, known as Lady Banks' rose, is a perennial ornamental crop and a versatile herb in traditional Chinese medicine. Given the lack of genomic resources, we assembled a HiFi and Nanopore sequencing-derived 458.58 Mb gap-free telomere-to-telomere high-quality genome with a scaffold N50 = 63.90 Mb. The genome of exhibited no lineage-specific whole-genome duplication compared with other Rosaceae. The phylogenomic analysis of 13 Rosaceae and through a comparative genomics study showed that numerous gene families were lineage-specific both before and after the diversification of Rosaceae. Some of these genes are candidates for new genes that have evolved from parental genes through fusion events. Fusion genes are divided into three types: Type-I and Type-II genes contain two parental genes that are generated by duplication, distributed in the same and different regions of the genome, respectively; and Type-III can only be detected in one parental gene. Here, Type-I genes are found to have more relaxed selection pressure and lower Ks values than Type-II, indicating that these newly evolved Type-I genes may play important roles in driving phenotypic evolution. Functional analysis exhibited that newly formed fusion genes can regulate the phenotype traits of plant growth and development, suggesting the functional significance of these genes. This study identifies new fusion genes that could be responsible for phenotype evolution and provides information on the evolutionary history of recently diverged species in the genus. Our data represents the major progress in understanding the new fusion genes evolution pattern of Rosaceae and provides an invaluable resource for phylogenomic studies in plants.

中文翻译：

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蔷薇科系统发育学研究为新基因的进化提供了见解


班克斯玫瑰，又名班克斯夫人玫瑰，是一种多年生观赏作物，也是一种多功能的中药草本植物。鉴于缺乏基因组资源，我们组装了 HiFi 和 Nanopore 测序衍生的 458.58 Mb 无间隙端粒到端粒高质量基因组，支架 N50 = 63.90 Mb。与其他蔷薇科植物相比，其基因组没有表现出谱系特异性的全基因组重复。对13个蔷薇科植物的系统发育分析和比较基因组学研究表明，在蔷薇科植物多样化之前和之后，许多基因家族都具有谱系特异性。其中一些基因是新基因的候选者，这些新基因是通过融合事件从亲代基因进化而来的。融合基因分为三种类型：I型和II型基因包含两个通过复制产生的亲本基因，分别分布在基因组的相同和不同区域； Type-III只能在一个亲本基因中检测到。这里，发现I型基因比II型基因具有更宽松的选择压力和更低的Ks值，表明这些新进化的I型基因可能在驱动表型进化中发挥重要作用。功能分析表明，新形成的融合基因可以调控植物生长发育的表型性状，提示这些基因的功能意义。这项研究确定了可能导致表型进化的新融合基因，并提供了该属中最近分化物种的进化历史信息。我们的数据代表了理解蔷薇科新融合基因进化模式的重大进展，并为植物系统发育学研究提供了宝贵的资源。