Identification and functional analysis of SNP from transcriptome of cobia (Rachycentron canadum) in response to hypoxia stress
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摘要: 为了研究低氧胁迫下军曹鱼肠道转录组中单核苷酸多态性(SNP)标记位点及SNP所在基因SNP-Unigene的作用，通过SOAPsnp软件对军曹鱼幼鱼对照组和低氧胁迫转录组测序结果进行SNP检测，并将其比对到GO、KOG、KEGG数据库进行功能注释。结果显示，军曹鱼转录组SNP位点分布在26 120条SNP-Unigene上，共检测到431 845个SNP位点，SNP平均发生频率约为1/171 bp；SNP-Unigene功能注释发现，在低氧胁迫条件下，军曹鱼SNP-Unigene主要涉及信号转导、传染病、癌症和内分泌系统等信号通路。进一步筛选到3 417条SNP-Unigene被注释到MAPK信号通路等35条与免疫相关的通路中。基于转录组差异基因分析，检测了其中7个重要免疫通路中18个免疫相关基因的SNP位点分布情况。同时，也检测了HIF-1信号通路中PIK3CA等8个差异基因的SNP位点分布情况。研究结果将为进一步挖掘免疫及低氧相关SNP的分子遗传标记奠定基础，为军曹鱼低氧适应机制的深入研究提供科学参考。Abstract: In order to mine single nucleotide polymorphism (SNP) sites relates to hypoxia stress and study the function of the gene SNP-Unigene from Rachycentron canadum. SOAPsnp software is mainly used to detect the SNP of the intestinal transcriptome sequencing results of cobia juveniles under hypoxia stress conditions, and then annotation of them in the databases of GO, KOG, and KEGG are compared. The results show that the transcriptome SNP locus are distributed on 26 120 SNP-Unigene, with a total of 431 845 SNP sites are detected, the average frequency of SNP occurrence is about 1/171 bp. SNP-Unigene functional annotation showes that the cobia is mainly involved in signal transduction, infectious disease, cancer and endocrine system under hypoxia stress. Further, 3 417 SNP-Unigene are annotated to 35 immune-related pathways including MAPK signaling pathway. Based on the transcriptome differential gene analysis, the distribution of SNP sites of 18 immune-related genes in 7 important immune pathways is examined. At the same time, the distribution of SNP sites of 8 differential genes such as PIK3CA in the HIF-1 signaling pathway is also detected. The research results will lay the foundation for further mining of the molecular genetic markers of immune and hypoxia-related SNPs, and provide a scientific reference for the in-depth study of cobia’s hypoxia adaptation mechanism.
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Key words:
- Rachycentron canadum /
- hypoxia stress /
- transcriptomics /
- immune gene /
- SNP
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表 1 SNP位点数量概况
Tab. 1 The number of the SNP sites
组别 CT组 HT组 合计 SNP-Unigene数 13 076 13 044 26 120 SNP位点总数 215 953 215 892 431 845 纯合SNP位点数 76 550 76 092 152 642 
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表 2 免疫防御相关SNP-Unigene的KEGG富集分析
Tab. 2 KEGG enrichment analysis of immune-related SNP-Unigene
KEGG信号通路 信号通路ID SNP-Unigene数目 MAPK信号通路 ko04010 262 神经活性配体−受体相互作用 ko04080 228 Rap1信号通路 ko04015 190 Ras信号通路 ko04014 164 Wnt信号通路 ko04310 144 细胞因子−细胞因子受体相互作用 ko04060 137 细胞凋亡 ko04210 130 mTOR信号通路 ko04150 129 吞噬体 ko04145 123 趋化因子信号通路 ko04062 117 血小板活化 ko04611 117 FoxO信号通路 ko04068 117 NOD样受体信号通路 ko04621 113 白细胞经内皮迁移 ko04670 101 TNF信号通路 ko04668 95 Jak-STAT信号通路 ko04630 93 T细胞受体信号通路 ko04660 92 TRP通道的炎症介质调节 ko04750 89 NF-κB信号通路 ko04064 81 TGF-β信号通路 ko04350 80 Fcγ-R介导的吞噬作用 ko04666 79 B细胞受体信号通路 ko04662 73 造血细胞系 ko04640 72 Toll样受体信号通路 ko04620 71 自然杀伤细胞介导的细胞毒性 ko04650 69 Notch信号通路 ko04330 63 PPAR信号通路 ko03320 56 IL-17信号通路 ko04657 55 补体和凝血级联 ko04610 53 Fc ε RI信号通路 ko04664 47 抗原处理与呈递 ko04612 47 RIG-I样受体信号通路 ko04622 45 Toll和Imd信号通路 ko04624 35 肠道免疫网络Ig A的产生 ko04672 27 细胞质DNA传感通路 ko04623 23 合计 3 417
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表 3 CT和HT转录组中差异表达免疫防御及低氧相关基因SNP位点分析
Tab. 3 SNP identified in differentially expressed immune and hypoxia-related genes in CT and HT transcriptomes
信号通路 基因名称 低氧后表达
水平CT-SNP
数目HT-SNP
数目MAPK信号通路 IL1R1 上调 4 4 ERBB3 上调 5 5 CACNA1E 上调 4 4 Wnt信号通路 FZD3 下调 3 1 LRP5 下调 5 5 PLCB2 上调 10 11 PLCB3 下调 7 7 NFATC4 上调 6 6 mTOR信号通路 LPIN1 上调 9 9 LPIN2 下调 3 3 DDIT4 上调 2 2 Jak-STAT信号通路 GHR 下调 8 8 LEPR 上调 5 5 IL4RA 上调 9 9 NOD样受体信号通路 TRPM7 下调 17 17 Toll和Imd信号通路 ANK3 上调 18 18 NF-κB信号通路 BTK 下调 3 3 TNFRSF11A 下调 2 2 HIF-1信号通路 PIK3CA 下调 5 4 HK1 上调 4 4 EPAS1 下调 3 3 GAPDH 下调 2 2 EDN1 下调 1 1 ENO3 下调 1 1 ANGPT1 上调 4 4 ANGPT2 上调 1 1
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