Characterization and comparative analysis of the complete chloroplast genome sequence from Prunus avium ‘Summit’

Abstract

BackgroundSweet cherry (Prunus avium) is one of the most popular of the temperate fruits. Previous studies have demonstrated that there were several haplotypes in the chloroplast genome of sweet cherry cultivars. However, none of chloroplast genome of a sweet cherry cultivar were yet released, and the phylogenetic relationships among Prunus based on chloroplast genome data were unclear.MethodsIn this study, we assembled and annotated the complete chloroplast genome of a sweet cherry cultivar P. avium ‘Summit’ from high-throughput sequencing data. Gene Ontology (GO) terms were assigned to classify the function of the annotated genes. Maximum likelihood (ML) trees were constructed to reveal the phylogenetic relationships within Prunus species, using LSC (large single-copy) regions, SSC (small single-copy) regions, IR (inverted repeats) regions, CDS (coding sequences), intergenic regions, and whole cp genome datasets, respectively.ResultsThe complete plastid genome was 157, 886 bp in length with a typical quadripartite structure of LSC (85,990 bp) and SSC (19,080 bp) regions, separated by a pair of IR regions (26,408 bp). It contained 131 genes, including 86 protein-coding genes, 37 transfer RNA genes and 8 ribosomal RNA genes. A total of 77 genes were assigned to three major GO categories, including molecular function, cellular component and biological process categories. Comparison with other Prunus species showed that P. avium ‘Summit’ was quite conserved in gene content and structure. The non-coding regions, ndhc-trnV, rps12-trnV and rpl32-trnL were the most variable sequences between wild Mazzard cherry and ‘Summit’ cherry. A total of 73 simple sequence repeats (SSRs) were identified in ‘Summit’ cherry and most of them were mononucleotide repeats. ML phylogenetic tree within Prunus species revealed four clades: Amygdalus, Cerasus, Padus, and Prunus. The SSC and IR trees were incongruent with results using other cp data partitions. These data provide valuable genetic resources for future research on sweet cherry and Prunus species.

Comparative analysis and phylogenetic investigation of Hong Kong Ilex chloroplast genomes

“…For this reason, the pseudogene ycf1Ψ was created and overlapped with ndhF. This phenomenon has also been found in other angiosperms, such as Salvia and Prunus 39,40 . Based on the variation of the IR expansion, we were able to divide the Ilex studied into four different groups.…”

Chloroplast Genome Evolution in Four Montane Zingiberaceae Taxa in China

“…Cautleya also possesses the longest LSC region among the included taxa, which suggests that large changes in the rps19 of Cautleya should be the result of LSC region expansion and repair. Previous studies have suggested that rps19 cannot be completely removed from the IRa region through the expansion of LSC or IR regions ( Raman and Park, 2015 ; Lu et al, 2016 ; Zhao X. et al, 2019 ; Androsiuk et al, 2020 ). Therefore, the complete loss of rps19 in Cautleya is more likely than the suppression of rps19 duplication by the LSC region expansion.…”

“…The loss of rps19 has also been observed in a few other dicot taxa (e.g., Morus , Nicotiana , Vitis , and Tetrastigma ) but is relatively rare in monocots ( Ravi et al, 2006 ; Li et al, 2015 ), which suggests that rps19 is more likely to be lost or pseudogenized in dicots. The changes in rps19 could be due to (1) partial gene duplication ( Lu et al, 2016 ; Zhao X. et al, 2019 ) or (2) the contraction and expansion of IR regions ( Zhao X. et al, 2019 ). It was suggested that there are two evolutionary mechanisms of the IR region boundary: the small amplitude amplification of the boundary gene and the recombination repair of the boundary of the LSC region.…”

Comparative chloroplast genomes of Prunus subgenus Cerasus (Rosaceae): insights into sequence variations and phylogenetic relationships

“…In particular, seven regions (trnG-GCC -trnR-UCU , trnR-UCU -atpA, psbZ-trnG-GCC , trnH-GUG -psbA, trnT-UGU -trnL-UAA , rpl32-trnL-UAG and trnM-CAU -atpE) showed an unusually high level of variation above 10% (Table 3). In addition, previous study has also showed that rpl32-trnL-UAG exhibited divergence between wild and cultivated sweet cherry (Zhao et al 2019a(Zhao et al , 2019b. Consequently, these regions might be further tested in the studies on population diversity.…”

“…We also downloaded 22 available cp genomes of Prunus, comprising P. avium (Zhao et al 2019a), P. campanulata, P. emarginata (Chen et al 2019a), P. cerasoides (Xu et al 2018), P. conradinae (Yan et al 2020), P. dictyoneura (Liu et al 2019), P. dielsiana (Zhao et al 2019b), P. discoidea (Li et al 2019), P. canescens (Chen et al 2019b), P. jamasakura (Yi et al 2020), P. matuurae (Sun and Liu. 2019), P. kumanoensis (Sun et al 2019a), P. maximowiczii, P. pensylvanica (Zhang et al 2019), P. pseudocerasus (Feng et al 2018), P. rufa (Li et al 2020b), P. serrulata, P. spachiana (Sheng et al 2020), P. speciosa (Sun et al 2019b), P. subhirtella, P. takesimensis (Cho et al 2018), and P. yedoensis (Cho et al 2015), then used for subsequent comparative analyses.…”