摘要
为研究虹鳟Oncorhynchus mykiss ep300/crebbp基因家族的拷贝数变异、功能分化及与低氧应答的关联,通过TBLASTN和BLASTP搜索及重构进化树,确定该家族的拷贝数及与其直系同源的斑马鱼Danio rerio基因,基于对原始转录组测序数据的统计获得这些拷贝的组织表达谱及共表达基因,并对共表达基因进行GO富集分析,最后通过CDD搜索、多重序列比对及三维结构建模比较这些拷贝所编码蛋白质的变异程度。结果表明:虹鳟的ep300/crebbp家族有8个成员(ep300aa~ep300bb,crebbpaa~crebbpbb),其均由全基因组重复事件所形成,对应于斑马鱼的4个成员,可分为4对ohnologs;不同的ohnolog对之间在组织表达谱、编码蛋白质的一级结构和三级结构存在较大差异,而同一对ohnologs内部的2个拷贝在这些方面差异较小;这8个成员拥有数量不等的独有共表达基因,这些共表达基因所富集的与结合、修饰、应对压力/刺激和耐低氧相关的GO条目的数量均存在较大差异;ep300ba和ep300bb属于一对ohnologs,但它们编码的蛋白质保守结构域中存在35处变异,数量远大于其他ohnolog对,且只有ep300bb的共表达基因能富集到与应对压力/刺激和耐低氧相关的GO条目。研究表明,相较于其他ep300/crebbp家族成员,虹鳟ep300bb的进化速度较快,且与耐低氧性能相关性更大,可作为虹鳟遗传改良的重要候选基因。
To probe into copy number variation,functional divergence and correlation with hypoxia response of ep300/crebbp gene family in rainbow trout Oncorhynchus mykiss,TBLASTN and BLASTP search and reconstruction of phylogenetic tree were firstly conducted,based on which the members and their orthologs in zebrafish Danio rerio were determined.Tissue expression profiles and co-expressed genes of these copies were analyzed based on original transcriptome sequencing data,and GO enrichment analyses of these co-expressed genes were also conducted.The degree of variation among proteins encoded by these copies was compared by CDD search,multiple sequence alignment and three-dimensional structural modeling.The results showed that there were eight ep300/crebbp members in rainbow trout(ep300aa-ep300bb,crebbpaa-crebbpbb),which were all formed by whole genome duplication events and could be divided into four ohnolog pairs corresponding to the four members in D.rerio.There were significant differences in tissue expression profiles,and primary and tertiary structures of encoded proteins between different ohnolog pairs,much smaller differences between two copies within an ohnolog pair.These eight members had different numbers of unique co-expressed genes,and the number of GO terms enriched by these gene collections related to binding,modification,stress/stimulus-response and hypoxia tolerance were also varied greatly.ep300ba and ep300bb belong to an ohnolog pair,and yet their encoded proteins were varied in 35 positions in conserved domains,with the far greater number than other ohnolog pairs.Furthermore,only co-expressed genes of ep300bb enriched GO terms related to stress/stimulus-response and hypoxia tolerance.The findings suggest that ep300bb can serve as an important candidate gene for genetic improvement of rainbow trout due to its great evolution rate and stronger correlation with hypoxia tolerance than other ep300/crebbp members.
作者
王宪宗
刘青
李澍
WANG Xianzong;LIU Qing;LI Shu(College of Animal Science, Shanxi Agricultural University, Taigu 030801, China;Agriculture and Rural Affairs Bureau of Lüliang City, Lüliang 033099, China)
出处
《大连海洋大学学报》
CAS
CSCD
北大核心
2022年第3期376-385,共10页
Journal of Dalian Ocean University
基金
山西省高等学校科技创新项目(2020L0158)
山西农业大学科技创新项目(2017YJ05)。
