Bian C1,*, Hu Y2,*, Ravi V3,*, Kuznetsova IS4,*, Shen X4,*, Mu X2,*, Sun Y1,*, You X1, Li J1,, Li X5, Qiu Y1,, Tay BH3,, Thevasagayam NM4, Komissarov AS6, Trifonov V7, Kabilov M8, Tupikin A8, Luo J2, Liu Y2, Song H2, Liu C2, Wang X2,, Gu D2, Yang Y2, Li W1, Polgar G9, Fan G1,, Zeng P1,, Zhang H1,, Xiong Z1,, Tang Z1,, Peng C1,, Ruan Z1,, Yu H1,, Chen J1,, Fan M1,, Huang Y1, Wang M1, Zhao X1,, Hu G1, Yang H1,, Wang J1,, Wang J1,, Xu X1,, Song L10, Xu G11, Xu P11,, Xu J1,, O’Brien SJ6, Orbán L4†, Venkatesh B3† & Shi Q1†.
1 BGI-Shenzhen, Shenzhen 518083, China.
2 Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
3 Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore.
4 Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
5 Realbio Genomics Institute, Shanghai 200050, China.
6 Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, Russia.
7 Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
8 Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
9 Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, BE1410
10 Dalian Ocean University, Dalian 116023, China.
11 Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
* contributed equally to this work.
† Corresponding authors
Published online in Scientific Reports on 19 April 2016.
The Asian arowana (Scleropages formosus), one of the world’s most expensive cultivated ornamental fish, 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.
Figure 1 : Whole-genome sequences and transcriptomes of three varieties of arowana (golden, red and green) were generated and used for comparative analyses with other vertebrate genomes.
Figure 2 : Characteristics of the Asian arowana (golden variety) genome. Concentric circles from the outside: (A) Chromosome length (Mb) and numbers. Chromosome numbers were assigned based on the linkage groups. (B) Distribution of gene density in 1 Mb non-overlapping windows. (C) Expression level of genes in skin tissue of the golden arowana. High yellow peaks indicate strong expression. (D) Distribution of repeat density in 1Mb non-overlapping windows. Deeper green colour indicates higher repeat density. (E) Distribution of GC content in 1 Mb non-overlapping windows. Darker blue colour indicates higher GC content. The pink lines represent the inner synteny blocks.
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