Comparative Chloroplast Genome Analyses of the Winter-Blooming Eastern Asian Endemic Genus Chimonanthus (Calycanthaceae) With Implications For Its Phylogeny and Diversification

• Published in: Frontiers in genetics 2021-11, Vol.12, p.709996-709996
• Main Authors: Jamal, Abbas, Wen, Jun, Ma, Zhi-Yao, Ahmed, Ibrar, Abdullah, Chen, Long-Qing, Nie, Ze-Long, Liu, Xiu-Qun
• Format: Article
• Language: English
• Subjects: chloroplast genomics; correlations; divergence time; Genetics; incipient radiation; phylogeny; subtropical forest biome assembly
• ISSN: 1664-8021; 1664-8021
• DOI: 10.3389/fgene.2021.709996

of Calycanthaceae is a small endemic genus in China, with unusual winter-blooming sweet flowers widely cultivated for ornamentals and medicinal uses. The evolution of plastomes and its phylogenetic relationships remain unresolved due to limited availability of genetic resources. Here, we report fully assembled and annotated chloroplast genomes of five species. The chloroplast genomes of the genus (size range 153,010 - 153,299 bp) reveal high similarities in gene content, gene order, GC content, codon usage, amino acid frequency, simple sequence repeats, oligonucleotide repeats, synonymous and non-synonymous substitutions, and transition and transversion substitutions. Signatures of positive selection are detected in and genes in . The correlations among substitutions, InDels, and oligonucleotide repeats reveal weak to strong correlations in distantly related species at the intergeneric levels, and very weak to weak correlations among closely related species. Chloroplast genomes are used to reconstruct a well-resolved phylogenetic tree, which supports the monophyly of . Within , and form one clade, while , , , and constitute another clade. appears paraphyletic and is closely related to and , suggesting the need to reevaluate the species delimitation of . and diverged in mid-Oligocene; the radiation of extant species was dated to the mid-Miocene, while diverged from other species in the late Miocene. , , and are inferred to have diverged in the Pleistocene of the Quaternary period, suggesting recent speciation of a relict lineage in the subtropical forest regions in eastern China. This study provides important insights into the chloroplast genome features and evolutionary history of and family Calycanthaceae.