| 张纬宇，陈再忠，温 彬，高建忠.神仙鱼透明鳃盖转录组解析[J].广东农业科学,2024,51(4):54-64 |
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神仙鱼透明鳃盖转录组解析 |
| Transcriptome Analysis of Transparent Gill Covers of Pterophyllum scalare |
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| DOI：10.16768/j.issn.1004-874X.2024.04.005 |
| 中文关键词: 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 |
| 英文关键词: ZHANG Weiyu,CHEN Zaizhong,WEN Bin,GAO Jianzhong |
| 基金项目: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） |
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| 中文摘要: |
| 【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、1 个叶酸碳池、苯丙氨酸代谢、核苷酸代谢、泛醌和其他萜类化合物 - 醌生物合成等 7 条生物通路中。【结论】利用转录组学测序技术获得与神仙鱼透明鳃盖性状相关的 432 个基因，这些基因主要参与 12 条信号通路。研究结果将为神仙鱼透明鳃盖性状相关基因的挖掘和功能研究提供参考。 |
| 英文摘要: |
| 【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, 200 303 transcripts were obtained, corresponding to 123 178 unigenes. After deredundancy analysis, a total of 147 932 transcripts are obtained, corresponding to 108 070 unigenes, with an average length of 991.85 bp and N50 is 2 430 bp. (2) A total of 40 180 unigenes were annotated in the NR, KEGG, eggNOG, GO, Pfam, and Swiss-Prot databases, accounting for 37.98% of the total, of which 10 747 genes were annotated simultaneously in 6 databases, accounting for 26.75% of the total. (3) TGC relative to OGC has a total of 432 DEGs, of which TGC significantly up-regulated 267 genes and down-regulated 165 genes relative to OGC. (4) GO enrichment results showed that 432 DEGs were mainly enriched in 5 biological pathways: IMP biosynthesis, IMP metabolism, “de novo” IMP biosynthesis, amino acid binding, and modified amino acid binding. (5) KEGG enrichment results showed that 432 DEGs were mainly enriched in 7 biological pathways: neuroactive ligand-receptor interaction, tyrosine metabolism, purine metabolism, a carbon pool of folate, phenylalanine metabolism, nucleotide metabolism, ubiquinone and other terpene-quinone biosynthesis. 【Conclusion】432 genes related to the transparent gill cover trait of P. scalare were obtained by transcriptomic sequencing, which were mainly involved in 12 signaling pathways. The results will provide reference for the mining and functional study of genes related to transparent gill cover trait in P. scalare. |
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