背景:ACO(1-氨基环丙烷-1-羧酸)是植物乙烯合成途径中的关键酶,影响植物生物学的关键方面,如开花,果实成熟,和种子发育。
目的:本研究旨在鉴定具有代表性的玫瑰科基因组中的ACO基因,通过整合同理信息来重建它们的系统发育关系,并研究其在果实发育过程中的表达模式和网络。
方法:我们使用专门的隐马尔可夫模型(HMM),基于ACO基因编码蛋白的序列属性,系统地鉴定和分析玫瑰科植物科12个代表性物种的ACO基因家族成员。通过转录组分析,我们描述了ACO基因在六个不同的玫瑰科果实中的表达模式。
结果:我们的调查显示,62种ACO基因分布在被调查的玫瑰科物种中,以主要在细胞质内表达的亲水性蛋白质为特征。系统发育分析将这些ACO基因分为三个可辨别的类别,即I类,二级,和第三类。通过共线性评估进一步审查表明这些类别之间缺乏共线性关系,突出每个类别中保守基序和启动子类型的变化。转录组分析揭示了与未显示呼吸爆发的水果相比,ACO基因在表达水平和趋势上的显着差异。采用加权基因共表达网络分析(WGCNA),我们发现,枇杷果实中ACO基因的共表达相关性与苹果中观察到的明显不同。我们的发现,源自基因本体论(GO)富集结果,表明ACO基因及其共表达的对应物参与了与枇杷中萜类代谢和碳水化合物合成有关的生物过程。此外,我们对基因调控网络(GRN)的探索强调了GNAT转录因子(Ejapchr1G00010380)在控制枇杷果实中ACO基因(Ejapchr10G00001110)过表达中的潜在关键作用。
结论:构建的ACO蛋白HMM为鉴定植物ACO蛋白提供了一种精确和系统的方法,促进系统发育重建。来自代表性玫瑰科果实的ACO基因表现出不同的表达和调控模式,保证进一步的功能表征。
BACKGROUND: ACO (1-aminocyclopropane-1-carboxylic acid) serves as a pivotal enzyme within the plant ethylene synthesis pathway, exerting influence over critical facets of plant biology such as flowering, fruit ripening, and seed development.
OBJECTIVE: This study aims to identify ACO genes from representative Rosaceae genomes, reconstruct their phylogenetic relationships by integrating synteny information, and investigate their expression patterns and networks during fruit development.
METHODS: we utilize a specialized Hidden Markov Model (HMM), crafted on the sequence attributes of ACO gene-encoded proteins, to systematically identify and analyze ACO gene family members across 12 representative species within the Rosaceae botanical family. Through transcriptome analysis, we delineate the expression patterns of ACO genes in six distinct Rosaceae fruits.
RESULTS: Our investigation reveals the presence of 62 ACO genes distributed among the surveyed Rosaceae species, characterized by hydrophilic proteins predominantly expressed within the cytoplasm. Phylogenetic analysis categorizes these ACO genes into three discernible classes, namely Class I, Class II, and Class III. Further scrutiny via collinearity assessment indicates a lack of collinearity relationships among these classes, highlighting variations in conserved motifs and promoter types within each class. Transcriptome analysis unveils significant disparities in both expression levels and trends of ACO genes in fruits exhibiting respiratory bursts compared to those that do not. Employing Weighted Gene Co-Expression Network Analysis (WGCNA), we discern that the co-expression correlation of ACO genes within loquat fruit notably differs from that observed in apples. Our findings, derived from Gene Ontology (GO) enrichment results, signify the involvement of ACO genes and their co-expressed counterparts in biological processes linked to terpenoid metabolism and carbohydrate synthesis in loquat. Moreover, our exploration of gene regulatory networks (GRN) highlights the potential pivotal role of the GNAT transcription factor (Ejapchr1G00010380) in governing the overexpression of the ACO gene (Ejapchr10G00001110) within loquat fruits.
CONCLUSIONS: The constructed HMM of ACO proteins offers a precise and systematic method for identifying plant ACO proteins, facilitating phylogenetic reconstruction. ACO genes from representative Rosaceae fruits exhibit diverse expression and regulative patterns, warranting further function characterizations.