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

Consolata Nanjala,Elijah Mbandi Mkala,Qing-Feng Wang,Vincent Okelo Wanga,Cai-Fei Zhang,Emmanuel Nyongesa Waswa,Millicent Akinyi Oulo,Elizabeth Syowai Mutinda,Yan Wang,Wyclif Ochieng Odago,Guang-Wan Hu

doi:10.3389/fpls.2021.814833

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.

Highlights

Hoya is the second largest genus in Apocynaceae-Asclepiadoideae with at least 300 species, after Ceropegia L. (Bruyns et al, 2017)
173.84 GB of paired-end quality reads were obtained from Illumina sequencing for the 31 Hoya group species from China (Table 1)
All plastomes showed the quasitripartite structure characteristic for Dischidia and Hoya with a strongly reduced small single copy (SSC) and significantly enlarged inverted repeats (IR) regions (Figures 1A,B). Their lengths varied in sizes ranging from 175,404 bp in Hoya lacunosa to 179,069 bp in H. ariadna, mainly because of length variation in large single copy (LSC) (80,795 bp in H. liangii to 92,072 bp in Hoya sp2 ZCF6006)

Summary

Introduction

Hoya is the second largest genus in Apocynaceae-Asclepiadoideae with at least 300 species, after Ceropegia L. (ca. 357 species) (Bruyns et al, 2017). Analysis of Hoya Plastomes margins, pollinia with pellucid margins, and elongated, slender, and fusiform seeds with hairs attached at their terminal part (Omlor, 1998). Due to their showy flowers, ease of growing, and popularity as ornamental plants, they have been grown in botanical gardens around the world. Dischidia is a genus closely related to the genus Hoya found in South East Asia. It consists of approximately 80 species (Livshultz et al, 2005). Some species have oil-rich structures in the seeds that are attractive to ants and may facilitate seed dispersal (Rintz, 1980)

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