神仙鱼透明鳃盖转录组解析  

Transcriptome Analysis of Transparent Gill Covers of Pterophyllum scalare

作　　者：张纬宇 陈再忠[1] 温彬[1] 高建忠[1] ZHANG Weiyu;CHEN Zaizhong;WEN Bin;GAO Jianzhong(College of Fisheries and Life Science,Shanghai Ocean University/Key Laboratory of Freshwater Aquatic Genetic Resources,Ministry of Agriculture and Rural Affairs/Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources,Ministry of Education/Shanghai Engineering Research Center of Aquaculture/National Demonstration Centre for Experimental Fisheries Science Education,Shanghai 201306,China)

机构地区：[1]上海海洋大学水产与生命学院/农业农村部淡水水产种质资源重点实验室/水产种质资源发掘与利用教育部重点实验室/上海水产养殖工程技术研究中心/水产科学国家级实验教学示范中心,上海201306

出　　处：《广东农业科学》2024年第4期54-64,共11页Guangdong Agricultural Sciences

基　　金：上海市自然科学基金(20ZR1423600);上海扬帆人才计划项目(19YF1419400);国家自然科学基金(31902376)。

摘　　要：【目的】神仙鱼透明性状具有很高的经济价值和科研价值。探究神仙鱼透明鳃盖(Transparent gill cover,TGC)和不透明鳃盖(Opaque gill cover,OGC)之间的差异表达基因(Differential expression genes,DEG),并挖掘影响神仙鱼透明鳃盖性状的相关信号通路,可为后续筛选调控神仙鱼透明鳃盖性状的关键基因并开展相关机制研究提供理论基础。【方法】选取红顶三色品系神仙鱼的鳃盖组织为研究材料,OGC和TGC各选取6个样本。基于Illumina Novaseq 6000测序平台进行转录组学测序,利用Fastp对原始测序数据进行质控,利用Trinity软件对质控后的数据进行从头组装获得转录本(Transcript)和对应的单基因(Unigene),利用CD-HIT软件和BUSCO软件分别对初始组装序列进行去冗余分析和结果评估。去冗余后的Unigene基于序列同源性进行功能注释。利用RSEM软件计算每个样本中Unigene的表达量。使用DESeq2软件计算OGC和TGC之间的DEG。使用Goatools软件和KOBAS软件对DEG分别进行GO和KEGG通路富集分析。【结果】(1)测序数据质控后每个样本测序碱基平均错误率均低于0.1%,Q20均高于97.78%,Q30均高于93.58%,测序质量可靠。从头组装后获得200 303个Transcript,对应123 178个Unigene。组装后数据去冗余后共获得147 932个Transcript,对应108 070个Unigene,平均长度为991.85 bp,N50为2 430 bp。(2)共有40 180个Unigene在NR、KEGG、eggNOG、GO、Pfam、Swiss-Prot数据库中获得功能注释,占总体的37.98%,其中10 747个基因在6个数据库中同时被注释,占总体的26.75%。(3)TGC相对于OGC共432个DEG,其中TGC相对于OGC显著上调267个基因、下调165个基因。(4)GO富集结果显示,432个DEG主要富集在IMP生物合成过程、IMP代谢过程、“从头”IMP生物合成过程、氨基酸结合、修饰氨基酸结合等5条生物通路中。(5)KEGG富集结果显示,432个DEG主要富集在神经活性配体-受体相互作用、酪氨酸代谢、嘌呤代谢、【Objective】The transparent traits in Pterophyllum scalare has high economic and scientific value.This article aims to explore the differential expression genes(DEG)between transparent gill cover(TGC)and opaque gill cover(OGC)tissues of P.scalare,and explore the relevant signaling pathways affecting the transparent gill cover traits of P.scalare,so as to provide a theoretical basis for the subsequent screening of key genes regulating the transparent gill cover trait of P.scalare and related mechanism studies.【Method】The gill cover tissue of P.scalare(strain:red-topped tri-color)was selected as the research material,and 6 samples were selected from each group of OGC and TGC.Transcriptomic sequencing was carried out based on the Illumina Novaseq 6000 sequencing platform with using Fastp to perform quality control on raw sequencing data.The transcript and the corresponding single gene(Unigene)were obtained by de novo assembling of quality control data by Trinity software,and the initial assembly sequence was deredundancy analysis and result evaluation by CD-HIT software and BUSCO software,respectively.After redundancy,unigene were functionally annotated based on sequence homology.RSEM software was used to calculate the expression of unigene in each sample.DEGs between OGC and TGC were calculated using DESeq2 software.GO and KEGG pathway enrichment analysis was performed on DEGs using Goatools software and KOBAS software,respectively.【Result】(1)After quality control of sequencing data,the average error rate of each sample sequencing base was less than 0.1%,Q20 was higher than 97.78%,and Q30 was higher than 93.58%,and the sequencing quality was reliable.After de novo assembling,200303 transcripts were obtained,corresponding to 123178 unigenes.After deredundancy analysis,a total of 147932 transcripts are obtained,corresponding to 108070 unigenes,with an average length of 991.85 bp and N50 is 2430 bp.(2)A total of 40180 unigenes were annotated in the NR,KEGG,eggNOG,GO,Pfam,and Swiss-Prot databases,accounting

关 键 词：神仙鱼 转录组学 透明性状 差异表达基因 GO富集分析 KEGG富集分析 

分 类 号：S917.4[农业科学—水产科学]