Characterization of the plastid genome of Cratoxylum species (Hypericaceae) and new insights into phylogenetic relationships

Abstract

To expand the genomic information of Hypericaceae, particularly on Cratoxylum, we characterized seven novel complete plastid genomes (plastomes) of five Cratoxylum and two of its allied taxa, including C. arborescens, C. formosum subsp. formosum, C. formosum subsp. pruniflorum, C. maingayi, C. sumatranum, Hypericum hookerianum, and Triadenum breviflorum. For Cratoxylum, the plastomes ranged from 156,962 to 157,792 bp in length. Genomic structure and gene contents were observed in the five plastomes, and were comprised of 128–129 genes, which includes 83–84 protein-coding (CDS), 37 tRNA, and eight rRNA genes. The plastomes of H. hookerianum and T. breviflorum were 138,260 bp and 167,693 bp, respectively. A total of 110 and 127 genes included 72 and 82 CDS, 34 and 37 tRNA, as well as four and eight rRNA genes. The reconstruction of the phylogenetic trees using maximum likelihood (ML) and Bayesian inference (BI) trees based on the concatenated CDS and internal transcribed spacer (ITS) sequences that were analyzed separately have revealed the same topology structure at genus level; Cratoxylum is monophyletic. However, C. formosum subsp. pruniflorum was not clustered together with its origin, raising doubt that it should be treated as a distinct species, C. pruniflorum based on molecular evidence that was supported by morphological descriptions.

Complete Chloroplast Genome of Hypericum perforatum and Dynamic Evolution in Hypericum (Hypericaceae)

“…However, the chloroplast genome size displayed striking variations among the five Hypericum species. The genome size of T. breviflorum and Cratoxylum cochinchinense, the sister groups of Hypericum, were 167,693 bp and 157,103 bp, respectively [28,29]. These results indicate that the smaller genome size of Hypericum was contracted during the evolutionary process, according to the phylogenetic relationships of Hypericaceae.…”

The chloroplast genome sequences of Ipomoea alba and I. obscura (Convolvulaceae): genome comparison and phylogenetic analysis

“…When compared to the nuclear-based phylogenetic tree, the molecular placement of I. alba is congruent to that using the complete chloroplast genome sequence; I. alba is also strongly resolved as the species to diverge before I. hederacea , I. purpurea , and I. quamoclit when using the combined dataset of ITS and waxy sequences 14 , and is placed in the same group as I. hederacea , I. indica , I. nil , and I. purpurea , being the first to diverge among the five species under ser. Quamoclit, based on the phylogenetic tree reconstructed using 605 putative single-copy nuclear regions 64 . However, as the clade represented by I. biflora , I. tiliifolia , and I. obscura should contain some other species derived from Argyreiinae 21 , based on the limited sampling size used in this study, we can only verify that I. obscura is grouped with I. tiliifolia when analysed using the ITS sequences based on the finding by Ref.…”

A New Source and Large Quantity of Resveratrol in Cratoxylum Species and Their Activities on Normal Human and Cancer Cells

“…Blume; C. formosum (Jack) Dyer, ssp formosum ; C. formosum (Jack) Dyer, ssp pruniflorum ; C. maingayi Dyer and C. sumatranum ssp. neriifolium Kurz [ 1 , 2 ]. Accordingly, Juanda et al [ 3 ] reported that the Cratoxylum genus includes six accepted species distributed in Southeast Asia.…”