- Background: Limited access to genetic information has greatly hindered our understanding of the molecular evolution, phylogeny, and differentiation time 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. - The average GC content of the complete cp genomes in the 12 species was 36.80%. - We found that the structure of the subg. - There was not rearrangement of the complete cp genome in the 12 subg. - Amygdalus species. - (Rosaceae), a subgenus of the genus Prunus L. - persica has over one thousand years of cultural history and is one of the five. - Full list of author information is available at the end of the article. - The aims of the present study were to: (1) explore the complete cp genome sequence of 12 subg. - The complete cp genome sequence of 12 subg. - The complete cp genome sequence of the 12 subg. - 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. - The complete cp genome structure of 12 subg. - However, all species had eight genes located at the border of the IR region, i.e., rpl22, rps19, and rpl2 at LSC/IRb. - The complete cp genome structure and order of the 12 subg. - 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. - There was no re- arrangement in the complete cp genomes of the 12 subg.. - There were 308 dispersed repeats, 259 palin- drome repeats, and 199 tandem repeats, which accounted for and 25.98% of the total re- peats, respectively. - There were 55–65 SSRs in the complete cp genome sequences of the 12 subg. - The top- ologies of the maximum likelihood (ML) and Bayesian. - The complete cp genomes of subg. - The 12 subg. - In this study, the complete cp genomes of the 12 subg.. - 2) indicates that the number of the repeat unit is 2. - 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 . - This high GC content could be caused by the high GC content of the rRNA gene sequences located in IR regions. - The complete cp genomes of the 12 subg.. - Size increases of plastomes are usually caused by expansion of the IR regions, which are the most con- served regions in the complete cp genome [34]. - Our re- sults showed that the cpDNA structure of the 12 subg.. - Amygdalus species slightly different from each other, al- though they all have eight genes located at the border of the IR region, i.e., rpl22, rps19, and rpl2 at LSC/IRb. - The ex- pansion of the IR region into the rps19 and ycf1 genes is also present in Cardiocrinum and Amana [35, 36].. - 2 Comparison of the borders for LSC, SSC, and IR regions of complete chloroplast genomes of 12 subg. - Amygdalus species.. - We identified 55–65 SSRs in the complete cp genomes of the 12 subg. - Development of the cp phylogeny and time estima- tion provides new evidence for future comparative evo- lutionary studies [29], and there have been an increasing number of studies using complete cp genome sequences to assess phylogenetic relationships among angiosperms [27, 39]. - classification of the 12 subg. - In morphological cladistic analysis, the appearance, shape, and other characteristics of the 12 subg. - There are differences in the morphological tree structure and molecular phylogeny of the Rosaceae family and relationships among various genera. - The divergence time of the 12 subg. - The Rosaceae pat- terns indicate that hybridization and polyploidy may have played a pivotal role in the early evolution of the family in the Eocene [43], which indicated that the Rosaceae was different about Eocene (53–36.5 Mya), they are similar to the results of our study.. - of the complete cp genome in the 12 species was 36.80%. - In addition, it was found that the structure of the subg. - There was no rearrangement in the complete cp of the 12 subg. - The voucher specimens were placed in the herbarium of the School of Life Science, Yulin Uni- versity, and the spare materials were placed in an ultra- low temperature refrigerator at − 80 °C (for accession. - The modified hexadecyl trimethyl ammonium bromide method [44, 45] was used to extract the total genomic DNA of the 9 species. - Subsequently, we used agarose gel electrophoresis to select the size of the fragment and performed polymerase chain reaction for sequencing li- brary preparation. - complete cp genome. - Ttexas.edu/dogma/) was used to annotate the complete cp genomes of the nine col- lected subg. - Mean divergence time of the nodes were shown next to the nodes while the blue bars correspond to the 95% highest posterior density (HPD). - Chloroplast genome sequence comparative analysis The complete cp genome sequences of the 12 subg.. - The differences of complete cp genome se- quences of the 12 subg. - the complete cp genomes were. - First, the complete cp genomes of the 45 species were exam- ined by multiple sequence alignment in MAFFT using the PhyloSuite software [57, 58]. - pseudocerasus were outgroups in reconstruction of the BI phylogenetic tree. - “Empirical” was set of the basic frequency, and the strict molecular clock model was selected. - We estimated the divergence time of the 12 subg.. - Pollen morphology of the Maddenia clade of Prunus and its taxonomic and phylogenetic implications. - https://doi.org/10.1111/j x.. - https://doi.org/10.1007/s . - Conspect and chorology of the genera Amygdalus L. - https://doi.org/10.1016/j.. - https://doi.org/10.1007/. - https://doi.org/10.21273/JA SHS . - The complete chloroplast genome of the Amygdalus ferganensis (Rosaceae) in Xinjiang, China. - https://doi.org . - https://doi.. - https://doi.org/10.1016/S . - https://doi.org/10.1016/j.foodhyd . - https://doi.org/10.1016/j.cropro . - https://doi.org/10.1016/j.biocontrol . - The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. - https://doi.org/10.1 007/s . - Comparative analysis of the complete chloroplast genome among Prunus mume, P. - https://doi.org/10.1186/. - Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae). - doi.org/10.3390/molecules22020249.. - doi.org/10.1007/s y.. - Phylogenetic relationships of the Fern Cyrtomium falcatum (Dryopteridaceae) from Dokdo Island based on chloroplast genome sequencing. - https://doi.org/10.3390/. - Molecular phylogeny of the genus Amygdalus (Rosaceae) based on nrDNA ITS and cpDNA trnS-trnG sequences. - https://doi.org/10.1038/. - Polyphyly of the Padus group of Prunus (Rosaceae) and the evolution of biogeographic disjunctions between eastern Asia and eastern North America. - https://doi.org X-1-18.. - Characterization of the complete chloroplast genome of the Chinese cherry Prunus pseudocerasus (Rosaceae). - https://doi.org/10.1093/bioinformatics/bts199.. - https://doi.org/10.1093/nar/gkt289.. - https://doi.org/10.1093/molbev/mst010.. - https://doi.org/10.1093/bioinformatics/14.9.. - https://doi.org/10.1093/. - doi.org/10.1093/sysbio/syq010.. - https://doi.org/10.1093/ve/vey1016.. - https://doi.org/10.1093/molbev/msx116.. - https://doi.org/10.1016/j.ecolind . - https://doi.org/10.1073/pnas . - https://doi.org/10.1093/aob/mcv159.. - Expanded phylogenetic and dating analyses of the apples and their relatives (Pyreae, Rosaceae). - https://doi.org/10.1016/j.ympev
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