Chromosome-level genome assembly of the glass catfish(Kryptopterus vitreolus)reveals molecular clues to its transparent phenotypeOACSTPCD
Glass catfish(Kryptopterus vitreolus)are notable in the aquarium trade for their highly transparent body pattern.This transparency is due to the loss of most reflective iridophores and light-absorbing melanophores in the main body,although certain black and silver pigments remain in the face and head.To date,however,the molecular mechanisms underlying this transparent phenotype remain largely unknown.To explore the genetic basis of this transparency,we constructed a chromosome-level haplotypic genome assembly for the glass catfish,encompassing 32 chromosomes and 23344 protein-coding genes,using PacBio and Hi-C sequencing technologies and standard assembly and annotation pipelines.Analysis revealed a premature stop codon in the putative albinism-related tyrp1b gene,encoding tyrosinase-related protein 1,rendering it a nonfunctional pseudogene.Notably,a synteny comparison with over 30 other fish species identified the loss of the endothelin-3(edn3b)gene in the glass catfish genome.To investigate the role of edn3b,we generated edn3b^(−/−)mutant zebrafish,which exhibited a remarkable reduction in black pigments in body surface stripes compared to wild-type zebrafish.These findings indicate that edn3b loss contributes to the transparent phenotype of the glass catfish.Our high-quality chromosome-scale genome assembly and identification of key genes provide important molecular insights into the transparent phenotype of glass catfish.These findings not only enhance our understanding of the molecular mechanisms underlying transparency in glass catfish,but also offer a valuable genetic resource for further research on pigmentation in various animal species.
Chao Bian;Rui-Han Li;Zhi-Qiang Ruan;Wei-Ting Chen;Yu Huang;Li-Yue Liu;Hong-Ling Zhou;Cheong-Meng Chong;Xi-Dong Mu;Qiong Shi
Laboratory of Aquatic Genomics,College of Life Sciences and Oceanography,Shenzhen University,Shenzhen,Guangdong 518057,China Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species,Ministry of Agriculture and Rural Affairs,Guangdong Modern.Recreational Fisheries Engineering Technology Center,Pearl River Fisheries Research Institute,Chinese Academy of Fishery Sciences,Guangzhou,Guangdong 510380,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,Shenzhen,Guangdong 518081,ChinaShenzhen 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 CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization&Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province,Chengdu Institute of Biology,Chinese Academy of Sciences,Chengdu,Sichuan 610041,ChinaShenzhen 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,ChinaSchool of Life Sciences,Jiaying University,Meizhou,Guangdong 514015,ChinaShenzhen 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,ChinaChina Zebrafish Resource Center,National Aquatic Biological Resource Center,State Key Laboratory of Freshwater Ecology and Biotechnology,Institute of Hydrobiology,Chinese Academy of Science,Wuhan,Hubei 430072,ChinaShenzhen Branch,Guangdong Laboratory for Lingnan Modern Agriculture,Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs,Agricultural Genomics Institute at Shenzhen,Chinese Academy of Agricultural Sciences,Shenzhen,Guangdong 518116,ChinaState Key Laboratory of Quality Research in Chinese Medicine,Institute of Chinese Medical Sciences,University of Macao,Macao,Macao 999078,ChinaKey Laboratory of Prevention and Control for Aquatic Invasive Alien Species,Ministry of Agriculture and Rural Affairs,Guangdong Modern.Recreational Fisheries Engineering Technology Center,Pearl River Fisheries Research Institute,Chinese Academy of Fishery Sciences,Guangzhou,Guangdong 510380,ChinaLaboratory of Aquatic Genomics,College of Life Sciences and Oceanography,Shenzhen University,Shenzhen,Guangdong 518057,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,Shenzhen,Guangdong 518081,China Center for Aquatic Genomics,College of Life Sciences,Neijiang Normal University,Neijiang,Sichuan 641100,China
水产学
Glass catfishWhole-genome sequencingedn3b−/−mutantTransparent phenotype
《Zoological Research》 2024 (5)
P.1027-1036,10
supported by the National Key Research and Development Program of China(2022YFE0139700,2023YFE0205100)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(20220202)Guangdong Provincial Special Fund for Modern Agriculture Industry Technology Innovation Team(2023KJ150)China-ASEAN Maritime Cooperation Fund(CAMC-2018F)National Freshwater Genetic Resource Center(FGRC18537)Guangdong Rural Revitalization Strategy Special Provincial Organization and Implementation Project Funds(2022-SBH-00-001)。
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