@Article{phyton.2024.051559,
AUTHOR = {Riwa Mahai, Rongpeng Liu, Xiaolang Du, Zejing Mu, Xiaoyun Wang, Jun Yuan},
TITLE = {Comparative and Phylogenetic Analysis of the Complete Chloroplast Genomes of 19 Species in Rosaceae Family},
JOURNAL = {Phyton-International Journal of Experimental Botany},
VOLUME = {93},
YEAR = {2024},
NUMBER = {6},
PAGES = {1203--1219},
URL = {http://www.techscience.com/phyton/v93n6/57206},
ISSN = {1851-5657},
ABSTRACT = {Rosaceae represents a vast and complex group of species, with its classification being intricate and contentious. The taxonomic placement of many species within this family has been a subject of ongoing debate. The study utilized the Illumina platform to sequence 19 plant species from 10 genera in the Rosaceae. The cp genomes, varying in size from 153,366 to 159,895 bp, followed the typical quadripartite organization consisting of a large single-copy (LSC) region (84,545 to 87,883 bp), a small single-copy (SSC) region (18,174 to 19,259 bp), and a pair of inverted repeat (IR) regions (25,310 to 26,396 bp). These genomes contained 132–138 annotated genes, including 87 to 93 protein-coding genes (PCGs), 37 tRNA genes, and 8 rRNA genes using MISA software, 52 to 121 simple sequence repeat (SSR) loci were identified. <i>D. arbuscular</i> contained the least of SSRs and did not have hexanotides, <i>A. lineata</i> contained the richest SSRs. Long terminal repeats (LTRs) were primarily composed of palindromic and forward repeat sequences, meanwhile, The richest LTRs were found in <i>Argentina lineata</i>. Except for <i>Argentina</i> lineata, <i>Fragariastrum eriocarpum</i>, and <i>Prunus trichostoma</i>, which varied in gene type and position on both sides of the boundary, the remaining species were found to be mostly conserved according to IR boundary analysis. The examination of the Ka/Ks ratio revealed that only the infA gene had a value greater than 1, indicating that this gene was primarily subjected to positive selection during evolution. Additionally, 9 hotspots of variation were identified in the LSC and SSC regions. Phylogenetic analysis confirmed the scientific validity of the genus Prunus L. <i>sensu</i> lato (s.l.) within the Rosaceae family. The separation of the three genera <i>Argentina</i> Hill, <i>Fragariastrum</i> Heist. ex Fabr. and <i>Dasiphora</i> Raf. from <i>Potentilla</i> L. may be a more scientific classification. These results offer fresh perspectives on the taxonomy of the Rosaceae.},
DOI = {10.32604/phyton.2024.051559}
}