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

Bian, Chao; Hu, Yinchang; Ravi, Vydianathan; Kuznetsova, Irina M.; Shen, Xueyan; Mu, Xuemei; Sun, Yu; You, Xinxin; Li, Jia; Li, Xiaofeng; Qiu, Ying; Tay, Boon-Hui; Thevasagayam, Natascha May; Komissarov, Aleksey; Trifonov, Vladimir A.; Kabilov, Мarsel R.; Tupikin, Alexey E.; Luo, Jingjing; Liu, Yi; Song, Hongmei; Liu, Chao; Wang, Xuejie; Gu, Donghong; Yang, Yexin; Li, Wujiao; Polgar, Gianluca; Fan, Guangyi; Zeng, Peng; Zhang, He; Xiong, Zijun; Tang, Zhujing; Peng, Chao; Ruan, Zhiqiang; Yu, Hui; Chen, Jieming; Fan, Mingjun; Huang, Yu; Wang, Min; Zhao, Xiaomeng; Hu, Guojie; Yang, Huanming; Wang, Jian; Wang, Jun; Xu, Xun; Song, Linsheng; Xu, Gaosi; Xu, Pao; Xu, Junmin; O’Brien, Stephen J.; Orbán, László; Venkatesh, Byrappa; Shi, Qiong

doi:10.1038/srep24501

Cited by 95 publications

(110 citation statements)

References 97 publications

(142 reference statements)

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“…Previously, we have generated two mapping families by crossing two pairs of these F1 hybrid brooders. The fostering methods of arowana are described in detail in our related work 4 . We used 94 F2 progenies and their parents for RAD sequencing to construct the high-density genetic map.…”

Section: Methodsmentioning

confidence: 99%

“…Details for the disciplines of filtering were described in our related work 4 . The SOAPfilter v2.2 software (http://soap.genomics.org.cn/index.html) with the optimized parameters (-y -p -g 1 -o clean -M 2 -f 0) was chosen to remove low-quality bases and PCR-replicates as well as adaptor sequences.…”

Section: Methodsmentioning

confidence: 99%

“…A raw sequencing read with a total length of L bp contains (L-K+1) k -mers 7 . Details of the k- mer analysis were provided in our related work 4 . Finally, we estimated that the genome sizes of the golden, red and green varieties are 822, 949 and 897 Mb, respectively.…”

Section: Methodsmentioning

confidence: 99%

“…Our previous study published in Scientific Reports 4 has reported a primary genome assembly of a female golden arowana and the draft genomes of the green and red varieties. The genomic and transcriptome comparisons among these three varieties have interpreted the possible molecular mechanism of colour variations.…”

Section: Background and Summarymentioning

confidence: 99%

“…In our previous work 4 , annotated genome sequences of the golden, red and green arowana varieties were uploaded to GenBank under the GenBank assembly accession numbers GCA_001624265.1 (Data Citation 1), GCA_001624255.1 (Data Citation 2) and GCA_001624245.1 (Data Citation 3), respectively. The RAD-seq raw read files were stored at NCBI SRA under experiment accession numbers SRX1728941 to SRX1728946 (Data Citation 4).…”

Section: Data Recordsmentioning

confidence: 99%

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A chromosome-level genome assembly of the Asian arowana, Scleropages formosus

Bian

et al. 2016

Sci Data

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Asian arowana (Scleropages formosus), an ancient teleost belonging to the Order Osteoglossomorpha, has been a valuable ornamental fish with some varieties. However, its biological studies and breeding germplasm have been remarkably limited by the lack of a reference genome. To solve these problems, here we report high-quality genome sequences of three common varieties of Asian arowana (the golden, red and green arowana). We firstly generated a chromosome-level genome assembly of the golden arowana, on basis of the genetic linkage map constructed with the restriction site-associated DNA sequencing (RAD-seq). In addition, we obtained draft genome assemblies of the red and green varieties. Finally, we annotated 22,016, 21,256 and 21,524 protein-coding genes in the genome assemblies of golden, red and green varieties respectively. Our data were deposited in publicly accessible repositories to promote biological research and molecular breeding of Asian arowana.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Background and Summarymentioning

confidence: 99%

Section: Data Recordsmentioning

confidence: 99%

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A chromosome-level genome assembly of the Asian arowana, Scleropages formosus

Bian

et al. 2016

Sci Data

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Fish Genomics

Huang¹,

Bian²,

Liu³

et al. 2020

Encyclopedia of Marine Biotechnology

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Diversification of Hox Gene Clusters in Osteoglossomorph Fish in Comparison to Other Teleosts and the Spotted Gar Outgroup

Martin

Holland

2017

J Exp Zool Pt B

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An ancient genome duplication (TGD or 3R) occurred in teleost fish after divergence from the lineage leading to gar. This genome duplication is shared by the three extant teleost lineages: Osteoglossomorpha (bony-tongues), Elopomorpha (eels and tarpons), and Clupeocephala (a large clade including salmon, carp, medaka, zebrafish, cichlids, pufferfish, stickleback, and ∼26,000 other species). After TGD, different clupeocephalan species retained different gene duplicates; this is seen clearly in Hox gene clusters but extends to all genes. Since divergent resolution of TGD paralogs is a potential driving force for speciation, it is possible this contributed to diversification of this clade. The extent to which divergent resolution of TGD paralogs occurred within Osteoglossomorpha has not been investigated in detail, and Hox cluster organization has been reported for just two species: Pantodon buchholzi (Pantodontidae) and Scleropages formosus (Osteoglossidae). We applied survey-scale genome sequencing and de novo assembly to three further osteoglossomorph taxa: Osteoglossum bicirrhosum (Osteoglossidae), Chitala ornata (Notopteridae), and Gnathonemus petersii (Mormyridae). We find that each retained more Hox genes than clupeocephalan taxa (excluding those that underwent additional genome duplication), but fewer than eels. Several Hox genes are missing in all teleosts, including duplicates of two Hox genes present in the slow evolving pre-TGD genome of the spotted gar. We find divergent resolution through individual gene losses, and whole cluster losses have been rampant across osteoglossomorphs, despite their extant species paucity. We suggest that reciprocal gene loss following TGD was probably insufficient to drive the exceptional diversification of teleosts.

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

Cited by 95 publications

References 97 publications

A chromosome-level genome assembly of the Asian arowana, Scleropages formosus

A chromosome-level genome assembly of the Asian arowana, Scleropages formosus

Fish Genomics

Diversification of Hox Gene Clusters in Osteoglossomorph Fish in Comparison to Other Teleosts and the Spotted Gar Outgroup

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