Analysis of the Complete Plastomes of 31 Species of Hoya Group: Insights Into Their Comparative Genomics and Phylogenetic Relationships

Abstract

<i>Hoya</i> is a genus in Apocynaceae-Asclepiadoideae, known for its showy wax flowers, making it a popular ornamental plant. However, phylogenetic relationships among most <i>Hoya</i> species are not yet fully resolved. In this study, we sequenced 31 plastomes of <i>Hoya</i> group species using genome skimming data and carried out multiple analyses to understand genome variation to resolve the phylogenetic positions of some newly sequenced Chinese endemic species. We also screened possible hotspots, <i>trnT-trnL-trnF, psba-trnH</i>, and <i>trnG-UCC</i>, <i>ndhF</i>, <i>ycf1, matK, rps16</i>, and <i>accD</i> genes that could be used as molecular markers for DNA barcoding and species identification. Using maximum likelihood (ML) and Bayesian Inference (BI), a species phylogeny was constructed. The newly assembled plastomes genomes showed the quasi-tripartite structure characteristic for <i>Hoya</i> and <i>Dischidia</i> with a reduced small single copy (SSC) and extremely enlarged inverted repeats (IR). The lengths ranged from 175,404 bp in <i>Hoya lacunosa</i> to 179,069 bp in <i>H. ariadna</i>. The large single copy (LSC) regions ranged from 80,795 bp (<i>Hoya liangii</i>) to 92,072 bp (<i>Hoya_</i>sp2<i>_</i>ZCF6006). The massively expanded IR regions were relatively conserved in length, with the small single-copy region reduced to a single gene, <i>ndhF</i>. We identified 235 long dispersed repeats (LDRs) and ten highly divergent hotspots in the 31 <i>Hoya</i> plastomes, which can be used as DNA barcodes for species identification. The phylogeny supports <i>Clemensiella</i> as a distinct genus. <i>Hoya ignorata</i> is resolved as a relative to Clade VI species. This study discloses the advantages of using Plastome genome data to study phylogenetic relationships.