Pyrus (pear) is among the most nutritious fruits and contains fibers that have great health benefits to humans. It is mostly cultivated in temperate regions globally and is highly subjected to biotic and abiotic stresses which affect its yield. Pheophorbide a oxygenase (PAO) is an essential component of the chlorophyll degradation system and contributes to the senescence of leaves. It is responsible for opening the pheophorbide a porphyrin macrocycle and forming the main fluorescent chlorophyll catabolite However, this gene family and its members have not been explored in Pyrus genomes. Here we report a pangenome-wide investigation has been conducted on eight Pyrus genomes: Cuiguan, Shanxi Duli, Zhongai 1, Nijisseiki, Yunhong No.1, d’Anjou, Bartlett v2.0, and Dangshansuli v.1.1. The phylogenetic history, their gene structure, conservation patterns of motifs, their distribution on chromosomes, and gene duplication are studied in detail which shows the intraspecific structural conservation as well as evolutionary patterns of Pyrus PAOs. Cis-elements, protein–protein interactions (PPI), and the Gene Ontology (GO) enrichment analyses show their potential biological functions. Furthermore, their expression in various tissues, fruit hardening conditions, and drought stress conditions is also studied. Based on phylogenetics, the identified PAOs were divided into four groups. The expansion of this gene family in Pyrus is caused by both tandem and segmental duplication. Moreover, positive and negative selection pressure equally directed the gene’s duplication process. The Pyrus PAO genes were enriched in hormones-related, light, development, and stress-related elements. RNA-seq data analysis showed that PAOs have varied levels of expression under diseased and abiotic stress conditions. The 3D structures of PAOs are also predicted to get more insights into functional conservation. Our research can be used further to get a deeper knowledge of the PAO gene family in Pyrus and to guide future research on improving the genetic composition of Pyrus to enhance stress tolerance.

中文翻译：

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八个梨基因组脱镁叶绿酸 a 加氧酶 (PAO) 基因的比较基因组学分析及其在梨多重胁迫反应中的调控作用

梨（梨）是最有营养的水果之一，含有对人类健康有益的纤维。它主要在全球温带地区种植，并且高度受到生物和非生物胁迫的影响，从而影响其产量。脱镁叶绿酸加氧酶 (PAO) 是叶绿素降解系统的重要组成部分，有助于叶子的衰老。它负责打开脱镁叶绿酸卟啉大环并形成主要的荧光叶绿素分解代谢物。然而，该基因家族及其成员尚未在梨属基因组中进行探索。在这里，我们报告了对八个梨属基因组进行的全基因组研究：翠冠、山西杜里、中爱1号、二十世纪、云红一号、d'Anjou、Bartlett v2.0和砀山素里v.1.1。详细研究了 Pyrus PAO 的系统发育历史、基因结构、基序的保守模式、它们在染色体上的分布和基因复制，显示了 Pyrus PAO 的种内结构保守性和进化模式。顺式-元素、蛋白质-蛋白质相互作用（PPI）和基因本体（GO）富集分析显示了它们潜在的生物学功能。此外，还研究了它们在各种组织、果实硬化条件和干旱胁迫条件下的表达。根据系统发育学，已鉴定的 PAO 分为四类。梨属中该基因家族的扩展是由串联和片段复制引起的。此外，正选择压力和负选择压力同样引导基因的复制过程。梨树聚氧化酶基因富含与激素相关、光、发育和压力相关的元素。 RNA-seq数据分析表明聚氧化酶在患病和非生物胁迫条件下具有不同的表达水平。 PAO 的 3D 结构预计也能对功能保护有更多的了解。我们的研究可进一步用于更深入地了解梨属中的 PAO 基因家族，并指导未来改善梨属遗传组成以增强抗逆性的研究。