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

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 - Sci Rep (2016)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen 518083, China.

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.

No MeSH data available.


Related in: MedlinePlus

Evolution of the teleost karyotype.(A) Thirteen pre-TGD reduced ancestral chromosomes are indicated as coloured bars. Genomic regions originating from the same ancestral chromosomes are depicted in the same colour. Green, red and blue arrows represent translocation, fusion and fission events, respectively. The numbers in each branch of tree are the estimated divergence times. The predicted ancestral chromosomes of medaka were modified from Kasahara’s study38. Circos plots show syntenic relationships between the linkage groups of spotted gar and chromosomes of arowana (B) zebrafish (C) and medaka (D). Spotted gar chromosome numbers are shown in red whereas those of arowana, zebrafish and medaka are shown in black.
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f4: Evolution of the teleost karyotype.(A) Thirteen pre-TGD reduced ancestral chromosomes are indicated as coloured bars. Genomic regions originating from the same ancestral chromosomes are depicted in the same colour. Green, red and blue arrows represent translocation, fusion and fission events, respectively. The numbers in each branch of tree are the estimated divergence times. The predicted ancestral chromosomes of medaka were modified from Kasahara’s study38. Circos plots show syntenic relationships between the linkage groups of spotted gar and chromosomes of arowana (B) zebrafish (C) and medaka (D). Spotted gar chromosome numbers are shown in red whereas those of arowana, zebrafish and medaka are shown in black.

Mentions: Reconstruction of the ancestral teleost karyotype and models of teleost genome evolution have been previously proposed based on genomes of clupeocephalan teleosts such as Tetraodon and medaka43839. We aligned the arowana and human genomes, and identified 61 doubly conserved synteny (DCS, Supplementary Table 15) blocks, which is consistent with previous studies438. Comparison of the teleost ancestor chromosomes (from ref. 38) with those of golden arowana, revealed 12 major rearrangements comprising two fissions, three fusions and seven translocation events specific to the arowana (and possibly the whole Osteoglossomorph) lineage (Fig. 4A).


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

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 - Sci Rep (2016)

Evolution of the teleost karyotype.(A) Thirteen pre-TGD reduced ancestral chromosomes are indicated as coloured bars. Genomic regions originating from the same ancestral chromosomes are depicted in the same colour. Green, red and blue arrows represent translocation, fusion and fission events, respectively. The numbers in each branch of tree are the estimated divergence times. The predicted ancestral chromosomes of medaka were modified from Kasahara’s study38. Circos plots show syntenic relationships between the linkage groups of spotted gar and chromosomes of arowana (B) zebrafish (C) and medaka (D). Spotted gar chromosome numbers are shown in red whereas those of arowana, zebrafish and medaka are shown in black.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4835728&req=5

f4: Evolution of the teleost karyotype.(A) Thirteen pre-TGD reduced ancestral chromosomes are indicated as coloured bars. Genomic regions originating from the same ancestral chromosomes are depicted in the same colour. Green, red and blue arrows represent translocation, fusion and fission events, respectively. The numbers in each branch of tree are the estimated divergence times. The predicted ancestral chromosomes of medaka were modified from Kasahara’s study38. Circos plots show syntenic relationships between the linkage groups of spotted gar and chromosomes of arowana (B) zebrafish (C) and medaka (D). Spotted gar chromosome numbers are shown in red whereas those of arowana, zebrafish and medaka are shown in black.
Mentions: Reconstruction of the ancestral teleost karyotype and models of teleost genome evolution have been previously proposed based on genomes of clupeocephalan teleosts such as Tetraodon and medaka43839. We aligned the arowana and human genomes, and identified 61 doubly conserved synteny (DCS, Supplementary Table 15) blocks, which is consistent with previous studies438. Comparison of the teleost ancestor chromosomes (from ref. 38) with those of golden arowana, revealed 12 major rearrangements comprising two fissions, three fusions and seven translocation events specific to the arowana (and possibly the whole Osteoglossomorph) lineage (Fig. 4A).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, Shenzhen 518083, China.

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.

No MeSH data available.


Related in: MedlinePlus