title: The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts.
abstract: The Asian arowana (Scleropages formosus), one of the world's most expensive cultivated ornamental fishes, is an endangered species. It represents an ancient lineage of teleosts: the Osteoglossomorpha. Here, we provide a high-quality chromosome-level reference genome of a female golden-variety arowana using a combination of deep shotgun sequencing and high-resolution linkage mapping. In addition, we have also generated two draft genome assemblies for the red and green varieties. Phylogenomic analysis supports a sister group relationship between Osteoglossomorpha (bonytongues) and Elopomorpha (eels and relatives), with the two clades together forming a sister group of Clupeocephala which includes all the remaining teleosts. The arowana genome retains the full complement of eight Hox clusters unlike the African butterfly fish (Pantodon buchholzi), another bonytongue fish, which possess only five Hox clusters. Differential gene expression among three varieties provides insights into the genetic basis of colour variation. A potential heterogametic sex chromosome is identified in the female arowana karyotype, suggesting that the sex is determined by a ZW/ZZ sex chromosomal system. The high-quality reference genome of the golden arowana and the draft assemblies of the red and green varieties are valuable resources for understanding the biology, adaptation and behaviour of Asian arowanas.
authors.affiliation: Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen 518083, China.|BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Bian
authors.affiliation: Key Laboratory of Tropical &Subtropical Fishery Resource Application &Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
authors.forename: Yinchang
authors.initials: Y
authors.lastname: Hu
authors.affiliation: Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore.
authors.forename: Vydianathan
authors.initials: V
authors.lastname: Ravi
authors.affiliation: Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.|Laboratory of Chromosome Structure and Function, Department of Cytology and Histology, Biological Faculty, Saint Petersburg State University, Saint-Petersburg 198504, Russia.
authors.forename: Inna S
authors.initials: IS
authors.lastname: Kuznetsova
authors.affiliation: Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
authors.forename: Xueyan
authors.initials: X
authors.lastname: Shen
authors.affiliation: Key Laboratory of Tropical &Subtropical Fishery Resource Application &Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
authors.forename: Xidong
authors.initials: X
authors.lastname: Mu
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen 518083, China.|BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Xinxin
authors.initials: X
authors.lastname: You
authors.affiliation: Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen 518083, China.|BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Jia
authors.initials: J
authors.lastname: Li
authors.affiliation: Realbio Genomics Institute, Shanghai 200050, China.
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Li
authors.affiliation: Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen 518083, China.|BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Qiu
authors.affiliation: Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore.
authors.forename: Boon-Hui
authors.initials: BH
authors.lastname: Tay
authors.affiliation: Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
authors.forename: Natascha May
authors.initials: NM
authors.lastname: Thevasagayam
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg 199004, Russia.
authors.forename: Aleksey S
authors.initials: AS
authors.lastname: Komissarov
authors.affiliation: Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.|Novosibirsk State University, Novosibirsk 630090, Russia.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Trifonov
authors.affiliation: Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
authors.forename: Marsel
authors.initials: M
authors.lastname: Kabilov
authors.affiliation: Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
authors.forename: Alexey
authors.initials: A
authors.lastname: Tupikin
authors.affiliation: Key Laboratory of Tropical &Subtropical Fishery Resource Application &Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
authors.forename: Jianren
authors.initials: J
authors.lastname: Luo
authors.affiliation: Key Laboratory of Tropical &Subtropical Fishery Resource Application &Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Key Laboratory of Tropical &Subtropical Fishery Resource Application &Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
authors.forename: Hongmei
authors.initials: H
authors.lastname: Song
authors.affiliation: Key Laboratory of Tropical &Subtropical Fishery Resource Application &Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Liu
authors.affiliation: Key Laboratory of Tropical &Subtropical Fishery Resource Application &Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
authors.forename: Xuejie
authors.initials: X
authors.lastname: Wang
authors.affiliation: Key Laboratory of Tropical &Subtropical Fishery Resource Application &Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
authors.forename: Dangen
authors.initials: D
authors.lastname: Gu
authors.affiliation: Key Laboratory of Tropical &Subtropical Fishery Resource Application &Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
authors.forename: Yexin
authors.initials: Y
authors.lastname: Yang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Wujiao
authors.initials: W
authors.lastname: Li
authors.affiliation: Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, BE1410 Brunei Darussalam.
authors.forename: Gianluca
authors.initials: G
authors.lastname: Polgar
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Guangyi
authors.initials: G
authors.lastname: Fan
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Zeng
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: He
authors.initials: H
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Zijun
authors.initials: Z
authors.lastname: Xiong
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Zhujing
authors.initials: Z
authors.lastname: Tang
authors.affiliation: Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen 518083, China.|BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Peng
authors.affiliation: Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen 518083, China.|BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Ruan
authors.affiliation: Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen 518083, China.|BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Hui
authors.initials: H
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authors.affiliation: Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen 518083, China.|BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Jieming
authors.initials: J
authors.lastname: Chen
authors.affiliation: Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen 518083, China.|BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Mingjun
authors.initials: M
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authors.affiliation: Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen 518083, China.|BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Huang
authors.affiliation: Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen 518083, China.|BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Min
authors.initials: M
authors.lastname: Wang
authors.affiliation: Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen 518083, China.|BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Xiaomeng
authors.initials: X
authors.lastname: Zhao
authors.affiliation: Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen 518083, China.|BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Guojun
authors.initials: G
authors.lastname: Hu
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|James D. Watson Institute of Genome Science, Hangzhou 310008, China.|Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|James D. Watson Institute of Genome Science, Hangzhou 310008, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|James D. Watson Institute of Genome Science, Hangzhou 310008, China.|Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
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authors.initials: X
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authors.affiliation: Dalian Ocean University, Dalian 116023, China.
authors.forename: Linsheng
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authors.affiliation: Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
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authors.affiliation: Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
authors.forename: Pao
authors.initials: P
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authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|BGI-Zhenjiang Institute of Hydrobiology, Zhenjiang 212000, China.
authors.forename: Junmin
authors.initials: J
authors.lastname: Xu
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg 199004, Russia.|Oceanographic Center, Nova Southeastern University Ft. Lauderdale, Ft Lauderdale, Florida 33004, USA.
authors.forename: Stephen J
authors.initials: SJ
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authors.affiliation: Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.|Department of Animal Sciences and Breeding, Georgikon Faculty, University of Pannonia, H-8230 Keszthely, Hungary.|Centre for Comparative Genomics, Murdoch University, Murdoch, 6150 Australia.
authors.forename: László
authors.initials: L
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authors.affiliation: Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore.
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authors.affiliation: Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen 518083, China.|BGI-Shenzhen, Shenzhen 518083, China.|BGI-Zhenjiang Institute of Hydrobiology, Zhenjiang 212000, China.
authors.forename: Qiong
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mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D005260:Female; D005399:Fishes / Q000235:genetics*; D016678:Genome; D018895:Microsatellite Repeats / Q000235:genetics; D010802:Phylogeny; D012730:Sex Chromosomes / Q000235:genetics