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Yin Y, Zhang Y, Hua Z, Wu A, Pan X, Yang J, Wang X. Muscle transcriptome analysis provides new insights into the growth gap between fast- and slow-growing Sinocyclocheilus grahami. Front Genet 2023; 14:1217952. [PMID: 37538358 PMCID: PMC10394708 DOI: 10.3389/fgene.2023.1217952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023] Open
Abstract
Sinocyclocheilus grahami is an economically valuable and famous fish in Yunnan Province, China. However, given its slow growth (40 g/2 years) and large growth differences among individuals, its growth performance needs to be improved for sustainable future use, in which molecular breeding technology can play an important role. In the current study, we conducted muscle transcriptomic analysis to investigate the growth gaps among individuals and the mechanism underlying growth within 14 fast- and 14 slow-growth S. grahami. In total, 1,647 differentially expressed genes (DEGs) were obtained, including 947 up-regulated and 700 down-regulated DEGs in fast-growth group. Most DEGs were significantly enriched in ECM-receptor interaction, starch and sucrose metabolism, glycolysis/gluconeogenesis, pyruvate metabolism, amino acids biosynthesis and metabolism, peroxisome, and PPAR signaling pathway. Some genes related to glycogen degradation, glucose transport, and glycolysis (e.g., adipoq, prkag1, slc2a1, agl, pygm, pgm1, pfkm, gapdh, aldoa, pgk1, pgam2, bpgm, and eno3) were up-regulated, while some genes related to fatty acid degradation and transport (e.g., acox1, acaa1, fabp1b.1, slc27a1, and slc27a2) and amino acid metabolism (e.g., agxt, shmt1, glula, and cth) were down-regulated in the fast-growth group. Weighted gene co-expression network analysis identified col1a1, col1a2, col5a1, col6a2, col10a1, col26a1, bglap, and krt15 as crucial genes for S. grahami growth. Several genes related to bone and muscle growth (e.g., bmp2, bmp3, tgfb1, tgfb2, gdf10, and myog) were also up-regulated in the fast-growth group. These results suggest that fast-growth fish may uptake adequate energy (e.g., glucose, fatty acid, and amino acids) from fodder, with excess energy substances used to synthesize collagen to accelerate bone and muscle growth after normal life activities are maintained. Moreover, energy uptake may be the root cause, while collagen synthesis may be the direct reason for the growth gap between fast- and slow-growth fish. Hence, improving food intake and collagen synthesis may be crucial for accelerating S. grahami growth, and further research is required to fully understand and confirm these associations.
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Affiliation(s)
- Yanhui Yin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yuanwei Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zexiang Hua
- Fishery Technology Extension Station of Yunnan, Kunming, Yunnan, China
| | - Anli Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xiaofu Pan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Junxing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xiaoai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
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Sun CF, Zhang XH, Dong JJ, You XX, Tian YY, Gao FY, Zhang HT, Shi Q, Ye X, Shi Q, Ye X. Whole-genome resequencing reveals recent signatures of selection in five populations of largemouth bass ( Micropterus salmoides). Zool Res 2023; 44:78-89. [PMID: 36349358 PMCID: PMC9841193 DOI: 10.24272/j.issn.2095-8137.2022.274] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Largemouth bass ( Micropterus salmoides) is an economically important fish species in North America, Europe, and China. Various genetic improvement programs and domestication processes have modified its genome sequence through selective pressure, leaving nucleotide signals that can be detected at the genomic level. In this study, we sequenced 149 largemouth bass fish, including protospecies (imported from the US) and improved breeds (four domestic breeding populations from China). We detected genomic regions harboring certain genes associated with improved traits, which may be useful molecular markers for practical domestication, breeding, and selection. Subsequent analyses of genetic diversity and population structure revealed that the improved breeds have undergone more rigorous genetic changes. Through selective signal analysis, we identified hundreds of putative selective sweep regions in each largemouth bass line. Interestingly, we predicted 103 putative candidate genes potentially subjected to selection, including several associated with growth (p sst1 and grb10), early development ( klf9, sp4, and sp8), and immune traits ( pkn2, sept2, bcl6, and ripk2). These candidate genes represent potential genomic landmarks that could be used to improve important traits of biological and commercial interest. In summary, this study provides a genome-wide map of genetic variations and selection footprints in largemouth bass, which may benefit genetic studies and accelerate genetic improvement of this economically important fish.
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Affiliation(s)
- Cheng-Fei Sun
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Xin-Hui Zhang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun-Jian Dong
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Xin-Xin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan-Yuan Tian
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Feng-Ying Gao
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - He-Tong Zhang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China,E-mail:
| | - Xing Ye
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China,
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Yang S, Leng S, Li Y, Wang X, Zhang Y, Wu A, Gao Y, Wu J, Zeng X, Du X, Pan X. Identification and functional characteristics of two TLR5 subtypes in S. grahami. FISH & SHELLFISH IMMUNOLOGY 2022; 131:707-717. [PMID: 36309325 DOI: 10.1016/j.fsi.2022.10.041] [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: 08/02/2022] [Revised: 10/10/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
TLR5, as a member of Toll-like receptors (TLRs) family in mammals, is responsible for recognizing bacterial flagellin and initiating innate immunity, but its function is still unclear in fish species. In this study, two family members of TLR5 were cloned and identified from Sinocyclocheilus grahami (S. grahami), named sgTLR5a and sgTLR5b. The length of coding sequence of sgTLR5a and sgTLR5b is 2,622 bp and 2,658 bp, encoding 873 and 885 amino acids, respectively. Molecular phylogenetic analysis indicates that sgTLR5a and sgTLR5b have the closest genetic relationship with TLR5M (membrane-type) of Cyprinus carpio and Schizothorax prenanti, respectively. sgTLR5a and sgTLR5b were widely expressed in various tested tissues, of which the expression levels were the highest in skin tissue. After stimulations of Aeromonas hydrophila (A. hydrophila) and flagellin, the expression levels of sgTLR5a and sgTLR5b in liver, spleen and head kidney tissues were strongly up-regulated, but LPS stimulation only increased the expression of sgTLR5b in these tissues. The luciferase reporter assay displayed that sgTLR5a and sgTLR5b could specifically recognize bacterial flagellin and A. hydrophila and activate the downstream NF-κB signaling pathway in HEK293T cells. Moreover, the overexpression of sgTLR5a and sgTLR5b in EPC cells up-regulated the expression levels of IL-8 and TNF. sgTLR5a and sgTLR5b were observed to locate in the intracellular region by confocal microscope. Interestingly, we found that the NF-κB signaling pathway was positively regulated by co-transfecting sgTLR5a or sgTLR5b with TLR trafficking chaperone sgUNC93B1. In conclusion, our results reveal sgTLR5a and sgTLR5b may play an important role in antibacterial response by activating the NF-κB signaling pathway.
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Affiliation(s)
- Shiyong Yang
- Department of Aquaculture, College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, PR China
| | - Sizhu Leng
- Department of Engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, PR China
| | - Yunkun Li
- Department of Engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, PR China
| | - Xiaoai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, PR China; Yunnan Key Laboratory of Plateau Fish Breeding, Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, PR China
| | - Yuanwei Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, PR China; Yunnan Key Laboratory of Plateau Fish Breeding, Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, PR China
| | - Anli Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, PR China; Yunnan Key Laboratory of Plateau Fish Breeding, Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, PR China
| | - Yanfeng Gao
- Chengdu Zoo, Chengdu, 610081, Sichuan, PR China
| | - Jiayun Wu
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, PR China
| | - Xianyin Zeng
- Department of Engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, PR China
| | - Xiaogang Du
- Department of Engineering and Applied Biology, College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, PR China.
| | - Xiaofu Pan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, PR China; Yunnan Key Laboratory of Plateau Fish Breeding, Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, PR China.
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Xin WG, Li XD, Lin YC, Jiang YH, Xu MY, Zhang QL, Wang F, Lin LB. Whole genome analysis of host-associated lactobacillus salivarius and the effects on hepatic antioxidant enzymes and gut microorganisms of Sinocyclocheilus grahami. Front Microbiol 2022; 13:1014970. [PMID: 36386721 PMCID: PMC9648147 DOI: 10.3389/fmicb.2022.1014970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/12/2022] [Indexed: 09/29/2023] Open
Abstract
As a fish unique to Yunnan Province in China, Sinocyclocheilus grahami hosts abundant potential probiotic resources in its intestinal tract. However, the genomic characteristics of the probiotic potential bacteria in its intestine and their effects on S. grahami have not yet been established. In this study, we investigated the functional genomics and host response of a strain, Lactobacillus salivarius S01, isolated from the intestine of S. grahami (bred in captivity). The results revealed that the total length of the genome was 1,737,623 bp (GC content, 33.09%), comprised of 1895 genes, including 22 rRNA operons and 78 transfer RNA genes. Three clusters of antibacterial substances related genes were identified using antiSMASH and BAGEL4 database predictions. In addition, manual examination confirmed the presence of functional genes related to stress resistance, adhesion, immunity, and other genes responsible for probiotic potential in the genome of L. salivarius S01. Subsequently, the probiotic effect of L. salivarius S01 was investigated in vivo by feeding S. grahami a diet with bacterial supplementation. The results showed that potential probiotic supplementation increased the activity of antioxidant enzymes (SOD, CAT, and POD) in the hepar and reduced oxidative damage (MDA). Furthermore, the gut microbial community and diversity of S. grahami from different treatment groups were compared using high-throughput sequencing. The diversity index of the gut microbial community in the group supplemented with potential probiotics was higher than that in the control group, indicating that supplementation with potential probiotics increased gut microbial diversity. At the phylum level, the abundance of Proteobacteria decreased with potential probiotic supplementation, while the abundance of Firmicutes, Actinobacteriota, and Bacteroidota increased. At the genus level, there was a decrease in the abundance of the pathogenic bacterium Aeromonas and an increase in the abundance of the potential probiotic bacterium Bifidobacterium. The results of this study suggest that L. salivarius S01 is a promising potential probiotic candidate that provides multiple benefits for the microbiome of S. grahami.
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Affiliation(s)
- Wei-Gang Xin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Yunnan Kunming, China
- Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Yunnan, Kunming, China
| | - Xin-Dong Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Yunnan Kunming, China
- Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Yunnan, Kunming, China
| | - Yi-Cen Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Yunnan Kunming, China
- Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Yunnan, Kunming, China
| | - Yu-Hang Jiang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Yunnan Kunming, China
- Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Yunnan, Kunming, China
| | - Mei-Yu Xu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Yunnan Kunming, China
- Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Yunnan, Kunming, China
| | - Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Yunnan Kunming, China
- Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Yunnan, Kunming, China
| | - Feng Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Yunnan Kunming, China
- Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Yunnan, Kunming, China
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Yunnan Kunming, China
- Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Yunnan, Kunming, China
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Zhu C, Liu H, Pan Z, Cheng L, Sun Y, Wang H, Chang G, Wu N, Ding H, Zhao H, Zhang L, Yu X. Insights into chromosomal evolution and sex determination of Pseudobagrus ussuriensis (Bagridae, Siluriformes) based on a chromosome-level genome. DNA Res 2022; 29:6647841. [PMID: 35861402 PMCID: PMC9358014 DOI: 10.1093/dnares/dsac028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/20/2022] [Indexed: 12/01/2022] Open
Abstract
Pseudobagrus ussuriensis is an aquaculture catfish with significant sexual dimorphism. In this study, a chromosome-level genome with a size of 741.97 Mb was assembled for female P. ussuriensis. A total of 26 chromosome-level contigs covering 97.34% of the whole-genome assembly were obtained with an N50 of 28.53 Mb and an L50 of 11. A total of 24,075 protein-coding genes were identified, with 91.54% (22,039) genes being functionally annotated. Based on the genome assembly, four chromosome evolution clusters of catfishes were identified and the formation process of P. ussuriensis chromosomes was predicted. A total of 55 sex-related quantitative trait loci (QTLs) with a phenotypic variance explained value of 100% were located on chromosome 8 (chr08). The QTLs and other previously identified sex-specific markers were located in a sex-determining region of 16.83 Mb (from 6.90 to 23.73 Mb) on chr08, which was predicted as the X chromosome. The sex-determining region comprised 554 genes, with 135 of which being differently expressed between males and females/pseudofemales, and 16 candidate sex-determining genes were screened out. The results of this study provided a useful chromosome-level genome for genetic, genomic and evolutionary studies of P. ussuriensis, and also be useful for further studies on sex-determination mechanism analysis and sex-control breeding of this fish.
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Affiliation(s)
- Chuankun Zhu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Haiyang Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences , Guangzhou 510380, China
| | - Zhengjun Pan
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Lei Cheng
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang Fisheries Research Institute, Chinese Academy of Fishery Sciences , Harbin 150070, China
| | - Yanhong Sun
- Wuhan Aquaculture Science Research Institute , Wuhan 430207, China
| | - Hui Wang
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Guoliang Chang
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Nan Wu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Huaiyu Ding
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Haitao Zhao
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University , Huai’an 223300, China
| | - Lei Zhang
- Key Laboratory of Fishery Sustainable Development and Water Environment Protection of Huai’an City, Huai’an Sub Center of the Institute of Hydrobiology, Chinese Academy of Sciences , Huai’an 223002, China
| | - Xiangsheng Yu
- Huai’an Fisheries Technical Guidance Station , Huai’an 223001, China
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Huang Y, Li J, Bian C, Li R, You X, Shi Q. Evolutionary Genomics Reveals Multiple Functions of Arylalkylamine N-Acetyltransferase in Fish. Front Genet 2022; 13:820442. [PMID: 35664299 PMCID: PMC9160868 DOI: 10.3389/fgene.2022.820442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 04/15/2022] [Indexed: 11/21/2022] Open
Abstract
As an important hormone, melatonin participates in endocrine regulation of diverse functions in vertebrates. Its biosynthesis is catalyzed by four cascaded enzymes, among them, arylalkylamine N-acetyltransferase (AANAT) is the most critical one. Although only single aanat gene has been identified in most groups of vertebrates, researchers including us have determined that fish have the most diverse of aanat genes (aanat1a, aanat1b, and aanat2), playing various potential roles such as seasonal migration, amphibious aerial vision, and cave or deep-sea adaptation. With the rapid development of genome and transcriptome sequencing, more and more putative sequences of fish aanat genes are going to be available. Related phylogeny and functional investigations will enrich our understanding of AANAT functions in various fish species.
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Affiliation(s)
- Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
- *Correspondence: Yu Huang, ; Qiong Shi,
| | - Jia Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB-Ugent Center for Plant Systems Biology, Ghent, Belgium
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
- BGI Education Center, College of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, China
| | - Ruihan Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
- BGI Education Center, College of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, China
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
- BGI Education Center, College of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, China
- *Correspondence: Yu Huang, ; Qiong Shi,
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Li R, Wang X, Bian C, Gao Z, Zhang Y, Jiang W, Wang M, You X, Cheng L, Pan X, Yang J, Shi Q. Whole-Genome Sequencing of Sinocyclocheilus maitianheensis Reveals Phylogenetic Evolution and Immunological Variances in Various Sinocyclocheilus Fishes. Front Genet 2021; 12:736500. [PMID: 34675964 PMCID: PMC8523889 DOI: 10.3389/fgene.2021.736500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/06/2021] [Indexed: 12/02/2022] Open
Abstract
An adult Sinocyclocheilus maitianheensis, a surface-dwelling golden-line barbel fish, was collected from Maitian river (Kunming City, Yunnan Province, China) for whole-genome sequencing, assembly, and annotation. We obtained a genome assembly of 1.7 Gb with a scaffold N50 of 1.4 Mb and a contig N50 of 24.7 kb. A total of 39,977 protein-coding genes were annotated. Based on a comparative phylogenetic analysis of five Sinocyclocheilus species and other five representative vertebrates with published genome sequences, we found that S. maitianheensis is close to Sinocyclocheilus anophthalmus (a cave-restricted species with similar locality). Moreover, the assembled genomes of S. maitianheensis and other four Sinocyclocheilus counterparts were used for a fourfold degenerative third-codon transversion (4dTv) analysis. The recent whole-genome duplication (WGD) event was therefore estimated to occur about 18.1 million years ago. Our results also revealed a decreased tendency of copy number in many important genes related to immunity and apoptosis in cave-restricted Sinocyclocheilus species. In summary, we report the first genome assembly of S. maitianheensis, which provides a valuable genetic resource for comparative studies on cavefish biology, species protection, and practical aquaculture of this potentially economical fish.
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Affiliation(s)
- Ruihan Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Xiaoai Wang
- State Key Laboratory of Genetic Resources and Evolution, The Innovative Academy of Seed Design, Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Chao Bian
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Zijian Gao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Yuanwei Zhang
- State Key Laboratory of Genetic Resources and Evolution, The Innovative Academy of Seed Design, Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wansheng Jiang
- Hunan Engineering Laboratory for Chinese Giant Salamander's Resource Protection and Comprehensive Utilization, and Key Laboratory of Hunan Forest and Chemical Industry Engineering, Jishou University, Zhangjiajie, China
| | - Mo Wang
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Faculty of Biodiversity Conservation, Southwest Forestry University, Kunming, China
| | - Xinxin You
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | | | - Xiaofu Pan
- State Key Laboratory of Genetic Resources and Evolution, The Innovative Academy of Seed Design, Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Junxing Yang
- State Key Laboratory of Genetic Resources and Evolution, The Innovative Academy of Seed Design, Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qiong Shi
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
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