fan J, Lin C, Li Z, Shi M, He F, Bai L, Fu Y, Deng Z, Guo H, Li H, Li Q, Xu Y, Lan T, Hou Z, Xia Y, Yang S. Population Genomics Reveals Elevated Inbreeding and Accumulation of Deleterious Mutations in White Raccoon Dogs. BIOLOGY 2025; 14:30. [PMID: 39857261 PMCID: PMC11760849 DOI: 10.3390/biology14010030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2024] [Revised: 12/18/2024] [Accepted: 12/31/2024] [Indexed: 01/27/2025]
Abstract
The formation of animal breeds usually begins with a small subsample from their ancestral population. Deleterious mutations accumulate in the population under genetic drift, inbreeding, and artificial selection during the development and maintenance of traits desired by humans. White raccoon dogs are among the most popular breeds of farmed raccoon dogs, but white raccoon dogs are more susceptible to disease and have a lower reproductive ability. However, the accumulation of deleterious mutations in this white breed is largely unknown. By analyzing and comparing whole-genome sequencing data from 20 white raccoon dogs and 38 normal raccoon dogs, we detected an increased occurrence of loss-of-function (LoF) mutations in white raccoon dogs compared with normal raccoon dogs. With the finding of a significantly higher dosage of homozygous missense mutations in the white raccoon dog genome, we detected a greater fitness cost in white raccoon dogs. Although a much higher FROH level for ROH fragments longer than 1 Mb has been reported in white raccoon dogs, we did not detect a genetic signal of genetic purging in white raccoon dogs. This study provides valuable genomic resources and new insights into the accumulation of mutation loads in farmed raccoon dogs.
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Affiliation(s)
- Yinping Tian
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Y.T.); (Y.L.); (Y.M.); (J.L.); (J.F.); (C.L.); (L.B.); (Y.F.); (H.L.); (Y.X.); (T.L.); (Z.H.)
| | - Yu Lin
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Y.T.); (Y.L.); (Y.M.); (J.L.); (J.F.); (C.L.); (L.B.); (Y.F.); (H.L.); (Y.X.); (T.L.); (Z.H.)
| | - Yue Ma
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Y.T.); (Y.L.); (Y.M.); (J.L.); (J.F.); (C.L.); (L.B.); (Y.F.); (H.L.); (Y.X.); (T.L.); (Z.H.)
| | - Jiayi Li
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Y.T.); (Y.L.); (Y.M.); (J.L.); (J.F.); (C.L.); (L.B.); (Y.F.); (H.L.); (Y.X.); (T.L.); (Z.H.)
| | - Sunil Kumar Sahu
- BGI Research, Wuhan 430074, China;
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China;
| | - Jiale Fan
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Y.T.); (Y.L.); (Y.M.); (J.L.); (J.F.); (C.L.); (L.B.); (Y.F.); (H.L.); (Y.X.); (T.L.); (Z.H.)
| | - Chen Lin
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Y.T.); (Y.L.); (Y.M.); (J.L.); (J.F.); (C.L.); (L.B.); (Y.F.); (H.L.); (Y.X.); (T.L.); (Z.H.)
| | - Zhiang Li
- College of Life Science, Northeast Forestry University, Harbin 150040, China; (Z.L.); (Q.L.)
| | - Minhui Shi
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China;
| | - Fengping He
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China;
| | - Lianduo Bai
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Y.T.); (Y.L.); (Y.M.); (J.L.); (J.F.); (C.L.); (L.B.); (Y.F.); (H.L.); (Y.X.); (T.L.); (Z.H.)
| | - Yuan Fu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Y.T.); (Y.L.); (Y.M.); (J.L.); (J.F.); (C.L.); (L.B.); (Y.F.); (H.L.); (Y.X.); (T.L.); (Z.H.)
| | - Zhangwen Deng
- Guangxi Zhuang Autonomous Region Forest Inventory and Planning Institute, Nanning 530011, China;
| | - Huabing Guo
- Forest Inventory and Planning Institute of Jilin Province, Changchun 130022, China;
| | - Haimeng Li
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Y.T.); (Y.L.); (Y.M.); (J.L.); (J.F.); (C.L.); (L.B.); (Y.F.); (H.L.); (Y.X.); (T.L.); (Z.H.)
- Heilongjiang Key Laboratory of Complex Traits and Protein Machines in Organisms, Harbin 150040, China
| | - Qiye Li
- College of Life Science, Northeast Forestry University, Harbin 150040, China; (Z.L.); (Q.L.)
| | - Yanchun Xu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Y.T.); (Y.L.); (Y.M.); (J.L.); (J.F.); (C.L.); (L.B.); (Y.F.); (H.L.); (Y.X.); (T.L.); (Z.H.)
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
| | - Tianming Lan
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Y.T.); (Y.L.); (Y.M.); (J.L.); (J.F.); (C.L.); (L.B.); (Y.F.); (H.L.); (Y.X.); (T.L.); (Z.H.)
- Heilongjiang Key Laboratory of Complex Traits and Protein Machines in Organisms, Harbin 150040, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
| | - Zhijun Hou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Y.T.); (Y.L.); (Y.M.); (J.L.); (J.F.); (C.L.); (L.B.); (Y.F.); (H.L.); (Y.X.); (T.L.); (Z.H.)
| | - Yanling Xia
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Y.T.); (Y.L.); (Y.M.); (J.L.); (J.F.); (C.L.); (L.B.); (Y.F.); (H.L.); (Y.X.); (T.L.); (Z.H.)
| | - Shuhui Yang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (Y.T.); (Y.L.); (Y.M.); (J.L.); (J.F.); (C.L.); (L.B.); (Y.F.); (H.L.); (Y.X.); (T.L.); (Z.H.)
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Wang L, Yang H, Munyaradzia HB, Zhu W, Dong ZJ. The mRNA and protein datasets after cold stress of red tilapia. Sci Data 2024; 11:1177. [PMID: 39477964 PMCID: PMC11525570 DOI: 10.1038/s41597-024-04025-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Accepted: 10/22/2024] [Indexed: 11/02/2024] Open
Abstract
The cold stress during overwintering is considered the bottleneck of red tilapia industry. In this study, the water temperature (WT) was reduced by 2 °C per day from 20 °C to 8 °C in the cold (C) group. Then transcriptome of brain(B), gill(G), liver(L) and skin(S) tissues and proteome of G, L and S tissues were performed in C and Normal (N) (WT: 20 °C) group. 24 transcriptomes were completed, and 168.8 Gb data were obtained, with more than 5.89 Gb clean data of each sample. A total of 30499 annotation results were obtained with 3199, 4697, 4393, and 3382 differentially expressed mRNAs in NB_vs_CB, NG_vs_CG, NL_vs_CL, NS_vs_CS. 18 DIA proteomes were performed, and 6341 proteins were obtained with 178, 500 and 166 differentially expressed proteins in NG_vs_CG, NL_vs_CL, NS_vs_CS. Our datasets can be reused for key genes and proteins identification, omics joint analysis and regulatory mechanism analysis of low temperature or cold stress in fish, which will help understanding the regulatory mechanism and facilitate the molecular selective breeding of cold-resistant varieties of fish.
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Affiliation(s)
- Lanmei Wang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, Jiangsu, China.
- Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Wuxi, 214081, Jiangsu, China.
| | - Haoran Yang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, Jiangsu, China
| | | | - Wenbin Zhu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, Jiangsu, China
- Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Wuxi, 214081, Jiangsu, China
| | - Zai-Jie Dong
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, Jiangsu, China
- Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Wuxi, 214081, Jiangsu, China
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Song F, Yang Z, Shi L, Zheng D, Liang H, Wang L, Sun J, Luo J. Transcriptome analysis reveals candidate miRNAs involved in skin color differentiation of juvenile Plectropomus leopardus in response to different background colors. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 48:101141. [PMID: 37690214 DOI: 10.1016/j.cbd.2023.101141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 09/12/2023]
Abstract
Red skin color in Plectropomus leopardus is important to its ornamental and economic value. However, the color of P. leopardus can change during the rearing process, darkening and turning black due to the influence of environmental background color. The underlying molecular mechanisms that regulate this phenomenon remain unclear. MicroRNAs (miRNAs) are endogenous, small non-coding RNAs that play important roles in numerous biological processes, such as skin differentiation and color formation in many animals. Therefore, we performed miRNA sequencing of P. leopardus skin before (initial) and after rearing with three different background colors (white, black, and blue) using Illumina sequencing to identify candidate miRNAs that may contribute to skin color differentiation. In total, 154,271,376 clean reads were obtained, with over 92 % of them successfully mapped to the P. leopardus reference genome. The miRNA length distributions of all samples displayed peaks around a typical length of 22 nt. Within these sequences, 243 known and 287 novel miRNAs were identified. A total of 65 significantly differentially expressed miRNAs (DEMs) were identified (P < 0.05), including 40 known DEMs and 25 novel DEMs. These DEMs included novel_561, miR-141-3p, and miR-129-5p, whose target genes were primarily associated with pigmentation related processes, including tyrosine metabolism, melanogenesis, and the Wnt signaling pathway. These findings shed light on the potential roles of miRNAs in the darkening of skin color in P. leopardus, thus enhancing our understanding of the molecular mechanisms involved in skin pigmentation differentiation in this species.
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Affiliation(s)
- Feibiao Song
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Sanya Nanfan Research Institute of Hainan University, College of Marine Sciences, Hainan University, Haikou 570228, China.
| | - Zihang Yang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Sanya Nanfan Research Institute of Hainan University, College of Marine Sciences, Hainan University, Haikou 570228, China
| | - Liping Shi
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Sanya Nanfan Research Institute of Hainan University, College of Marine Sciences, Hainan University, Haikou 570228, China
| | - Da Zheng
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Sanya Nanfan Research Institute of Hainan University, College of Marine Sciences, Hainan University, Haikou 570228, China
| | - Huan Liang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Sanya Nanfan Research Institute of Hainan University, College of Marine Sciences, Hainan University, Haikou 570228, China
| | - Lei Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Sanya Nanfan Research Institute of Hainan University, College of Marine Sciences, Hainan University, Haikou 570228, China
| | - Junlong Sun
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Sanya Nanfan Research Institute of Hainan University, College of Marine Sciences, Hainan University, Haikou 570228, China
| | - Jian Luo
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Sanya Nanfan Research Institute of Hainan University, College of Marine Sciences, Hainan University, Haikou 570228, China.
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Li Z, Xu C, Yu H, Kong L, Liu S, Li Q. Effects of Dietary Cystine and Tyrosine Supplementation on Melanin Synthesis in the Pacific Oyster (Crassostrea gigas). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:537-547. [PMID: 37369882 DOI: 10.1007/s10126-023-10223-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 06/07/2023] [Indexed: 06/29/2023]
Abstract
Melanogenesis is a multistep process to produce melanin for dark pigmentation in skin coloration. Previous studies in vertebrates demonstrated that cystine and tyrosine amino acids are involved in the melanin synthesis. However, very little is known about the melanogenesis in bivalve. In this study, cystine supplementation for 30 days significantly upregulated the expression of CgB-aat1, CgCbs and CgTyr and pheomelanin content in the Pacific oyster Crassostrea gigas. Transmission electron microscope (TEM) results revealed more melanosomes in the connective tissue and melanin granules were secreted in epithelium of mantle. In contrast, tyrosine supplementation had no clear effect on melanogenesis except the gene expression changes of CgB-aat1 and CgCbs. In addition, prolonged supplementation of cystine or tyrosine for 60 days had a negative impact on melanogenesis. Indeed, after 60 days, expression of most of the melanin synthesis-related genes under study was decreased, and melanin content was significantly reduced, indicating that cystine and tyrosine might inhibit production of eumelanin and pheomelanin, respectively. In addition, in vitro analysis using primary cell culture from mantle tissue indicated that incubation with cystine, tyrosine, or B-AAT1 polypeptide, CBS/TYR recombinant proteins induced the increase of CgB-aat1 and CgCbs expression in a dose-dependent manner, suggesting the presence of a regulatory network in response to cystine and tyrosine amino acids intakes in pheomelanin synthesis-related gene expression. Taken together, these data indicate that cystine-CgB-aat1-CgCbs-CgTyr axis is a potential regulator of the pheomelanin biosynthesis pathway, and thus plays an important role in the mantle pigmentation in C. gigas. This work provides a new clue for selective cultivation of oyster strains with specific shell colors in bivalve breeding.
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Affiliation(s)
- Zhuanzhuan Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Chengxun Xu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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Li Z, Hu B, Du L, Hou C, Li Q. Involvement of B-aat1 and Cbs in regulating mantle pigmentation in the Pacific oyster (Crassostrea gigas). Mol Biol Rep 2023; 50:377-387. [PMID: 36335521 DOI: 10.1007/s11033-022-08037-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Shell color formation is an important physiological process in bivalves, the molecular genetic basis has potential application in bivalve aquaculture, but there is still remaining unclear about this issue. The cystine/glutamate transporter (Slc7a11) and cystathionine beta-synthase (Cbs) are integral genes in pheomelanin synthesis pathway, which is vital to skin pigmentation. METHODS AND RESULTS Here, the sequences of b (0, +) -type amino acid transporter 1 (B-aat1) and Cbs in Pacific oyster (Crassostrea gigas) (CgB-aat1, CgCbs) were characterized. Phylogenetically, the deduced amino acid sequences of CgB-aat1 and CgCbs both possessed conserved features. Genes were both ubiquitously expressed in six tested tissues with more abundant expression level in central mantle. Besides, the polyclonal antibodies of CgB-aat1, CgCbs, CgTyr, and CgTyrp2 were successfully prepared. Immunofluorescence analysis revealed that CgB-aat1 and CgCbs proteins were both expressed in gill rudiments of eyed-larvae and concentrated mainly in cytoplasm of epithelial cell and nerve axons in mantle. Additionally, after CgB-aat1 or CgCbs silencing, expressions at mRNA and protein levels of CgB-aat1 and CgCbs involved in pheomelanin synthesis were significantly suppressed, and CgTyr, CgTyrp1 and CgTyrp2 related to eumelanin synthesis were also down-regulated but no apparent differences, respectively. Moreover, micrographic examination found less brown-granules at mantle edge in CgB-aat1 interference group. CONCLUSION These results implied that pheomelanin synthesis was possible induced by CgB-aat1-CgTyr-CgCbs axis, and it played an essential role on mantle pigmentation in the oysters. These findings provide the useful genetic knowledge and enrich the physiological information for the shell color formation in bivalve aquaculture.
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Affiliation(s)
- Zhuanzhuan Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Biyang Hu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Lijie Du
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Chunhao Hou
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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Valette T, Leitwein M, Lascaux JM, Desmarais E, Berrebi P, Guinand B. Redundancy analysis, genome-wide association studies and the pigmentation of brown trout (Salmo trutta L.). JOURNAL OF FISH BIOLOGY 2023; 102:96-118. [PMID: 36218076 DOI: 10.1111/jfb.15243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
The association of molecular variants with phenotypic variation is a main issue in biology, often tackled with genome-wide association studies (GWAS). GWAS are challenging, with increasing, but still limited, use in evolutionary biology. We used redundancy analysis (RDA) as a complimentary ordination approach to single- and multitrait GWAS to explore the molecular basis of pigmentation variation in brown trout (Salmo trutta) belonging to wild populations impacted by hatchery fish. Based on 75,684 single nucleotide polymorphic (SNP) markers, RDA, single- and multitrait GWAS allowed the extraction of 337 independent colour patterning loci (CPLs) associated with trout pigmentation traits, such as the number of red and black spots on flanks. Collectively, these CPLs (i) mapped onto 35 out of 40 brown trout linkage groups indicating a polygenic genomic architecture of pigmentation, (ii) were found to be associated with 218 candidate genes, including 197 genes formerly mentioned in the literature associated to skin pigmentation, skin patterning, differentiation or structure notably in a close relative, the rainbow trout (Onchorhynchus mykiss), and (iii) related to functions relevant to pigmentation variation (e.g., calcium- and ion-binding, cell adhesion). Annotated CPLs include genes with well-known pigmentation effects (e.g., PMEL, SLC45A2, SOX10), but also markers associated with genes formerly found expressed in rainbow or brown trout skins. RDA was also shown to be useful to investigate management issues, especially the dynamics of trout pigmentation submitted to several generations of hatchery introgression.
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Davoudi P, Do DN, Rathgeber B, Colombo SM, Sargolzaei M, Plastow G, Wang Z, Karimi K, Hu G, Valipour S, Miar Y. Genome-wide detection of copy number variation in American mink using whole-genome sequencing. BMC Genomics 2022; 23:649. [PMID: 36096727 PMCID: PMC9468235 DOI: 10.1186/s12864-022-08874-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/05/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Copy number variations (CNVs) represent a major source of genetic diversity and contribute to the phenotypic variation of economically important traits in livestock species. In this study, we report the first genome-wide CNV analysis of American mink using whole-genome sequence data from 100 individuals. The analyses were performed by three complementary software programs including CNVpytor, DELLY and Manta. RESULTS A total of 164,733 CNVs (144,517 deletions and 20,216 duplications) were identified representing 5378 CNV regions (CNVR) after merging overlapping CNVs, covering 47.3 Mb (1.9%) of the mink autosomal genome. Gene Ontology and KEGG pathway enrichment analyses of 1391 genes that overlapped CNVR revealed potential role of CNVs in a wide range of biological, molecular and cellular functions, e.g., pathways related to growth (regulation of actin cytoskeleton, and cAMP signaling pathways), behavior (axon guidance, circadian entrainment, and glutamatergic synapse), lipid metabolism (phospholipid binding, sphingolipid metabolism and regulation of lipolysis in adipocytes), and immune response (Wnt signaling, Fc receptor signaling, and GTPase regulator activity pathways). Furthermore, several CNVR-harbored genes associated with fur characteristics and development (MYO5A, RAB27B, FGF12, SLC7A11, EXOC2), and immune system processes (SWAP70, FYN, ORAI1, TRPM2, and FOXO3). CONCLUSIONS This study presents the first genome-wide CNV map of American mink. We identified 5378 CNVR in the mink genome and investigated genes that overlapped with CNVR. The results suggest potential links with mink behaviour as well as their possible impact on fur quality and immune response. Overall, the results provide new resources for mink genome analysis, serving as a guideline for future investigations in which genomic structural variations are present.
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Affiliation(s)
- Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Duy Ngoc Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Bruce Rathgeber
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Stefanie M Colombo
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
- Select Sires Inc., Plain City, OH, USA
| | - Graham Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Karim Karimi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Guoyu Hu
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Shafagh Valipour
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada.
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Wang C, Lu B, Li T, Liang G, Xu M, Liu X, Tao W, Zhou L, Kocher TD, Wang D. Nile Tilapia: A Model for Studying Teleost Color Patterns. J Hered 2021; 112:469-484. [PMID: 34027978 DOI: 10.1093/jhered/esab018] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/08/2021] [Indexed: 11/12/2022] Open
Abstract
The diverse color patterns of cichlid fishes play an important role in mate choice and speciation. Here we develop the Nile tilapia (Oreochromis niloticus) as a model system for studying the developmental genetics of cichlid color patterns. We identified 4 types of pigment cells: melanophores, xanthophores, iridophores and erythrophores, and characterized their first appearance in wild-type fish. We mutated 25 genes involved in melanogenesis, pteridine metabolism, and the carotenoid absorption and cleavage pathways. Among the 25 mutated genes, 13 genes had a phenotype in both the F0 and F2 generations. None of F1 heterozygotes had phenotype. By comparing the color pattern of our mutants with that of red tilapia (Oreochromis spp), a natural mutant produced during hybridization of tilapia species, we found that the pigmentation of the body and eye is controlled by different genes. Previously studied genes like mitf, kita/kitlga, pmel, tyrb, hps4, gch2, csf1ra, pax7b, and bco2b were proved to be of great significance for color patterning in tilapia. Our results suggested that tilapia, a fish with 4 types of pigment cells and a vertically barred wild-type color pattern, together with various natural and artificially induced color gene mutants, can serve as an excellent model system for study color patterning in vertebrates.
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Affiliation(s)
- Chenxu Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Baoyue Lu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Tao Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Guangyuan Liang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Mengmeng Xu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Xingyong Liu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Linyan Zhou
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
| | - Thomas D Kocher
- the Department of Biology, University of Maryland, College Park, MD
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
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Vissio PG, Darias MJ, Di Yorio MP, Pérez Sirkin DI, Delgadin TH. Fish skin pigmentation in aquaculture: The influence of rearing conditions and its neuroendocrine regulation. Gen Comp Endocrinol 2021; 301:113662. [PMID: 33220300 DOI: 10.1016/j.ygcen.2020.113662] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 11/05/2020] [Accepted: 11/12/2020] [Indexed: 12/14/2022]
Abstract
Skin pigmentation pattern is a species-specific characteristic that depends on the number and the spatial combination of several types of chromatophores. This feature can change during life, for example in the metamorphosis or reproductive cycle, or as a response to biotic and/or abiotic environmental cues (nutrition, UV incidence, surrounding luminosity, and social interactions). Fish skin pigmentation is one of the most important quality criteria dictating the market value of both aquaculture and ornamental species because it serves as an external signal to infer its welfare and the culture conditions used. For that reason, several studies have been conducted aiming to understand the mechanisms underlying fish pigmentation as well as the influence exerted by rearing conditions. In this context, the present review focuses on the current knowledge on endocrine regulation of fish pigmentation as well as on the aquaculture conditions affecting skin coloration. Available information on Iberoamerican fish species cultured is presented.
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Affiliation(s)
- Paula G Vissio
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental. Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires. Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), CONICET, Buenos Aires, Argentina.
| | - Maria J Darias
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - María P Di Yorio
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental. Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires. Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), CONICET, Buenos Aires, Argentina
| | - Daniela I Pérez Sirkin
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental. Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires. Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), CONICET, Buenos Aires, Argentina
| | - Tomás H Delgadin
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental. Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires. Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), CONICET, Buenos Aires, Argentina
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