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

Chao Bian; Yinchang Hu; Vydianathan Ravi; Inna S. Kuznetsova; Xueyan Shen; Xidong Mu; Ying Sun; Xinxin You; Jia Li; Xiaofeng Li; Ying Qiu; Boon Hui Tay; Natascha May Thevasagayam; Aleksey S. Komissarov; Vladimir Trifonov; Marsel Kabilov; Alexey Tupikin; Jianren Luo; Yi Liu; Hongmei Song; Chao Liu; Xuejie Wang; Dangen Gu; Yexin Yang; Wujiao Li; Gianluca Polgar; Guangyi Fan; Peng Zeng; He Zhang; Zijun Xiong; Zhujing Tang; Chao Peng; Zhiqiang Ruan; Hui Yu; Jieming Chen; Mingjun Fan; Yu Huang; Min Wang; Xiaomeng Zhao; Guojun Hu; Huanming Yang; Jian Wang; Jun Wang; Xun Xu; Linsheng Song; Gangchun Xu; Pao Xu; Junmin Xu; Stephen J. O'Brien; László Orbán; Byrappa Venkatesh; Qiong Shi

doi:10.1038/srep24501

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

Chao Bian, Yinchang Hu, Vydianathan Ravi, Inna S. Kuznetsova, Xueyan Shen, Xidong Mu, Ying Sun, Xinxin You, Jia Li, Xiaofeng Li, Ying Qiu, Boon Hui Tay, Natascha May Thevasagayam, Aleksey S. Komissarov, Vladimir Trifonov, Marsel Kabilov, Alexey Tupikin, Jianren Luo, Yi Liu, Hongmei SongChao Liu, Xuejie Wang, Dangen Gu, Yexin Yang, Wujiao Li, Gianluca Polgar, Guangyi Fan, Peng Zeng, He Zhang, Zijun Xiong, Zhujing Tang, Chao Peng, Zhiqiang Ruan, Hui Yu, Jieming Chen, Mingjun Fan, Yu Huang, Min Wang, Xiaomeng Zhao, Guojun Hu, Huanming Yang, Jian Wang, Jun Wang, Xun Xu, Linsheng Song, Gangchun Xu, Pao Xu, Junmin Xu, Stephen J. O'Brien, László Orbán^*, Byrappa Venkatesh, Qiong Shi

^*Corresponding author af dette arbejde

Genomforskning og Molekylær Biomedicin

44 Citationer (Scopus)

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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.

Originalsprog	Engelsk
Artikelnummer	24501
Tidsskrift	Scientific Reports
Vol/bind	6
Antal sider	17
ISSN	2045-2322
DOI	https://doi.org/10.1038/srep24501
Status	Udgivet - 2016

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10.1038/srep24501Licens: CC BY

Bian_2016_The_asian_arowanaForlagets udgivne version, 2,03 MBLicens: CC BY

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Bian, C., Hu, Y., Ravi, V., Kuznetsova, I. S., Shen, X., Mu, X., Sun, Y., You, X., Li, J., Li, X., Qiu, Y., Tay, B. H., Thevasagayam, N. M., Komissarov, A. S., Trifonov, V., Kabilov, M., Tupikin, A., Luo, J., Liu, Y., ... Shi, Q. (2016). The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts. Scientific Reports, 6, [24501]. https://doi.org/10.1038/srep24501

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 2016, 'The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts', Scientific Reports, bind 6, 24501. https://doi.org/10.1038/srep24501

@article{164ac95858b64e8e94e9829bbbe25756,

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.",

author = "Chao Bian and Yinchang Hu and Vydianathan Ravi and Kuznetsova, {Inna S.} and Xueyan Shen and Xidong Mu and Ying Sun and Xinxin You and Jia Li and Xiaofeng Li and Ying Qiu and Tay, {Boon Hui} and Thevasagayam, {Natascha May} and Komissarov, {Aleksey S.} and Vladimir Trifonov and Marsel Kabilov and Alexey Tupikin and Jianren Luo and Yi Liu and Hongmei Song and Chao Liu and Xuejie Wang and Dangen Gu and Yexin Yang and Wujiao Li and Gianluca Polgar and Guangyi Fan and Peng Zeng and He Zhang and Zijun Xiong and Zhujing Tang and Chao Peng and Zhiqiang Ruan and Hui Yu and Jieming Chen and Mingjun Fan and Yu Huang and Min Wang and Xiaomeng Zhao and Guojun Hu and Huanming Yang and Jian Wang and Jun Wang and Xun Xu and Linsheng Song and Gangchun Xu and Pao Xu and Junmin Xu and O'Brien, {Stephen J.} and L{\'a}szl{\'o} Orb{\'a}n and Byrappa Venkatesh and Qiong Shi",

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T1 - The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts

AU - Bian, Chao

AU - Hu, Yinchang

AU - Ravi, Vydianathan

AU - Kuznetsova, Inna S.

AU - Shen, Xueyan

AU - Mu, Xidong

AU - Sun, Ying

AU - You, Xinxin

AU - Li, Jia

AU - Li, Xiaofeng

AU - Qiu, Ying

AU - Tay, Boon Hui

AU - Thevasagayam, Natascha May

AU - Komissarov, Aleksey S.

AU - Trifonov, Vladimir

AU - Kabilov, Marsel

AU - Tupikin, Alexey

AU - Luo, Jianren

AU - Liu, Yi

AU - Song, Hongmei

AU - Liu, Chao

AU - Wang, Xuejie

AU - Gu, Dangen

AU - Yang, Yexin

AU - Li, Wujiao

AU - Polgar, Gianluca

AU - Fan, Guangyi

AU - Zeng, Peng

AU - Zhang, He

AU - Xiong, Zijun

AU - Tang, Zhujing

AU - Peng, Chao

AU - Ruan, Zhiqiang

AU - Yu, Hui

AU - Chen, Jieming

AU - Fan, Mingjun

AU - Huang, Yu

AU - Wang, Min

AU - Zhao, Xiaomeng

AU - Hu, Guojun

AU - Yang, Huanming

AU - Wang, Jian

AU - Wang, Jun

AU - Xu, Xun

AU - Song, Linsheng

AU - Xu, Gangchun

AU - Xu, Pao

AU - Xu, Junmin

AU - O'Brien, Stephen J.

AU - Orbán, László

AU - Venkatesh, Byrappa

AU - Shi, Qiong

PY - 2016

Y1 - 2016

N2 - 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.

AB - 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.

U2 - 10.1038/srep24501

DO - 10.1038/srep24501

M3 - Journal article

C2 - 27089831

AN - SCOPUS:84973162658

SN - 2045-2322

VL - 6

JO - Scientific Reports

JF - Scientific Reports

M1 - 24501

ER -

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

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