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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

Characteristics of the reference genome of the golden Asian arowana.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 1Mb 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 1Mb non-overlapping windows. Darker blue colour indicates higher GC content. The pink lines represent the inner synteny blocks.
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f2: Characteristics of the reference genome of the golden Asian arowana.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 1Mb 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 1Mb non-overlapping windows. Darker blue colour indicates higher GC content. The pink lines represent the inner synteny blocks.

Mentions: Recently, a draft assembly of an Asian arowana (colour variety unknown) with an N50 scaffold length of 59 kb has been generated15. We sequenced the genomes of golden, red and green varieties of arowana to >100-fold coverage (Supplementary Tables 1 and 2) using the Illumina HiSeq2000 platform. Sequence reads from the three varieties were assembled separately (Supplementary Table 3) using SOAPdenovo216 resulting in N50 scaffold sizes of 5.96, 1.63 and 1.85 million bases (Mb), and genome assemblies spanning approximately 779, 753 and 759 Mb for the golden, red and green varieties, respectively, in agreement with their estimated genome sizes based on k-mer analyses (Table 1 and Supplementary Fig. 1). Evaluation using CEGMA17 and de novo-assembled transcripts showed that the three assemblies covered over 98% of core eukaryotic genes and 95% of gene regions (Supplementary Tables 4 and 5), confirming their high level of completeness and accuracy. We then indentified 829,293, 1,168,314 and 1,684,422 heterozygous single nucleotide polymorphisms (SNP) and detected the following heterozygosity levels: 1.01%, 1.23% and 1.88% in the golden, red and green arowana genomes, respectively. To further improve the quality of the golden variety genome assembly, we developed a high-density genetic map by restriction site-associated DNA sequencing (RAD-seq) using 94 F2 individuals that originated from red grade 1 and Malaysian golden arowana grandparents18. Subsequently, we identified 22,881 SNPs using the golden assembly as the reference, of which 5,617 refined SNPs and their corresponding scaffolds were clustered and embedded into 25 linkage groups (Fig. 2) spanning approximately 3,240 cM and 683 Mb (87.7% of the golden variety assembly; Supplementary Fig. 2 and Supplementary Table 6). The high-quality linkage group-anchored assembly of the golden variety of Asian arowana can be used as a reference genome, whereas the draft genomes of green and red varieties are suitable for comparative studies.


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)

Characteristics of the reference genome of the golden Asian arowana.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 1Mb 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 1Mb non-overlapping windows. Darker blue colour indicates higher GC content. The pink lines represent the inner synteny blocks.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2: Characteristics of the reference genome of the golden Asian arowana.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 1Mb 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 1Mb non-overlapping windows. Darker blue colour indicates higher GC content. The pink lines represent the inner synteny blocks.
Mentions: Recently, a draft assembly of an Asian arowana (colour variety unknown) with an N50 scaffold length of 59 kb has been generated15. We sequenced the genomes of golden, red and green varieties of arowana to >100-fold coverage (Supplementary Tables 1 and 2) using the Illumina HiSeq2000 platform. Sequence reads from the three varieties were assembled separately (Supplementary Table 3) using SOAPdenovo216 resulting in N50 scaffold sizes of 5.96, 1.63 and 1.85 million bases (Mb), and genome assemblies spanning approximately 779, 753 and 759 Mb for the golden, red and green varieties, respectively, in agreement with their estimated genome sizes based on k-mer analyses (Table 1 and Supplementary Fig. 1). Evaluation using CEGMA17 and de novo-assembled transcripts showed that the three assemblies covered over 98% of core eukaryotic genes and 95% of gene regions (Supplementary Tables 4 and 5), confirming their high level of completeness and accuracy. We then indentified 829,293, 1,168,314 and 1,684,422 heterozygous single nucleotide polymorphisms (SNP) and detected the following heterozygosity levels: 1.01%, 1.23% and 1.88% in the golden, red and green arowana genomes, respectively. To further improve the quality of the golden variety genome assembly, we developed a high-density genetic map by restriction site-associated DNA sequencing (RAD-seq) using 94 F2 individuals that originated from red grade 1 and Malaysian golden arowana grandparents18. Subsequently, we identified 22,881 SNPs using the golden assembly as the reference, of which 5,617 refined SNPs and their corresponding scaffolds were clustered and embedded into 25 linkage groups (Fig. 2) spanning approximately 3,240 cM and 683 Mb (87.7% of the golden variety assembly; Supplementary Fig. 2 and Supplementary Table 6). The high-quality linkage group-anchored assembly of the golden variety of Asian arowana can be used as a reference genome, whereas the draft genomes of green and red varieties are suitable for comparative studies.

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