基因的复制与丢失是物种基因组进化的重要途径，基因家族的扩增与物种的适应性进化、特异性状有关。蔷薇科共有124个属，包含花卉、果树等重要的经济作物。研究蔷薇属谱系特异性基因及物种特异性基因对理解蔷薇属的进化、性状产生等方面具有重要意义。本研究通过比较蔷薇属与蔷薇科其他物种的基因组鉴定了蔷薇属谱系特异性扩增的基因家族，分析其中IAN基因家族及RLK-Pelle_DLSV基因家族所在的蛋白激酶超家族的进化、功能，并开展了月季蛋白激酶RcMPK3的功能验证试验。主要研究结果如下：

特异性扩增基因分析：蔷薇属与草莓分化过程中发生扩增和收缩的基因功能富集表明蔷薇属增强了能量代谢及生物胁迫响应，同时降低信号转导及热胁迫响应，说明蔷薇属可能经历了获能途径减少、温度下降等环境变化。14个物种的特异性基因功能富集分析表明，物种特异性基因大多富集于核酸代谢、激素应答、刺激响应等通路。此外，59%的月季特异性基因参与逆境响应，并且更集中于非生物胁迫响应。对8个在蔷薇属特异性扩增的基因家族选择压及功能富集分析表明，大多数谱系特异性扩增基因受到纯化选择，集中于免疫防御、信号转导、生长发育和繁殖等通路。

IAN基因家族分析：对12个物种的IAN基因进行生物信息学分析。结果显示，在蔷薇属物种中IAN基因数量最多，在其余物种中数量较为保守。系统进化树显示拟南芥AtIAN9为蔷薇科所有IAN的同源基因。染色体分布与共线性说明IAN基因大多呈串联重复排列，其扩增与局部复制事件有关。顺式作用元件分析表明昼夜节律调节等元件为拟南芥IAN特有。逆境转录组表明月季IAN基因参与不同逆境的响应，说明月季IAN基因可能发生了功能分化。

蛋白激酶超家族分析：对月季蛋白激酶基因进行生物信息学分析。结果显示，月季中RLK-Pelle_DLSV、RLK-Pelle_LRK10L-2等亚家族的基因数量多于其他物种，其中RLK-Pelle_DLSV在蔷薇属中谱系特异性扩增。转录组及共表达网络说明月季通过不同途径响应不同逆境，其中RLK-Pelle家族介导月季对生物、非生物胁迫的响应，CMGC家族主要参与对非生物胁迫的响应。基于相较于草莓在月季中扩增的蛋白激酶亚家族及月季灰霉病转录组数据，选择可能参与月季对灰霉病的响应的RcMPK3基因验证功能。结果显示，干扰RcMPK3会导致月季花瓣灰霉病斑扩大，说明RcMPK3可能参与月季对灰霉病的响应。

蔷薇属谱系特异性基因主要集中于逆境响应，其中IAN基因家族在蔷薇属植物中扩增，并且可能产生了功能分化，月季蛋白激酶参与响应生物胁迫及非生物胁迫的机制不同，并且RcMPK3可能参与月季对灰霉病的响应。

Gene duplication and loss are important pathways for the evolution of species genomes, while the expansion of gene families are related to the adaptive evolution and specific traits of species. There are 124 genera in Rosaceae, including important economic crops such as fruit and flowers. The study of lineage-specific genes and species-specific genes in Rosa plays an important role in understanding the evolution and trait generation of Rosa. This study identified lineage-specific gene families and species-specific gene families in Rosa by comparing the genomes of Rosa with other species in Rosaceae, selected IAN gene family and protein kinase superfamily to analyse evolution and function. Rosa chinensis protein kinase RcMPK3 was verified in playing a role in response to gray mold in Rosa chinensis. The main research results are as follows:

Analysis of specific expanded gene: The functional enrichment analysis of expanded and contracted genes during the divergence between Rosa and Fragaria suggested that Rosa have enhanced energy metabolism and biological stress responses, while signal transduction and heat stress responses have been reduced, indicate Rosa may have experienced environmental changes such as reduced energy availability and temperature decline. Functional enrichment analysis of species-specific genes across 14 species showed that these genes were predominantly enriched in pathways related to nucleic acid metabolism, hormone responses, and stimulus responses. 59% of the Rosa chinensis specific genes were involved in stress responses, with a stronger bias toward abiotic stress responses. Selection pressure and functional enrichment analysis of 8 gene families specifically expanded in Rosa revealed that most lineage-specific expanded genes were under purifying selection and were enriched in pathways related to immune defense, signal transduction, growth and development, reproduction.

IAN gene family analysis: Bioinformatics analysis of IAN genes in 12 species was performed. The results showed that the number of IAN genes was the largest in Rosa, and was relatively conservative in the rest of the species. The phylogenetic tree showed that Arabidopsis thaliana AtIAN9 was the homologous gene of all IAN in Rosaceae. Chromosome distribution and colinearity showed that IAN genes were arranged in tandem repeats, indicating that the expansion of IAN genes was formed by local duplication events. Cis-acting element analysis showed that elements such as circadian rhythm regulation were unique to Arabidopsis thaliana IAN. The analysis results of the adversity transcriptome showed that IAN genes mediated responses to different adversities, indicating that Rosa chinensis IAN genes may have undergone functional differentiation.

Protein kinase superfamily analysis: A bioinformatics analysis was conducted on protein kinase genes in Rosa chinensis. The results showed that subfamilies such as RLK-Pelle_DLSV and RLK-Pelle_LRK10L-2 have greater number of genes in Rosa chinensis compared to other species, with RLK-Pelle_DLSV specifically undergoing lineage-specific expansion in the Rosa. Transcriptome data and co-expression network analyses indicated that Rosa chinensis responds to different stresses through distinct pathways. Specifically, the RLK-Pelle family mediates responses to both biotic and abiotic stresses, while the CMGC family is mainly involved in responses to abiotic stress. Based on the expanded protein kinase subfamilies in Rosa chinensis compared to Fragaria and transcriptome data under gray mold infection, the gene RcMPK3 was selected for functional validation due to its potential role in gray mold resistance. Functional analysis showed that silencing RcMPK3 led to an expansion of gray mold lesions on petals, suggesting that RcMPK3 may play a role in the defense response of Rosa chinensis against gray mold.

Lineage specific genes in Rosa were primarily enriched in stress response pathways. Among them, the IAN gene family have undergone expansion in Rosa and may have experienced functional divergence. In addition, protein kinases in Rosa chinensis were involved in responses to biotic and abiotic stresses through distinct mechanisms, and RcMPK3 is likely involved in the defense response of Rosa chinensis against gray mold.

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