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

Abstract

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.

Insights into the phylogenetic relationships and species boundaries of the Myricaria squamosa complex (Tamaricaceae) based on the complete chloroplast genome

“…6 ; Yang et al, 2023 ). Significant IR contractions of rps 19 and ycf 1 were observed, which were predicted as the main contributors to the overall variation observed among Myricaria chloroplast genomes, in line with reports for species in other genera, including Cerasus , Prunus and Rubus ( Yu et al, 2022 ; Wan et al, 2023 ). The comparative analysis and P i values test ( Figs.…”

“…A total of 114–115 unique genes were annotated in this study ( Tables 1 and S1 ), including four rRNA genes, 30 tRNA genes, and 80–81 CDSs, similar to previous reports ( Liu et al, 2020b ). There were some differences in the genes annotated in this study compared to previous studies, mainly reflected in CDSs, such as ycf genes ( Wan et al, 2023 ); specifically, the ycf 15 gene was detected in 32 Myricaria samples, but absent in three individuals (codes 7301, 3010 and 2912; Table S1 ). The discrepancy in the number of PCGs in the publicly-available Myricaria plastomes may be attributed to a different annotation strategy.…”

Complete plastid genome structure of thirteen Asian Justicia (Acanthaceae) species: comparative genomics and phylogenetic analyses

“…The codon usage bias of 20 amino acids among different species is similar (Fig. 2, Table S5), which is congruent with other angiosperms [67,90]. It is revealed that most protein-coding genes are generally identical, but accD, matK, ndhI, rpl22, rpl20, rpoA, rps16, rps18, ycf1 and ycf2 in J. grossa are obviously different from that in other Justicia plants in length and base variation (Table S3), suggesting J. grossa is different from other Justicia plants in plastid genes.…”

Complete chloroplast genome sequences of the ornamental plant Prunus Cistena and comparative and phylogenetic analyses with its closely related species

“…There were some related studies exposed ycf1 as a paramount pseudogene in plants, leading to incomplete duplication of the gene within IRs [31,36]. The ycf1 gene repeated twice in the chloroplast genome of P. Cistena, which was similar to other Prunus plants [22,37]. It has been testi ed that the introns play a signi cant role in regulating the expression of genes, which might control the gene expression level in different spatiotemporal [19,31,38].…”