Limits...
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

Phylogenetic relationship of the Asian arowana to other teleosts.(A) Alternative phylogenetic models for the branching order of Osteoglossomorpha, Elopomorpha and Clupeocephala. (B) Phylogenetic position of Asian arowana with respect to other teleost fishes. The trees are based on 418 one-to-one orthologues (294,783 nucleotide positions) from 12 vertebrates. Values shown at the nodes are Maximum Likelihood bootstrap percentages/Bayesian posterior probability values. The scale bar represents 0.1 substitutions per site.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4835728&req=5

f3: Phylogenetic relationship of the Asian arowana to other teleosts.(A) Alternative phylogenetic models for the branching order of Osteoglossomorpha, Elopomorpha and Clupeocephala. (B) Phylogenetic position of Asian arowana with respect to other teleost fishes. The trees are based on 418 one-to-one orthologues (294,783 nucleotide positions) from 12 vertebrates. Values shown at the nodes are Maximum Likelihood bootstrap percentages/Bayesian posterior probability values. The scale bar represents 0.1 substitutions per site.

Mentions: Previous studies based on morphological and molecular data have produced conflicting phylogenetic relationships among the three major lineages of teleosts. Morphological and fossil data have placed osteoglossomorphs22 or elopomorphs23 as the sister group to the remaining teleosts. Phylogenetic analysis based on 28S ribosomal RNA as well as a larger set of 4,682 protein-coding genes from jawed vertebrates placed elopomorphs as sister to osteoglossomorphs912. On the other hand, mitogenome-based phylogenetic analysis11 as well as a study based on 170 proteins extracted from a draft assembly of the Asian arowana15 have placed osteoglossomorphs as sister to the remaining teleosts. More recent phylogenetic studies based on nuclear genes813 or ultraconserved elements10 from a wide range of teleosts have suggested that Elopomorpha is the sister group to the remaining teleosts (Fig. 3A).


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)

Phylogenetic relationship of the Asian arowana to other teleosts.(A) Alternative phylogenetic models for the branching order of Osteoglossomorpha, Elopomorpha and Clupeocephala. (B) Phylogenetic position of Asian arowana with respect to other teleost fishes. The trees are based on 418 one-to-one orthologues (294,783 nucleotide positions) from 12 vertebrates. Values shown at the nodes are Maximum Likelihood bootstrap percentages/Bayesian posterior probability values. The scale bar represents 0.1 substitutions per site.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f3: Phylogenetic relationship of the Asian arowana to other teleosts.(A) Alternative phylogenetic models for the branching order of Osteoglossomorpha, Elopomorpha and Clupeocephala. (B) Phylogenetic position of Asian arowana with respect to other teleost fishes. The trees are based on 418 one-to-one orthologues (294,783 nucleotide positions) from 12 vertebrates. Values shown at the nodes are Maximum Likelihood bootstrap percentages/Bayesian posterior probability values. The scale bar represents 0.1 substitutions per site.
Mentions: Previous studies based on morphological and molecular data have produced conflicting phylogenetic relationships among the three major lineages of teleosts. Morphological and fossil data have placed osteoglossomorphs22 or elopomorphs23 as the sister group to the remaining teleosts. Phylogenetic analysis based on 28S ribosomal RNA as well as a larger set of 4,682 protein-coding genes from jawed vertebrates placed elopomorphs as sister to osteoglossomorphs912. On the other hand, mitogenome-based phylogenetic analysis11 as well as a study based on 170 proteins extracted from a draft assembly of the Asian arowana15 have placed osteoglossomorphs as sister to the remaining teleosts. More recent phylogenetic studies based on nuclear genes813 or ultraconserved elements10 from a wide range of teleosts have suggested that Elopomorpha is the sister group to the remaining teleosts (Fig. 3A).

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