# Conserved Plastid Genomes of _Pourthiaea_ Trees: Comparative Analyses and Phylogenetic Relationship
## 1 Introduction  
Rosaceae, one of the most diverse families within angiosperms, comprises 92 genera and 2,805 species [1]. It is currently split into three subfamilies: Amygdaloideae, Rosoideae, and Dryadoideae [2]. The _Pourthiaea_ Decne. is a deciduous woody genus in the subfamily Amygdaloideae. The genus encompasses about 11-22 species and is widely distributed across East Asia to Southeast Asia [3; 4; 5; 6]. Some species of _Pourthiaea_ are important ornamentally and greening trees in China and are frequently utilized in horticulture for their fascinating white flowers in spring followed by red fruits in autumn. Therefore, _Pourthiaea_ plays an indispensable and positive role in ecological construction in the central and southern regions of China. The genus _Pourthiaea_ was first described by [PERSON] in 1894, yet the taxonomy of _Pourthiaea_ has been controversial. In the early days, _Pourthiaea_ was once consideredeither as a section of _Photinia_[2; 3; 4; 7; 8], a synonym of _Aronia_[9], or a segregate genus from _Photinia_ based on morphological characteristics [10]. Until recently, a study first confirmed the monophyly and genus status of _Pourthiaea_ based on two plastid regions (_trnL-trn_F and _psbA-trn_H) and the nuclear ribosomal DNA ITS (nrDNA ITS) sequence [11]. Subsequent studies have once again confirmed the monophyly of _Pourthiaea_ based on molecular and morphological evidence [5; 6; 12]. The monophyly of _Pourthiaea_ shares some distinguishing morphological characteristics, namely deciduous leaves, Kribs'III-I heterogeneous rays in the wood, pedicels and warty peduncles, and clusters of stone cells surrounded by parenchomatous cells in the flesh of pomes [10; 13; 14]. Additionally, the species delimitation of _Pourthiaea_ remains challenging due to the highly variable morphological characteristics [5; 6; 15]. Therefore, more efficient and specific DNA barcodes are needed to explore the phylogeny of _Pourthiaea_ and discriminate them from related species. Typically, the plastid genome (plastome) structure of angiosperms is highly conserved; it is 120 kb-190 kb in size, including a small single-copy (SSC) region, a large single-copy (LSC) region, and two inverted repeat (IR) regions [16]. Variations in plastome size are primarily due to the expansion and contraction of IR regions [17; 18]. For example, the plastome of _Pelargonium_\(\times\)_hortorum_ is 217 kb in size with the IR region expanding to 75,741 bp [19], while _Pinus thunbergi_ is 119 kb in size, and the IR region is only 495 bp [20]. The IR regions of plastid genomes have even been confirmed to be complete or partial losses in some species [21; 22]. Moreover, the plastid genome always encodes 110-130 distinct genes. These include about eighty protein-coding genes (PCGs), about thirty transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes [21]. Nonetheless, gene loss has occurred in the plastid genomes of many plant lineages [16]. Owing to their smaller size compared to the nuclear genome, conserved genomic structure, lack of recombination, low rates of nucleotide substitutions, and usual uniparental inheritance [23], plastid genomes have been more commonly used to infer phylogenetic relationships of green plants [24; 25; 26]. Recent advances in genome skimming sequencing have facilitated the capture of complete plastomes and nuclear ribosomal DNA (nrDNA) sequences [27; 28; 29; 30]. Therefore, we preferred to use this method to obtain plastomes and nrDNA sequences in order to comprehensively investigate the phylogenetic relationships of the genus _Pourthiaea_. Herein, we first analyzed the complete plastid genome sequences of thirteen _Pourthiaea_ species, including ten reported plastomes and three newly sequenced genomes (_Pourthiaea beauverdiana, Pourthiaea parrofilia_, and _Pourthiaea villosa_).