The chloroplast genome of Amygdalus L. (Rosaceae) reveals the phylogenetic relationship and divergence time

Background Limited access to genetic information has greatly hindered our understanding of the molecular evolution, phylogeny, and differentiation time of subg. Amygdalus. This study reported complete chloroplast (cp) genome sequences of subg. Amygdalus, which further enriched the available valuable resources of complete cp genomes of higher plants and deepened our understanding of the divergence time and phylogenetic relationships of subg. Amygdalus. Results The results showed that subg. Amygdalus species exhibited a tetrad structure with sizes ranging from 157,736 bp (P. kansuensis) to 158,971 bp (P. davidiana), a pair of inverted repeat regions (IRa/IRb) that ranged from 26,137–26,467 bp, a large single-copy region that ranged from 85,757–86,608 bp, and a small single-copy region that ranged from 19,020–19,133 bp. The average GC content of the complete cp genomes in the 12 species was 36.80%. We found that the structure of the subg. Amygdalus complete cp genomes was highly conserved, and the 12 subg. Amygdalus species had an rps19 pseudogene. There was not rearrangement of the complete cp genome in the 12 subg. Amygdalus species. All 12 subg. Amygdalus species clustered into one clade based on both Bayesian inference and maximum likelihood. The divergence time analyses based on the complete cp genome sequences showed that subg. Amygdalus species diverged approximately 15.65 Mya. Conclusion Our results provide data on the genomic structure of subg. Amygdalus and elucidates their phylogenetic relationships and divergence time. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07968-6.


Introduction
Amygdalus L. (Rosaceae), a subgenus of the genus Prunus L. [1][2][3], is a small group within Prunus that includes approximately 24 species. Subg. Amygdalus species are mainly distributed in Iran and eastern Turkey, but a few are distributed in southeastern Europe, the Mediterranean region, Mongolia, and China [4,5]. Subg.
Amygdalus members are shrubs or small trees that mostly grow between 1000 and 2500 m above sea level in mountainous areas [5]. Many studies have elucidated various aspects of subg. Amygdalus members; for example, Maatallaha et al. [6] evaluated mineral nutrients, phenolic and volatile profiles, and antioxidant activities of peach cultivars and assessed their potential for use in cultivar improvement [5,7]. Moreover, subg. Amygdalus species are valuable fruit trees and can be common ornamental plants, among which P. persica has over one thousand years of cultural history and is one of the five oldest cultivated fruit species with distinct advantages in the world [8].
In recent years, members of subg. Amygdalus have become important subjects of many studies [9][10][11][12]. For example, P. dulcis produces a lot of simple gum exudates that are obtained from its trunk, branches, and fruits [13]. Prunus davidiana var. potaninii Rehd., as an important rootstock of drupe fruit trees in northwestern China, is a wild relative of P. davidiana [14]. Fang et al. [15] constructed regression equations between the ages and base diameters of P. mira by data processing system, and concluded that the populations of P. mira in Linzhi are declining; this species plays an important role in the germplasm improvement of cultivated peach. Prunus mira was also used to facilitate vegetation and rootstock recovery to mitigate land degradation in many areas because of its high tolerance to drought, cold, and barren soil [16]. Prunus kansuensis, which has strong cold resistance and high drought tolerance, can be used as ornamental woody plants. However, the yields of cultivars have recently been seriously affected by diseases and insect pests [17,18]. Yazbek and Oh [5] reconstructed and analyzed the phylogenetic relationships of subg. Amygdalus by DNA sequencing and morphology, and then evaluated the morphological characteristics used for the classification of subg. Amygdalus. Vafadar et al. [19] identified the pollen morphology of hybrids of subg. Amygdalus, and analyzed common pollen grain features. Several studies have conducted phylogenetic analysis on stone fruits based on internal transcribed spacer (ITS) technology using genetic distance thresholds [20][21][22]. However, a study also showed that accurate identification of species may be impacted by a single threshold [23]. DNA metabarcoding is limited by bias of polymerase chain reaction, resolution of barcoding, universality, and perfect degree of database [24]. The chloroplast (cp) genome of subg. Amygdalus species may be essential for illuminating the evolution of and distinguishing the subg. Amygdalus species. No studies have addressed phylogenetic relationships and estimated divergence time of subg. Amygdalus. The cp is an important self-replicating organelle that plays a vital role in photosynthesis and energy transformation [25,26]. Previous studies have shown that the cp genome, which is 115 kb-165 kb in sequence length, consists of a characteristic circular quadripartite structure that includes a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverted repeat (IRa and IRb) regions [27]. Furthermore, compared with the nuclear genome, angiosperm cps are highly conserved in gene composition and genome structure [28], and the structure of plastids, which have unique advantages in phylogenetic reconstruction, is stable, usually uniparental, haploid, and non-recombinant. In this study, complete cp genome sequences of 12 subg. Amygdalus species were compared and analyzed to explore their sequence characteristics and structural differences; these complete cp genome sequences provide additional valuable cp genomic resources of subg. Amygdalus. The aims of the present study were to: (1) explore the complete cp genome sequence of 12 subg. Amygdalus species; (2) clarify the subg. Amygdalus relationships in genus Prunus; and (3) estimate the divergence times of subg. Amygdalus.

Results
Comparative analysis of cp genomes of subg. Amygdalus species The complete cp genome sequence of 12 subg. Amygdalus species exhibited a circular DNA molecule with a typical quadripartite structure; they have a pair of inverted repeats regions (IRa and IRb), one LSC region, and one SSC region ( Fig. 1, Table 1). The complete cp genome sequence of the 12 subg. Amygdalus species ranged from 157,736 bp (P. kansuensis) to 158,971 bp (P. davidiana) in length. The IRa/IRb regions ranged from 26,137-26,467 bp, the LSC region ranged from 85,757-86,608 bp, and the SSC region ranged from 19,020-19,133 bp ( Fig. 1, Table 1). The average GC content of the complete cp genome in the 12 species was 36.80%, and the average GC content of the IR regions was 42.60% (Table 1). The cp genomes of the subg. Amygdalus species encoded a total of 131/133 genes, including 86 protein-coding genes (PCGs), 37/39 tRNA genes, and eight rRNA genes. In P. tenella, there were no petB and ycf3 genes. In P. davidiana var. potaninii Rehd., P. kansuensis, P. persica, P. dulcis, P. davidiana, and P. mongolica, there were two rps19 genes and the ycf15 gene was lost. The rps4 gene of P. ferganensis, P. mira, P. tenella, P. pedunculata, P. tangutica, and P. triloba were lost ( Table 1, Table 2). There were 18 intron-containing genes; the rps12, clpP, and ycf3 genes contained two introns, and the other genes had a single intron ( Table 2).

IR boundary changes and gene rearrangement
The complete cp genome structure of 12 subg. Amygdalus species differed. However, all species had eight genes located at the border of the IR region, i.e., rpl22, rps19, and rpl2 at LSC/IRb; ycf1 and ndhF at IRb/SSC; ycf1 at SSC/IRa; and rpl2 and trnH at IRa/LSC. The border between IRb and SSC extended into the rps19 genes, and the 12 subg. Amygdalus species have similar rps19 pseudogenes. The ycf1 gene of P. mongolica was completely located in the IRb region and was 58 bp away from the IRb/SSC border. The IRb/SSC border extended into the ycf1 genes in the other genomes with a short ycf1 pseudogene of 1-16 bp. The IRa region expanded into trnH (Fig. 2).
The complete cp genome structure and order of the 12 subg. Amygdalus species were relatively conservative; the genomes had high sequence similarity, but there were also some highly variable regions (Fig. 3). These variations mainly existed in non-coding regions. There were substantial differences in intergenic regions in the LSC and SSC regions, including trnH-psbA, trnK-rps16, petN-psbM, rps4-trnT, ndhC-trnV, ycf4-cemA, rps19-rpl2, trnS-trnG, and rpoB-trnC. In addition, there were differences in the coding region of the ycf1 gene and the intron region of the clpP gene.
The complete cp genome of P. dulcis was considered a reference sequence to compare the remaining subg. Amygdalus complete cp genomes. There was no rearrangement in the complete cp genomes of the 12 subg. Amygdalus species (Fig. 4).

Repeats and simple sequence repeats analysis
Palindromic repeats, dispersed repeats, and tandem repeats were identified in the complete cp genome sequences of 12 subg. Amygdalus species (Fig. 5, Table S1, & Table S2). The numbers and distributions of these three repeats of subg. Amygdalus were similar and conservative. There were 308 dispersed repeats, 259 palindrome repeats, and 199 tandem repeats, which accounted for 40.21, 33.81, and 25.98% of the total repeats, respectively. Prunus mira had the most repeats, including 24 dispersed repeats, 23 palindromic repeats, and 20 tandem repeats. P. triloba had the fewest repeats, including 24 dispersed repeats, 21 palindromic repeats, and 15 tandem repeats. The repeats were concentrated in the region of 24-127 bp; most were distributed in spacers or introns, although a few were distributed in gene regions.

Chloroplast phylogenetic and divergence time analysis
Phylogenetic trees were constructed based on the complete cp genome sequences of 45 species. The topologies of the maximum likelihood (ML) and Bayesian inference (BI) trees were nearly identical ( Fig. 7 & Table S4). All 12 subg. Amygdalus species formed a monophyletic clade that was sister to Maleae and Spiraeae. Colurieae, Rubeae, Roseae, Potentilleae, and Agrimonieae clustered into one clade.

Discussion
The complete cp genomes of subg. Amygdalus species are typical quadripartite structures with LSC, SSC, and two IR regions. These genomes were similar to the previously reported complete cp genomes of P. mume, P. armeniaca, and P. salicina [29]. The cp genomes of most plants are 120-160 kb in size [30], although those of a few plants are  kb in size; for example, the cp genomes of Orobanchaceae are 46-190 kb in size [31,32]. In our study, the cp genomes were conserved and similarly sized, with genomes sizes ranging from 157,736 bp in P. kansuensis to 158,971 bp in P. davidiana. The 12 subg. Amygdalus species encoded 130/133 genes. There Amygdalus species; this indicates that the complete cp genome structure is relatively stable, and that the overall evolution rate is low [33].
In this study, the complete cp genomes of the 12 subg. Amygdalus species ranged from 157,736 bp in P. tenella to 158,971 bp in P. kansuensis. There were differences of only 1235 bp, which indicated that subg. Amygdalus species are highly conservative. Furthermore, there were a total of 130/ 133 genes present in the complete cp genome of subg. Amygdalus, which included 85/86 PCGs, 37 tRNAs, and 8 rRNAs. The GC contents were similar to those of other  plants (such as angiosperms), which showed that they are highly conserved [27]. The average GC content of the complete cp genomes in the 12 species was 36.80%, which is similar to the findings of a previously study that studied Gynostemma species (GC content, 36.9-37.0%) [27]. This high GC content could be caused by the high GC content of the rRNA gene sequences located in IR regions. The function, order, and GC content of these genes are all highly conserved, which was also noted for other angiosperms [27]. The complete cp genomes of the 12 subg.
Amygdalus species had an average GC content of 36.80%, which is consistent with the results of Gynostemma species genomes [27], and may be caused by the a high GC content in IR regions [27].
Size increases of plastomes are usually caused by expansion of the IR regions, which are the most conserved regions in the complete cp genome [34]. Our results showed that the cpDNA structure of the 12 subg. Amygdalus species slightly different from each other, although they all have eight genes located at the border of the IR region, i.e., rpl22, rps19, and rpl2 at LSC/IRb; ycf1 and ndhF at IRb/SSC; ycf1 at SSC/IRa; and rpl2 and trnH at IRa/LSC. The border between the IRb and SSC extended into the rps19 genes, and there were rps19 pseudogenes in the 12 subg. Amygdalus species. The expansion of the IR region into the rps19 and ycf1 genes is also present in Cardiocrinum and Amana [35,36]. These significant differences may contribute to the SSRs are widely distributed throughout the genome and play important roles in genome recombination and rearrangement; in particular, polymorphic SSRs can be used to study genetic diversity, population structure, and biogeography within and between groups [37]. We identified 55-65 SSRs in the complete cp genomes of the 12 subg. Amygdalus species; on average, 82.40% of SSRs were located in the noncoding LSC or SSC regions, and 17.60% of SSRs were located in the protein-coding region. Furthermore, SSRs are dominated by single nucleotide repeats, and approximately 90% of single nucleotide repeats were A/T repeats in this study. A previous study revealed that the repeated sequences may play a very important role in sequence rearrangement of complete cp genomes [38]. The results of palindromic repeats, dispersed palindromic repeats, and tandem repeats showed that the number and distribution of these repeats in the 12 species of subg. Amygdalus species were similar and conservative. Prunus mira had a maximum of 24 scattered repeats, 23 palindromes, and 20 tandem repeats. P. triloba had the fewest repeats. Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridization, apomixis, presumed rapid radiation, and historical diversification [29]. Development of the cp phylogeny and time estimation provides new evidence for future comparative evolutionary studies [29], and there have been an increasing number of studies using complete cp genome sequences to assess phylogenetic relationships among angiosperms [27,39]. Our phylogenetic tree was based on complete cp genome data. The ML and BI methods were used to conduct phylogenetic analysis on the 12 subg. Amygdalus species. The phylogenetic trees indicated that the 12 subg. Amygdalus species were clearly closely related with high bootstrap support and posterior probabilities (Fig. 7). The results showed that the 12 subg. Amygdalus species were divided into one subclade, which consistent with results of Yazbek et al. [5]. In addition, the results are consistent with the traditional classification system; this indicated that the current classification of the 12 subg. Amygdalus species is reasonable, such as the classification used in the Flora of China (www.iplant.cn/frps). In morphological cladistic analysis, the appearance, shape, and other characteristics of the 12 subg. Amygdalus species were similar. However, Vafadar et al. [40] suggested that P. mira Koehne, P. davidiana (Carriere) Franch., P. triloba Ltdl., and P. tenella L. should be excluded from Amygdalus, and this may require further study. There are differences in the morphological tree structure and molecular phylogeny of the Rosaceae family and relationships among various genera. Therefore, these cp genome sequences will provide genetic information that may help elucidate the evolution of these species.
The divergence time of the 12 subg. Amygdalus was estimated. The results showed that the 12 subg. Amygdalus species shared a common ancestor around 22

Plant material sampling and chloroplast genomic DNA extraction
Fresh and healthy leaves were collected from adult P. pedunculate, P. mira, P. ferganensis, P. tangutica, P. tenella, P. triloba, P. mongolica, P. dulcis, and P. davidiana var. potaninii Rehd. plants in the field in northwest China ( Table 3). The voucher specimens were placed in the herbarium of the School of Life Science, Yulin University, and the spare materials were placed in an ultralow temperature refrigerator at − 80°C (for accession  Table 3; all nine subg. Amygdalus specimens were identified and sorted by Yizhong Duan). Prunus persica, P. davidiana, and P. kansuensis sequences were collected from the GenBank database (Table 1). The modified hexadecyl trimethyl ammonium bromide method [44,45] was used to extract the total genomic DNA of the 9 species. The extracted DNA was subjected to 0.5% agarose gel electrophoresis and ultraviolet spectrophotometer to check the quality. After passing the total genomic DNA test, fragment it with ultrasound; then, fragment purification and end repair were performed, A was added at the 3′ end, and the sequencing adapter was connected. Subsequently, we used agarose gel electrophoresis to select the size of the fragment and performed polymerase chain reaction for sequencing library preparation. The built library was first subjected to library quality inspection. The library that passed quality inspection was sequenced by Beijing Biomax Biotechnology Co., Ltd. (http://www.biomarker.com.cn/) using the Illumina HiSeq Xten-PE150 platform.

Chloroplast genome assembly and annotation
Raw sequencing read (raw read) data were stored in FASTQ format. The FASTQ data were filtered to obtain clean reads. For data filtering, reads were removed if: (1) they had an adapter; (2) the N content exceeded 10%; (3) they had a base value of less than 10 with a quality value exceeding 50%. The filtered reads were assembled using SOAPdenovo software [46] (http://soap.genomics.org.cn/soap denovo.html), and the assembly was then optimized according to the paired-end and overlap of reads result. For some gaps in the sequence, the assembly result was filled and corrected by SOAPdenovo software to obtain a   Table S4). a The numbers at nodes correspond to ML bootstrap percentages, (b) the number of the branches represent Bayesian posterior probability (PP) complete cp genome. The OrganellarGenomeDRAW (OGDraw) online annotation software [47] (http:// phylocluster.biosci. Ttexas.edu/dogma/) was used to annotate the complete cp genomes of the nine collected subg. Amygdalus species, and the remaining three species of subg. Amygdalus plants genomes were downloaded from the National Center for Biotechnology Information (NCBI) database ( Table 1). The complete cp genome of P. pseudocerasus Lindl. (NC030599) [48] was used as the reference and was manually revised and annotated with Geneious R8 software [49]. Finally, OGDraw visualization software  Chloroplast genome sequence comparative analysis The complete cp genome sequences of the 12 subg.
Amygdalus species were compared. The IR, LSC, and SSC areas, and their boundary information were compared; the online IRscope tool (https://irscope.shinyapps. io/irapp/) [51] was used to map the IR boundary contrast figure. The differences of complete cp genome sequences of the 12 subg. Amygdalus species were studied, and the P. dulcis genome was used as the reference sequence. Each complete cp genome sequence annotation file format of "bed" was converted, which were uploaded to the online analysis program mVISTA (http://genome. lbl.gov/vista/mvista/submit.shtml) [52], and the Shuffle-Lagan mode was selected for genome-wide comparison. The complete cp genome sequence was imported into Geneious R8 software, and the mauve plug-in was used to alignment of global [53]. The gene rearrangement was detected by collinearity analysis with P. dulcis (MT019559) as a reference sequence.
Chloroplast phylogenetic relationships and divergence time estimate

Chloroplast phylogenetic relationships
The complete cp genomes of 33 species from the NCBI database (https://www.ncbi.nlm.nih.gov/) and the 12 subg. Amygdalus species were selected to construct a phylogenetic tree; the complete cp genomes were obtained for nine species of Rosoideae, 19 species of Maleae, 1 species of Sporaeeae, 13 species of Amygdaleae, P. discoidea, P. maximowiczii, and P. pseudocerasus (for the NCBI accession numbers, see Table S4). First, the complete cp genomes of the 45 species were examined by multiple sequence alignment in MAFFT using the PhyloSuite software [57,58]. Subsequently, the comparison results were imported into the ModelFinder program [59], and Akaike information criterion was selected for nucleotide substitution model testing. Then, the ".nex" files in the result were imported into the MrBayes program [60] to build a phylogenetic tree based on the BI method. Prunus discoidea, P. maximowiczii, and P. pseudocerasus were outgroups in reconstruction of the BI phylogenetic tree. We chose the GTR model and GAMMA distribution, and a Markov chain Monte Carlo with one cold and three heated chains [61,62]. Analyses were run for 2,000,000 generations total, sampled once every 1000 generations, running end when the value of the average standard deviation of split frequencies was less than 0.01. We discarded the less than 25% of aging samples and constructed a consistent tree according to the remaining samples. Then, based on the Akaike information criterion, the ModelFinder program was run again to select the optimal nucleotide substitution model from the nucleotide substitution models suitable for BEAST 2 analysis. The results were imported into the IQ-TREE program [63]; the GTR + I + G + F4 model and an ultrafast bootstrap approximation algorithm were selected [64]. The number of re-sampling was 10,000, and the SH-aLRT test was enabled to re-sample 1000 times [65]. The consistent tree file ".contree" was imported into Figtree v1.4.4 software to view and edit the tree, and the output tree diagram was saved to the file [66].

Divergence time estimate
The BEAST v2.6.0 program [62] was used to estimate the divergence time of subg. Amygdalus. First, the MAFFT comparison results were imported to BEAUTi v2, and GTR + Gamma was selected as the nucleotide substitution model (shape = 0.241) [61]. "Empirical" was set of the basic frequency, and the strict molecular clock model was selected. Second, the "Yule Model" was used as the system tree model, and we set the number of iterations and sampling in the Markov chain Monte Carlo algorithm to 3,000,000 and 1000, respectively. Finally, the ".xml" file was obtained from BEAST v2.6.0 [62]. The result was imported into Tracer v1.7.1 software (http://tree.bio.ed.ac.uk /software/tracer/) to check the effective sample size; the effective sample size was greater than 200, which means the results were robust. We used the TreeAnnotator program (https://beast. community/index.html) [67] to perform optimal tree merging. Burn-in was set to 10%, the optimal tree was saved as the final result, and Figtree v1.4.4 software [66] was used to view phylogenetic trees with different time estimates.
We estimated the divergence time of the 12 subg. Amygdalus species with the TimeTree tool (http://www. timetree.org) [68] using the BI tree. We selected four nodes to determine the divergence time:  [70,77]. The standard deviation of four nodes was 1.0 Mya. Finally, we analyzed the dated phylogeny in Figtree, and the value of node representing the tMRCA and 95%HPD were displayed in Figtree to make the results more intuitive.
Additional file 1: Table S1. The repeats distribution in the chloroplast genomes of 12 subg. Amygdalus species. Table S2. The tandem repeats distribution in the chloroplast genomes of 12 subg. Amygdalus species. Table S3. Simple sequence repeats in the chloroplast genomes of 12 subg. Amygdalus species. Table S4. List of species accessions numbers were used in phylogenetic analysis.