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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

Immune characterization of croaker.(a) Proteins encoded by immune-relevant genes in croaker that are present in similar (green circles), higher (red circles) or lower (green circles with dashed outlines) numbers compared with other teleosts, and genes that are absent (grey circles with dashed outlines) in croaker. CIITA=major histocompatibility complex class II transactivator; GILT=gamma-interferon-inducible lysosomal thiol reductase; IFN=interferon; IL=interleukin; IRF=interferon regulatory factor; MHC=major histocompatibility complex; TNF=tumour necrosis factor; TLR=toll-like receptor. (b) Number of genes involved in the cellular component of the MHC class I protein complex (GO:0042612, blue bar) and the MHC class II protein complex (GO:0042613, red bar) in different teleosts. The exact numbers are shown on the top of each bar. The gene numbers in croaker that are significantly lower than those in stickleback are indicated by a single asterisk (P-value=0.08 for GO:0042613) or a double asterisk (P-value=0.0022 for GO:0042612) according to a proportion test.
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f2: Immune characterization of croaker.(a) Proteins encoded by immune-relevant genes in croaker that are present in similar (green circles), higher (red circles) or lower (green circles with dashed outlines) numbers compared with other teleosts, and genes that are absent (grey circles with dashed outlines) in croaker. CIITA=major histocompatibility complex class II transactivator; GILT=gamma-interferon-inducible lysosomal thiol reductase; IFN=interferon; IL=interleukin; IRF=interferon regulatory factor; MHC=major histocompatibility complex; TNF=tumour necrosis factor; TLR=toll-like receptor. (b) Number of genes involved in the cellular component of the MHC class I protein complex (GO:0042612, blue bar) and the MHC class II protein complex (GO:0042613, red bar) in different teleosts. The exact numbers are shown on the top of each bar. The gene numbers in croaker that are significantly lower than those in stickleback are indicated by a single asterisk (P-value=0.08 for GO:0042613) or a double asterisk (P-value=0.0022 for GO:0042612) according to a proportion test.

Mentions: Our results revealed a well-established innate immune system and a partially established adaptive immune system in croaker (Fig. 2a). We confirmed the presence of innate immunity-relevant genes encoding TLRs, ILs and TNFs in the croaker genome (Supplementary Table 9), which is consistent with previous studies1127282930. Meanwhile, TNF superfamilies of ligands and receptors showed expansion in croaker, suggesting that innate immunity is strengthened by extra copies of TNF-related genes.


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)

Immune characterization of croaker.(a) Proteins encoded by immune-relevant genes in croaker that are present in similar (green circles), higher (red circles) or lower (green circles with dashed outlines) numbers compared with other teleosts, and genes that are absent (grey circles with dashed outlines) in croaker. CIITA=major histocompatibility complex class II transactivator; GILT=gamma-interferon-inducible lysosomal thiol reductase; IFN=interferon; IL=interleukin; IRF=interferon regulatory factor; MHC=major histocompatibility complex; TNF=tumour necrosis factor; TLR=toll-like receptor. (b) Number of genes involved in the cellular component of the MHC class I protein complex (GO:0042612, blue bar) and the MHC class II protein complex (GO:0042613, red bar) in different teleosts. The exact numbers are shown on the top of each bar. The gene numbers in croaker that are significantly lower than those in stickleback are indicated by a single asterisk (P-value=0.08 for GO:0042613) or a double asterisk (P-value=0.0022 for GO:0042612) according to a proportion test.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2: Immune characterization of croaker.(a) Proteins encoded by immune-relevant genes in croaker that are present in similar (green circles), higher (red circles) or lower (green circles with dashed outlines) numbers compared with other teleosts, and genes that are absent (grey circles with dashed outlines) in croaker. CIITA=major histocompatibility complex class II transactivator; GILT=gamma-interferon-inducible lysosomal thiol reductase; IFN=interferon; IL=interleukin; IRF=interferon regulatory factor; MHC=major histocompatibility complex; TNF=tumour necrosis factor; TLR=toll-like receptor. (b) Number of genes involved in the cellular component of the MHC class I protein complex (GO:0042612, blue bar) and the MHC class II protein complex (GO:0042613, red bar) in different teleosts. The exact numbers are shown on the top of each bar. The gene numbers in croaker that are significantly lower than those in stickleback are indicated by a single asterisk (P-value=0.08 for GO:0042613) or a double asterisk (P-value=0.0022 for GO:0042612) according to a proportion test.
Mentions: Our results revealed a well-established innate immune system and a partially established adaptive immune system in croaker (Fig. 2a). We confirmed the presence of innate immunity-relevant genes encoding TLRs, ILs and TNFs in the croaker genome (Supplementary Table 9), which is consistent with previous studies1127282930. Meanwhile, TNF superfamilies of ligands and receptors showed expansion in croaker, suggesting that innate immunity is strengthened by extra copies of TNF-related genes.

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