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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

The karyotype of female Asian arowana contains a large, putative W chromosome.(A) A typical female karyotype showing 24 pairs of chromosomes, among them a pair with unequal sized chromosomes. A large acrocentric chromosome with a substantial heterochromatic block in the pericentromere region was identified as a putative W chromosome. Chromosome pairs 1–9 are metacentric/submetacentric (m/sm), 10–16 are subtelocentric (st) and 17–24 are acrocentric (a). (B) Chromomycin A3 staining. White arrowhead indicates the female-specific, putative W chromosome. (C) Metaphase chromosomes stained with DAPI (blue) and telomere probe (green). Bars are 5 μm for all panels.
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f5: The karyotype of female Asian arowana contains a large, putative W chromosome.(A) A typical female karyotype showing 24 pairs of chromosomes, among them a pair with unequal sized chromosomes. A large acrocentric chromosome with a substantial heterochromatic block in the pericentromere region was identified as a putative W chromosome. Chromosome pairs 1–9 are metacentric/submetacentric (m/sm), 10–16 are subtelocentric (st) and 17–24 are acrocentric (a). (B) Chromomycin A3 staining. White arrowhead indicates the female-specific, putative W chromosome. (C) Metaphase chromosomes stained with DAPI (blue) and telomere probe (green). Bars are 5 μm for all panels.

Mentions: We performed comparative analysis on the karyotype of six male and six female arowana individuals (Supplementary Tables 21 and 22). The results confirmed our earlier finding that the diploid chromosome number of arowana is 2 n = 48 (ref. 18). When the female karyotypes were compared to those of males (Fig. 5A), a large acrocentric chromosome with a substantial heterochromatic block in the pericentromeric region was identified (Fig. 5A) that showed the presence of a GC-rich region (Fig. 5B). This extra chromosome was present in all six females, but absent from the six males. The golden arowana reference genome was constructed in 25 linkage groups based on the RAD map (this study), which showed an apparent discrepancy with that of our earlier publication18 that reported 2 n = 48 as the male karyotype. We believe that this is due to the fact that the female assembly contains two differentiated sex chromosomes as separate units, thus resulting in an apparent increase of the haploid number of chromosomes.


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)

The karyotype of female Asian arowana contains a large, putative W chromosome.(A) A typical female karyotype showing 24 pairs of chromosomes, among them a pair with unequal sized chromosomes. A large acrocentric chromosome with a substantial heterochromatic block in the pericentromere region was identified as a putative W chromosome. Chromosome pairs 1–9 are metacentric/submetacentric (m/sm), 10–16 are subtelocentric (st) and 17–24 are acrocentric (a). (B) Chromomycin A3 staining. White arrowhead indicates the female-specific, putative W chromosome. (C) Metaphase chromosomes stained with DAPI (blue) and telomere probe (green). Bars are 5 μm for all panels.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f5: The karyotype of female Asian arowana contains a large, putative W chromosome.(A) A typical female karyotype showing 24 pairs of chromosomes, among them a pair with unequal sized chromosomes. A large acrocentric chromosome with a substantial heterochromatic block in the pericentromere region was identified as a putative W chromosome. Chromosome pairs 1–9 are metacentric/submetacentric (m/sm), 10–16 are subtelocentric (st) and 17–24 are acrocentric (a). (B) Chromomycin A3 staining. White arrowhead indicates the female-specific, putative W chromosome. (C) Metaphase chromosomes stained with DAPI (blue) and telomere probe (green). Bars are 5 μm for all panels.
Mentions: We performed comparative analysis on the karyotype of six male and six female arowana individuals (Supplementary Tables 21 and 22). The results confirmed our earlier finding that the diploid chromosome number of arowana is 2 n = 48 (ref. 18). When the female karyotypes were compared to those of males (Fig. 5A), a large acrocentric chromosome with a substantial heterochromatic block in the pericentromeric region was identified (Fig. 5A) that showed the presence of a GC-rich region (Fig. 5B). This extra chromosome was present in all six females, but absent from the six males. The golden arowana reference genome was constructed in 25 linkage groups based on the RAD map (this study), which showed an apparent discrepancy with that of our earlier publication18 that reported 2 n = 48 as the male karyotype. We believe that this is due to the fact that the female assembly contains two differentiated sex chromosomes as separate units, thus resulting in an apparent increase of the haploid number of chromosomes.

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