Allotetraploids play central roles in the field of polyploid breeding of freshwater fishes. The molecular basis underlying distant hybridization and individual differences between allotetraploids and their parents is largely unknown. In this study, we performed quantitative proteomics profiling in gonad and liver tissues between allotetraploid and its parents Red Crucian Carp (♀) and Common Carp (♂) respectively. Thousands of proteins were identified and quantified. Species and tissue specific analysis revealed that a large number of causal proteins are specifically regulated in gonad or liver tissue in allotetraploid and its parents respectively. Subsequently, integrative bioinformatics analyses including functional enrichment, pathway and network analyses were conducted. The results suggested a series of gonad and liver specifically regulated proteins such as LSM3, LSM7, PABPC1B and ALDH3A1, EHHADHB, ACAT2 play crucial roles in reproduction-related and metabolism-related pathways including “DNA replication”, “Spliceosome” and “Metabolic pathways”, “Biosynthesis of antibiotics”. Meanwhile, species specifically regulated proteins such as FMR1, MAO are involved in “RNA transport”, “Glycine, serine and threonine metabolism”. Herein, we established the first comprehensive proteomics knowledgebase for particular freshwater fishes. It may shed light on the molecular mechanisms underlying polyploidy breeding and individual differences and serve as an indispensable reference for further studies.

Significance

The molecular basis underlying distant hybridization and individual differences between allotetraploid and their parents Red Crucian Carp and Common Carp is largely unknown. Quantitative proteomics profiling integrated with multiple bioinformatics analysis revealed that a large number of causal proteins are specifically expressed in gonad or liver tissue in allotetraploid and its parents. Herein, we established the first comprehensive proteomics knowledgebase for particular freshwater fishes. It may shed light on the molecular mechanisms underlying polyploidy breeding and individual differences and serve as an indispensable reference for further associated studies.

中文翻译：

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基于异源四倍体和亲本的定量蛋白质组学进行物种和组织特异性分析

异源四倍体在淡水鱼类多倍体育种领域中起着核心作用。异源四倍体与其亲本之间远距离杂交和个体差异的潜在分子基础尚不清楚。在这项研究中，我们进行了定量蛋白质组学在异源四倍体及其家长红鲫（性腺之间，肝组织的剖析♀）和鲤鱼（♂） 分别。鉴定和定量了数千种蛋白质。物种和组织特异性分析表明，异源四倍体及其亲本的性腺或肝脏组织中分别有大量的致病蛋白受到特殊调节。随后，进行了包括功能增强，途径和网络分析在内的综合生物信息学分析。结果表明，一系列受性腺和肝脏特异性调节的蛋白，例如LSM3，LSM7，PABPC1B和ALDH3A1，EHHADHB，ACAT2在生殖相关和代谢相关途径（包括“ DNA复制”，“剪接体”和“代谢途径”）中发挥关键作用”，“抗生素的生物合成”。同时，物种专门调节蛋白质，例如FMR1，MAO参与“ RNA转运”，“甘氨酸，丝氨酸和苏氨酸代谢”。在此，我们建立了第一个针对特定淡水鱼类的综合蛋白质组学知识库。它可能阐明多倍体育种和个体差异的分子机制，并作为进一步研究必不可少的参考。

意义

异源四倍体与其亲本红Cru鱼和普通鲤鱼之间远距离杂交和个体差异的潜在分子基础在很大程度上是未知的。蛋白质组学定量分析与多种生物信息学分析相结合，揭示了大量因果蛋白在异源四倍体及其亲本的性腺或肝组织中特异性表达。在此，我们建立了第一个针对特定淡水鱼类的综合蛋白质组学知识库。它可能揭示了多倍体育种和个体差异的分子机制，并为进一步的相关研究提供了必不可少的参考。