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The draft genome of the large yellow croaker reveals well-developed innate immunity.

Wu C, Zhang D, Kan M, Lv Z, Zhu A, Su Y, Zhou D, Zhang J, Zhang Z, Xu M, Jiang L, Guo B, Wang T, Chi C, Mao Y, Zhou J, Yu X, Wang H, Weng X, Jin JG, Ye J, He L, Liu Y - Nat Commun (2014)

Bottom Line: Rapidly evolving genes under positive selection are significantly enriched in pathways related to innate immunity.We also confirm the existence of several genes and identify the expansion of gene families that are important for innate immunity.Our results may reflect a well-developed innate immune system in the large yellow croaker, which could aid in the development of wild resource preservation and mariculture strategies.

View Article: PubMed Central - PubMed

Affiliation: National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China.

ABSTRACT
The large yellow croaker, Larimichthys crocea, is one of the most economically important marine fish species endemic to China. Its wild stocks have severely suffered from overfishing, and the aquacultured species are vulnerable to various marine pathogens. Here we report the creation of a draft genome of a wild large yellow croaker using a whole-genome sequencing strategy. We estimate the genome size to be 728 Mb with 19,362 protein-coding genes. Phylogenetic analysis shows that the stickleback is most closely related to the large yellow croaker. Rapidly evolving genes under positive selection are significantly enriched in pathways related to innate immunity. We also confirm the existence of several genes and identify the expansion of gene families that are important for innate immunity. Our results may reflect a well-developed innate immune system in the large yellow croaker, which could aid in the development of wild resource preservation and mariculture strategies.

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Related in: MedlinePlus

Comparison of evolutionary features of croaker and other teleosts.(a) Phylogenetic tree and numbers of gene families under expansion (red)/contraction (green). Mya, million years ago. (b) Venn diagram showing unique and overlapping gene families in croaker, stickleback, torafugu and pufferfish. (c) Length of syntenic regions on each scaffold based on stickleback. Scaffolds are indicated by coverage ≥75% (red solid dots), 50%≤ coverage ≪75% (green solid dots) and coverage ≪50% (grey solid dots). Three blue dashed lines indicate coverage of 50, 75 and 100%, respectively, from bottom to top. (d) KEGG pathways to which rapidly evolving genes were mapped are indicated by pairs of median dN/dS ratios (black solid dots) in croaker and stickleback; significantly enriched (FDR≪0.05) rapidly evolving genes in KEGG pathways are highlighted for croaker (red solid dots), stickleback (green solid dots) or both (blue solid dots).
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f1: Comparison of evolutionary features of croaker and other teleosts.(a) Phylogenetic tree and numbers of gene families under expansion (red)/contraction (green). Mya, million years ago. (b) Venn diagram showing unique and overlapping gene families in croaker, stickleback, torafugu and pufferfish. (c) Length of syntenic regions on each scaffold based on stickleback. Scaffolds are indicated by coverage ≥75% (red solid dots), 50%≤ coverage ≪75% (green solid dots) and coverage ≪50% (grey solid dots). Three blue dashed lines indicate coverage of 50, 75 and 100%, respectively, from bottom to top. (d) KEGG pathways to which rapidly evolving genes were mapped are indicated by pairs of median dN/dS ratios (black solid dots) in croaker and stickleback; significantly enriched (FDR≪0.05) rapidly evolving genes in KEGG pathways are highlighted for croaker (red solid dots), stickleback (green solid dots) or both (blue solid dots).

Mentions: To determine the extent of genetic conservation among teleost fishes, we compared seven teleost fish genomes including croaker, stickleback, Atlantic cod, medaka, torafugu, pufferfish (Tetraodon nigroviridis) and zebrafish (Danio rerio). We identified 17,362 orthologous gene families shared between at least two teleost species, 1,524 of which were single-copy orthologues shared by all the studied species. Using these single-copy orthologues, we explored the phylogenetic relationships of the seven teleost fishes (Fig. 1a). The phylogenetic tree revealed that stickleback (order Gasterosteiformes) was most closely related to croaker (order Perciformes) with an estimated divergence time of 142 Myr ago. The order Tetraodontiformes, which torafugu and pufferfish belong to, is only slightly less closely related to croaker (Fig. 1a), and the separation was estimated to be 191 Myr ago. We studied the orthologue profiles of the four closely related teleosts (croaker, stickleback, torafugu and pufferfish) (Fig. 1b). A total of 3,461 gene families were shared among the four fishes, and stickleback, a close relative, had 5,867 overlapping gene families with croaker. We further explored the syntenic relationship between croaker and stickleback (Fig. 1c). From 21,012 pairwise blastp comparisons, we obtained 562 syntenic blocks in the croaker genome, which contained 6,597 orthologous croaker genes. These syntenic blocks spanned 485 scaffolds with a total length of 331 Mb (51.4% of the draft genome). Most syntenic regions have high coverage of the respective scaffolds (407 scaffolds with >50% coverage and 289 scaffolds with >75% coverage), confirming a conservation of synteny between croaker and stickleback (Fig. 1c).


The draft genome of the large yellow croaker reveals well-developed innate immunity.

Wu C, Zhang D, Kan M, Lv Z, Zhu A, Su Y, Zhou D, Zhang J, Zhang Z, Xu M, Jiang L, Guo B, Wang T, Chi C, Mao Y, Zhou J, Yu X, Wang H, Weng X, Jin JG, Ye J, He L, Liu Y - Nat Commun (2014)

Comparison of evolutionary features of croaker and other teleosts.(a) Phylogenetic tree and numbers of gene families under expansion (red)/contraction (green). Mya, million years ago. (b) Venn diagram showing unique and overlapping gene families in croaker, stickleback, torafugu and pufferfish. (c) Length of syntenic regions on each scaffold based on stickleback. Scaffolds are indicated by coverage ≥75% (red solid dots), 50%≤ coverage ≪75% (green solid dots) and coverage ≪50% (grey solid dots). Three blue dashed lines indicate coverage of 50, 75 and 100%, respectively, from bottom to top. (d) KEGG pathways to which rapidly evolving genes were mapped are indicated by pairs of median dN/dS ratios (black solid dots) in croaker and stickleback; significantly enriched (FDR≪0.05) rapidly evolving genes in KEGG pathways are highlighted for croaker (red solid dots), stickleback (green solid dots) or both (blue solid dots).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4263168&req=5

f1: Comparison of evolutionary features of croaker and other teleosts.(a) Phylogenetic tree and numbers of gene families under expansion (red)/contraction (green). Mya, million years ago. (b) Venn diagram showing unique and overlapping gene families in croaker, stickleback, torafugu and pufferfish. (c) Length of syntenic regions on each scaffold based on stickleback. Scaffolds are indicated by coverage ≥75% (red solid dots), 50%≤ coverage ≪75% (green solid dots) and coverage ≪50% (grey solid dots). Three blue dashed lines indicate coverage of 50, 75 and 100%, respectively, from bottom to top. (d) KEGG pathways to which rapidly evolving genes were mapped are indicated by pairs of median dN/dS ratios (black solid dots) in croaker and stickleback; significantly enriched (FDR≪0.05) rapidly evolving genes in KEGG pathways are highlighted for croaker (red solid dots), stickleback (green solid dots) or both (blue solid dots).
Mentions: To determine the extent of genetic conservation among teleost fishes, we compared seven teleost fish genomes including croaker, stickleback, Atlantic cod, medaka, torafugu, pufferfish (Tetraodon nigroviridis) and zebrafish (Danio rerio). We identified 17,362 orthologous gene families shared between at least two teleost species, 1,524 of which were single-copy orthologues shared by all the studied species. Using these single-copy orthologues, we explored the phylogenetic relationships of the seven teleost fishes (Fig. 1a). The phylogenetic tree revealed that stickleback (order Gasterosteiformes) was most closely related to croaker (order Perciformes) with an estimated divergence time of 142 Myr ago. The order Tetraodontiformes, which torafugu and pufferfish belong to, is only slightly less closely related to croaker (Fig. 1a), and the separation was estimated to be 191 Myr ago. We studied the orthologue profiles of the four closely related teleosts (croaker, stickleback, torafugu and pufferfish) (Fig. 1b). A total of 3,461 gene families were shared among the four fishes, and stickleback, a close relative, had 5,867 overlapping gene families with croaker. We further explored the syntenic relationship between croaker and stickleback (Fig. 1c). From 21,012 pairwise blastp comparisons, we obtained 562 syntenic blocks in the croaker genome, which contained 6,597 orthologous croaker genes. These syntenic blocks spanned 485 scaffolds with a total length of 331 Mb (51.4% of the draft genome). Most syntenic regions have high coverage of the respective scaffolds (407 scaffolds with >50% coverage and 289 scaffolds with >75% coverage), confirming a conservation of synteny between croaker and stickleback (Fig. 1c).

Bottom Line: Rapidly evolving genes under positive selection are significantly enriched in pathways related to innate immunity.We also confirm the existence of several genes and identify the expansion of gene families that are important for innate immunity.Our results may reflect a well-developed innate immune system in the large yellow croaker, which could aid in the development of wild resource preservation and mariculture strategies.

View Article: PubMed Central - PubMed

Affiliation: National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China.

ABSTRACT
The large yellow croaker, Larimichthys crocea, is one of the most economically important marine fish species endemic to China. Its wild stocks have severely suffered from overfishing, and the aquacultured species are vulnerable to various marine pathogens. Here we report the creation of a draft genome of a wild large yellow croaker using a whole-genome sequencing strategy. We estimate the genome size to be 728 Mb with 19,362 protein-coding genes. Phylogenetic analysis shows that the stickleback is most closely related to the large yellow croaker. Rapidly evolving genes under positive selection are significantly enriched in pathways related to innate immunity. We also confirm the existence of several genes and identify the expansion of gene families that are important for innate immunity. Our results may reflect a well-developed innate immune system in the large yellow croaker, which could aid in the development of wild resource preservation and mariculture strategies.

Show MeSH
Related in: MedlinePlus