Identification of genes related to blind side hypermelanosis of Cynoglossus semilaevis based on skin transcriptome sequencing
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摘要: 半滑舌鳎（Cynoglossus semilaevis）作为比目鱼（Pleuronectiformes）中的代表物种，是我国沿海地区重要的海水经济鱼类。半滑舌鳎体色异常的问题长期以来一直困扰着从业者。导致体色变化的原因多种多样，遗传因素是最根本原因。针对半滑舌鳎无眼侧黑化的研究多在环境、营养、生理、常见色素基因克隆等方面展开，新的功能基因挖掘工作欠缺。本研究选取半滑舌鳎不同体色皮肤进行转录组测序，通过差异基因GO和KEGG富集比对分析，在可能的6条黑色素相关的KEGG通路中筛查差异基因并对差异表达最为显著的10个基因进行了实时荧光定量聚合酶链式反应的验证。本研究找出了半滑舌鳎无眼侧黑化表达显著变化的5个功能基因，分别为txndc、alox15b、ptgs2、ptgisPTGIS、atp1a2a（p<0.05）。其中txndc、alox15b、ptgs2、ptgis基因在黑化组中表达水平高于对照组；功能方面，有3个基因均与花生四烯酸（AA）有一定的相关性，这为多不饱和脂肪酸参与半滑舌鳎体色异常的分子调控机制提供了一定的理论支持。Abstract: Cynoglossus semilaevis as a representative species of Pleuronectiformes, is an important marine economic fish in Chinese coastal areas. The abnormal body color of C. semilaevis has been perplexing the practitioners for a long time. There are many reasons leading to abnormal body color, among which the genetic factors are thought to be the most fundamental reasons. The present researches on hypermelanosis of the blind side of C. semilaevis mainly focus on environment, nutrition, physiology, cloning of known pigmental genes and so on, while the digging of new funtional genes is still lacking. In this study, skin samples with different colors of C. semilaevis are selected for transcriptome sequencing. Through GO and KEGG functional enrichment and comparative analysis of different genes, differential expressed genes are screened in six melanogenesis-related KEGG pathways and the top ten genes are verified by qPCR. In this study, we find five functional genes with significant changes in the hypermelanotic skin on the blind side of C. semilaevis, which refer to txndc, alox15b, ptgs2, ptgis, and atp1a2a (p<0.05). The expression levels of txndc, alox15b, ptgs2, and ptgis genes in the melanization group are higher than those in the control group. In terms of function, three of these five genes are related to arachidonic acid (AA) to some extent. This provides theoretical support for the hypothesis that nutritional regulation related to unsaturated fatty acids may be involved in the molecular mechanism of abnormal body color in C. semilaevis.
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Key words:
- skin /
- Cynoglossus semilaevis /
- hypermelanosis /
- arachidonic acid /
- transcriptome
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图 1 半滑舌鳎无眼侧黑化鱼体色特征
Fig. 1 The body color feature of the Cynoglossus semilaevis with no eye side blackened fish
图 3 半滑舌鳎正常皮肤与黑化皮肤样品间差异表达基因火山图和差异表达基因丰度热图
a. 红色点代表差异基因，黑色点代表被过滤掉的数据，Count为测得计量数；b. 纵向代表基因类型
Fig. 3 Volcano map of the number of differentially expressed genes and heat map of abundance of differentially expressed gene between normal and hypermelanotic skin samples of Cynoglossus semilaevis
a. The red dots represent differential expressed genes, the black dots represent the filtered date, Counts is the measured quantity; b. the vertical one represents genes
图 4 半滑舌鳎正常与黑化皮肤转录组测序差异基因富集注释的GO通路和KEGG通路
Fig. 4 GO pathways and KEGG pathways analysis of differential expressed genes enrichment annotations of transcriptome sequencing of normal and hypermelanotic skin of Cynoglossus semilaevis
图 5 6个候选体色相关mRNA在半滑舌鳎6个测序样品中的qPCR表达检测结果箱线图
蓝色CSC代表半滑舌鳎皮肤正常对照组定量结果，白色CSH代表半滑舌鳎皮肤黑化实验组相对表达结果
Fig. 5 Box plot of qPCR expression results of 6 candidate body color-related mRNAs in 6 sequencing samples of Cynoglossus semilaevis
The CSC represents the relative expression in skin of normal C. semilaevis in the control group, and the CSH represents the relative expression in the skin of hypermelanotic C. semilaevis in the experimental group
表 1 6个半滑舌鳎皮肤转录组测序样品过滤后数据产出及质控分析
Tab. 1 Clean reads output and quality control analysis of six Cynoglossus semilaevis skin transcriptome sequencing samples
样本
名称总有效读数 碱基
数目Q20质量
分值Q30质量
分值GC含量
百分比/%N碱基
含量csc1 65 031 072 9 725 97.03 92.20 47.68 0 csc2 73 612 170 10 981 96.83 91.93 48.19 0 csc3 66 089 004 9 886 96.95 91.96 48.81 0 csh1 79 487 970 11 897 97.25 92.55 47.61 0 csh2 70 698 406 10 579 97.31 92.72 48.38 0 csh3 61 545 522 9 208 97.02 92.04 48.22 0 
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表 2 6个半滑舌鳎皮肤转录组测序样品基因组比对统计表
Tab. 2 Genomic comparison statistics of six Cynoglossus semilaevis skin transcriptome sequencing samples
样品名称 总数目 唯一比对到参考基因组上的
测得条目数目及占比比对到参考基因组多处的
测得条目数目及占比不能比对到参考基因组的
测得条目数目及占比csh1 39 743 985 32 335 924(81.36%) 1 897 171(4.77%) 5 510 890(13.87%) csc1 32 515 536 24 786 485(76.23%) 1 145 579(3.52%) 6 583 472(20.25%) csh2 35 349 203 28 571 030(80.83%) 1 563 099(4.42%) 5 215 074(14.75%) csc2 36 806 085 28 143 927(76.47%) 1 482 619(4.03%) 7 179 539(19.51%) csc3 33 044 502 25 549 970(77.32%) 1 369 439(4.14%) 6 125 093(18.54%) csh3 30 772 761 24 553 311(79.79%) 1 291 583(4.20%) 4 927 867(16.01%)
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