The complete chloroplast genome of <i>Prunus clarofolia</i> (Rosaceae), a wild cherry endemic to China

Yan, Jiawen; Yu, Lin; Bai, Weiliang; Nie, Dongling; Xiong, Ying; Wu, Sizheng

doi:10.1080/23802359.2021.2016080

Cited by 1 publication

(4 citation statements)

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“…Microcerasus also showed a significant difference from other taxa (Table S7) (Yü et al, 1986;Webster and Looney, 1996), which were grouped with Amygdalus, Armeniaca, and Prunus as a subclade in this study (Figure 6). These relationships were also reported in previous studies (Chen et al, 2018;Zhang et al, 2021;Li et al, 2022). Microcerasus showed close evolutionary relationships to Amygdalus (P. tenella, P. pedunculata, and P. triloba) and Armeniaca (P. mume, P. mandshurica, and P. armeniaca) species.…”

Section: Evolutionary and Phylogenetic Analysissupporting

confidence: 89%

“…Therefore, although the IR regions are highly conserved for stabilizing the cp genome structure (Figure 2) (Marechal and Brisson, 2010), some changes (especially in rps19, ndhF, and ycf1) are evident at the IR border areas among Cerasus species, in line with reports for other species and genera. We annotated 115 unique genes in this study (Table 2), which is similar to the findings reported for other Prunus plastomes with 110-115 unique genes (Xue et al, 2019;Wang et al, 2021;Zhang et al, 2021;Li et al, 2022). There were four rRNA genes detected (4.5S rRNA, 5S rRNA, 16S rRNA, and 23S rRNA), which coincides with reports for land plants (Sugiura, 1992).…”

Section: Cerasus Cp Genome Features and Genomic Variationsupporting

confidence: 86%

“…In this study, the 11 Cerasus cp genomes presented a typical quadripartite structure (LSC, SSC, IRA, and IRB), as reported for other Prunus species (Xue et al, 2019;Zhang et al, 2021;Li et al, 2022) and land plants (Wicke et al, 2011;Zhang et al, 2017;Liu et al, 2020). The Cerasus cp genome size (157,571-158,830 bp) was similar to that of previously reported Prunus species such as P. pseudocerasus (157,834 bp), P. dielsiana (158,005 bp), P. clarofolia (157,899 bp), P. mira (158,153 bp), and P. salicina (157,916 bp) (Feng et al, 2018;Bao et al, 2019;Xue et al, 2019;Zhao et al, 2019;Li et al, 2022). This indicated that the length of the cp sequence is relatively conserved with only moderate variation among species of the Prunus genus.…”

Section: Cerasus Cp Genome Features and Genomic Variationsupporting

confidence: 82%

“…Because of its evolutionarily conserved structure, sequence length, and constituent genes, the cp genome has been widely used in analyses of genetic variation and phylogeny with moderate base replacement (Palmer, 1985;Ravi et al, 2007;Wicke et al, 2011). In this study, the 11 Cerasus cp genomes presented a typical quadripartite structure (LSC, SSC, IRA, and IRB), as reported for other Prunus species (Xue et al, 2019;Zhang et al, 2021;Li et al, 2022) and land plants (Wicke et al, 2011;Zhang et al, 2017;Liu et al, 2020). The Cerasus cp genome size (157,571-158,830 bp) was similar to that of previously reported Prunus species such as P. pseudocerasus (157,834 bp), P. dielsiana (158,005 bp), P. clarofolia (157,899 bp), P. mira (158,153 bp), and P. salicina (157,916 bp) (Feng et al, 2018;Bao et al, 2019;Xue et al, 2019;Zhao et al, 2019;Li et al, 2022).…”

Section: Cerasus Cp Genome Features and Genomic Variationsupporting

confidence: 63%

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Evolutionary and phylogenetic analyses of 11 Cerasus species based on the complete chloroplast genome

et al. 2023

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The subgenus Cerasus, one of the most important groups in the genus Prunus sensu lato, comprises over 100 species; however, the taxonomic classification and phylogenetic relationships of Cerasus remain controversial. Therefore, it is necessary to reconstruct the phylogenetic tree for known Cerasus species. Here, we report the chloroplast (cp) genome sequences of 11 Cerasus species to provide insight into evolution of the plastome. The cp genomes of the 11 Cerasus species (157,571–158,830 bp) displayed a typical quadripartite circular structure. The plastomes contain 115 unique genes, including 80 protein-coding genes, four ribosomal RNAs, and 31 transfer RNAs. Twenty genes were found to be duplicated in inverted repeats as well as at the boundary. The conserved non-coding sequences showed significant divergence compared with the coding regions. We found 12 genes and 14 intergenic regions with higher nucleotide diversity and more polymorphic sites, including matK, rps16, rbcL, rps16-trnQ, petN-psbM, and trnL-trnF. During cp plastome evolution, the codon profile has been strongly biased toward the use of A/T at the third base, and leucine and isoleucine codons appear the most frequently. We identified strong purifying selection on the rpoA, cemA, atpA, and petB genes; whereas ccsA, rps19, matK, rpoC2, ycf2 and ndhI showed a signature of possible positive selection during the course of Cerasus evolution. In addition, we further analyzed the phylogenetic relationships of these species with 57 other congenic related species.Through reconstructing the Cerasus phylogeny tree, we found that true cherry is similar to the flora of China forming a distinct group, from which P. mahaleb was separated as an independent subclade. Microcerasus was genetically closer to Amygdalus, Armeniaca, and Prunus (sensu stricto) than to members of true cherry, whereas P. japonica and P. tomentosa were most closely related to P. triloba and P. pedunculata. However, P. tianshanica formed a clade with P. cerasus, P. fruticosa, P. cerasus × P. canescens ‘Gisela 6’, and P. avium as a true cherry group. These results provide new insights into the plastome evolution of Cerasus, along with potential molecular markers and candidate DNA barcodes for further phylogenetic and phylogeographic analyses of Cerasus species.

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Section: Evolutionary and Phylogenetic Analysissupporting

confidence: 89%