AUTHOR=Guan Bicai , Wen Jianteng , Guo Hanjing , Liu Yizhen 

TITLE=Comparative and phylogenetic analyses based on the complete chloroplast genome of Cornus subg. Syncarpea (Cornaceae) species

JOURNAL=Frontiers in Plant Science

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1306196

DOI=10.3389/fpls.2024.1306196

ISSN=1664-462X

ABSTRACT=<p>This study presents a comprehensive analysis of the chloroplast (cp) genomes of <italic>Cornus</italic> species, including comparative and phylogenetic evaluations, as well as examinations of their genomic structure and composition. The cp genomes exhibit a typical circular quadripartite structure and demonstrate highly similar gene order and genomic structure. The complete cp genome size of the 10 taxa in this study is 156,965 bp to 157,383 bp, where the length of the large single-copy (LSC) region is 86,296 bp to 86,691 bp, small single-copy (SSC) region is 18,386 bp to 18,454 bp, and inverted repeat (IR) region is 23,143 bp to 26,112 bp. A total of 131 genes were found, including 86 protein-coding genes (PCGs), eight rRNA genes, and 37 tRNA genes. The mean GC content of the 10 taxa is 38.145%, where the LSC region is 36.396%, the SSC region is 32.372%, and the IR region is 43.076%. Despite the relatively conserved nature of the cp genome within the species of <italic>Cornus</italic>, 25–31 simple sequence repeats (SSRs) were identified in the 10 taxa in our study. The SSRs were found to be distributed in the LSC, SSC, and IR regions in <italic>Cornus hongkongensis</italic> subsp. <italic>hongkongensis</italic>, <italic>C. hongkongensis</italic> subsp. <italic>elegans</italic>, <italic>C. hongkongensis</italic> subsp. <italic>gigantea</italic>, and <italic>C. hongkongensis</italic> subsp. <italic>tonkinensis</italic>, while the SSR was not found in the IR region of the other six taxa. Thus, whole cp genomics is a valuable tool for species identification, taxonomic clarification, and genomic evolutionary analysis. Furthermore, our findings reveal that <italic>C. hongkongensis</italic> and <italic>C. hongkongensis</italic> subsp. <italic>gigantea</italic>, along with <italic>Cornus kousa</italic> and <italic>Cornus elliptica</italic>, form sister groups. Notably, <italic>C. hongkongensis</italic> subsp. <italic>ferruginea</italic> and <italic>C. hongkongensis</italic> subsp. <italic>melanotricha</italic> did not exhibit affinity with <italic>C. hongkongensis</italic> subsp. <italic>hongkongensis</italic>. Our study furnishes essential data for further research on their classification and provides novel insights into the relationship within <italic>Cornus</italic> subg. <italic>Syncarpea</italic>.</p>