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

Abstract

Hoya is a genus in Apocynaceae-Asclepiadoideae, known for its showy wax flowers, making it a popular ornamental plant. However, phylogenetic relationships among most Hoya species are not yet fully resolved. In this study, we sequenced 31 plastomes of Hoya 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, trnT-trnL-trnF, psba-trnH, and trnG-UCC, ndhF, ycf1, matK, rps16, and accD 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 Hoya and Dischidia with a reduced small single copy (SSC) and extremely enlarged inverted repeats (IR). The lengths ranged from 175,404 bp in Hoya lacunosa to 179,069 bp in H. ariadna. The large single copy (LSC) regions ranged from 80,795 bp (Hoya liangii) to 92,072 bp (Hoya_sp2_ZCF6006). The massively expanded IR regions were relatively conserved in length, with the small single-copy region reduced to a single gene, ndhF. We identified 235 long dispersed repeats (LDRs) and ten highly divergent hotspots in the 31 Hoya plastomes, which can be used as DNA barcodes for species identification. The phylogeny supports Clemensiella as a distinct genus. Hoya ignorata is resolved as a relative to Clade VI species. This study discloses the advantages of using Plastome genome data to study phylogenetic relationships.

Thirteen complete chloroplast genomes of the costaceae family: insights into genome structure, selective pressure and phylogenetic relationships

“…1 ). They shared similar GC content, protein-coding genes, rRNAs and most of the tRNAs, which also had been found in other flowering plants [ 24 – 26 , 28 – 35 ]. Although these 13 genomes were highly conserved, intron loss, gene duplication and gene loss appeared in this study, for instance, trnG-UCC had no intron in the genome of C. beckii , while the rest 12 genomes contained one intron in this tRNA gene, suggesting that intron loss had occurred during the evolutionary history of C. beckii .…”

“…The ratio (ω = dN/dS) has been widely used for measuring selective pressure [ 30 – 31 , 33 – 35 ]. The ω ratio > 1 represents positive selection, while ω < 1 represents purifying selection [ 31 , 32 ].…”

Structural Characterization of the Acer ukurunduense Chloroplast Genome Relative to Related Species in the Acer Genus

“…The phylogenetic analysis based on sequencing data from different molecular markers ndhF/rpl32 and rpl32/trnL-UAG is also separate in the families Aristidoideae and Eragrostideae, and in the genuses Fagopyrum and Dolomiaea , respectively ( Shen et al, 2020 ; Fan et al, 2021 ; Kuan Liu et al, 2021 ; Guo et al, 2022 ). The ycf1 has been employed to assist in inferring the evolution of Pinus , Hoya , and Curcuma ( Liang et al, 2020 ; Odago et al, 2021 ; Zeb et al, 2022 ). Those highly variable regions can be crucial molecular markers for closely related plants and contribute to generally phylogenetic relationship analysis research in the Acer genus.…”

Genome Skimming with Nanopore Sequencing Precisely Determines Global and Transposon DNA Methylation in Vertebrates

“…Genome skimming has been used for diverse purposes including plastid genome assembly, parasite identification, evolutionary biology in extinct species, and is gaining software tools for phylogenetic analyses. 3,[19][20][21][22] Classical genome skimming focuses on mitochondrial genome recovery for species or individual identification but does not typically utilize the nuclear portion of the skimmed reads or their DNA methylation. There are only five reports of nanopore sequencing used for genome skimming in animals at the time of publication, none of which examine the epigenome.…”