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26120条SNP-Unigene上,共检测到431845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3417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。
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 26120 SNP-Unigene,with a total of 431845 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,3417 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.
作者
杨二军
杨林桐
王维政
黄建盛
张健东
王忠良
陈刚
Yang Erjun;Yang Lintong;Wang Weizheng;Huang Jiansheng;Zhang Jiandong;Wang Zhongliang;Chen Gang(Fishery College,Guangdong Ocean University,Zhanjiang 524088,China;Southern Marine Science and Engineering Guangdong Laboratory(Zhanjiang),Zhanjiang 524025,China;Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals,Zhanjiang 524088,China)
出处
《海洋学报》
CAS
CSCD
北大核心
2022年第1期113-124,共12页
基金
南方海洋科学与工程广东省实验室(湛江)资助项目(ZJW-2019-06)
财政部和农业农村部:国家现代农业产业技术体系资助项目(CARS-47)
广东海洋大学本科生创新创业团队项目(CCTD201804)。
