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PMID: 27089831 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts.

Scientific reports ·Vol. 6 ·2016-04-19 ·Pages 24501

Bian C, Hu Y, Ravi V, Kuznetsova IS, Shen X, Mu X, Sun Y, You X, Li J, Li X, Qiu Y, Tay BH, Thevasagayam NM, Komissarov AS, Trifonov V, Kabilov M, Tupikin A, Luo J, Liu Y, Song H, Liu C, Wang X, Gu D, Yang Y, Li W, Polgar G, Fan G, Zeng P, Zhang H, Xiong Z, Tang Z, Peng C, Ruan Z, Yu H, Chen J, Fan M, Huang Y, Wang M, Zhao X, Hu G, Yang H, Wang J, Wang J, Xu X, Song L, Xu G, Xu P, Xu J, O'Brien SJ, Orbán L, Venkatesh B, Shi Q

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.

MeSH Terms
Animals Evolution, Molecular Female Fishes/genetics Genome Microsatellite Repeats/genetics Phylogeny Sex Chromosomes/genetics
Authors & Affiliations
52 authors, click to expand affiliations / ORCID
Bian Chao
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.
Hu Yinchang
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.
Ravi Vydianathan
Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore.
Kuznetsova Inna S
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.
Shen Xueyan
Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
Mu Xidong
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.
Sun Ying
BGI-Shenzhen, Shenzhen 518083, China.
You Xinxin
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.
Li Jia
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.
Li Xiaofeng
Realbio Genomics Institute, Shanghai 200050, China.
Qiu Ying
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.
Tay Boon-Hui
Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore.
Thevasagayam Natascha May
Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
Komissarov Aleksey S
Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg 199004, Russia.
Trifonov Vladimir
Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia. | Novosibirsk State University, Novosibirsk 630090, Russia.
Kabilov Marsel
Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
Tupikin Alexey
Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
Luo Jianren
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.
Liu Yi
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.
Song Hongmei
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.
Liu Chao
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.
Wang Xuejie
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.
Gu Dangen
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.
Yang Yexin
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.
Li Wujiao
BGI-Shenzhen, Shenzhen 518083, China.
Polgar Gianluca
Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, BE1410 Brunei Darussalam.
Fan Guangyi
BGI-Shenzhen, Shenzhen 518083, China.
Zeng Peng
BGI-Shenzhen, Shenzhen 518083, China.
Zhang He
BGI-Shenzhen, Shenzhen 518083, China.
Xiong Zijun
BGI-Shenzhen, Shenzhen 518083, China.
Tang Zhujing
BGI-Shenzhen, Shenzhen 518083, China.
Peng Chao
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.
Ruan Zhiqiang
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.
Yu Hui
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.
Chen Jieming
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.
Fan Mingjun
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.
Huang Yu
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.
Wang Min
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.
Zhao Xiaomeng
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.
Hu Guojun
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.
Yang Huanming
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.
Wang Jian
BGI-Shenzhen, Shenzhen 518083, China. | James D. Watson Institute of Genome Science, Hangzhou 310008, China.
Wang Jun
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.
Xu Xun
BGI-Shenzhen, Shenzhen 518083, China.
Song Linsheng
Dalian Ocean University, Dalian 116023, China.
Xu Gangchun
Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
Xu Pao
Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
Xu Junmin
BGI-Shenzhen, Shenzhen 518083, China. | BGI-Zhenjiang Institute of Hydrobiology, Zhenjiang 212000, China.
O'Brien Stephen J
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.
Orbán László
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.
Venkatesh Byrappa
Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore.
Shi Qiong
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.
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Article Info
Journal
Scientific reports
Abbr.
Sci Rep
ISSN
2045-2322
DOI
10.1038/srep24501
Published
2016-04-19
Epub
2016-00-19
Pages
24501
Language
English
Region
England
NLM ID
101563288
PMCID
PMC4835728
Subset
IM
External Links
PubMed source DOI: 10.1038/srep24501 PMC Full Text View journal details
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