Plastome evolution and organisation in the Hoya group (Apocynaceae)

Abstract

The genus Hoya is highly diverse and many of its species are popular ornamental plants. However, the relationships between Hoya and related genera (the Hoya group) are not fully resolved. In this study, we report 20 newly sequenced plastomes of species in the Hoya group. The complete plastomes vary in length from 175,405 to 178,525 bp while the LSCs vary from 90,248 to 92,364 bp and the complete SSCs vary from 2,285 to 2,304 bp, making the SSC in the Hoya group one of the shortest known in the angiosperms. The plastome structure in the Hoya group is characterised by a massive increase in the size of the inverted repeats as compared to the outgroups. In all ingroup species, the IR/SSC boundary moved from ycf1 to ndhF while this was not observed in outgroup taxa, making it a synapomorphy for the Hoya group. We have also assembled the mitogenome of Hoya lithophytica, which, at 718,734 bp, is the longest reported in the family. The phylogenetic analysis using exons from 42 taxa in the Hoya group and three outgoups confirms that the earliest divergent genus in the Hoya group is Papuahoya, followed by Dischidia. The relationship between Dischidia and the clade which includes all Hoya and Oreosparte taxa, is not fully supported. Oreosparte is nested in Hoya making it paraphyletic unless Clemensiella is recognised as a separate genus.

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

“…Our plastome matrix of 72 protein-coding genes and 57 species based on ML and Bayesian analyses (Figure 5) represented the most extensive sampling of the protein-coding genes to date and was mainly in congruence with the previous results (Wanntorp et al, 2006(Wanntorp et al, , 2014Rodda et al, 2020a;Rodda and Niissalo, 2021).…”

“…We sequenced complete plastomes of 31 species of the Wei et al (2020), and Rodda and Niissalo (2021). We aim to compare and characterize the cp genomes among selected species of Hoya, identify and select molecular markers suitable for population genetics, reconstruct the species relationships of the six extant clades of the Hoya group.…”

“…Most interclade relationships remained ambiguous even in the study by Rodda et al (2020a) with more samples. Using first phylogenomic data from complete plastomes ( Rodda and Niissalo, 2021 ) further resolved the interclade and some intra-clade relationships and re-defined Hoya s.str. as comprising only Clade III–VI ( Rodda and Niissalo, 2021 ).…”

“…Using first phylogenomic data from complete plastomes ( Rodda and Niissalo, 2021 ) further resolved the interclade and some intra-clade relationships and re-defined Hoya s.str. as comprising only Clade III–VI ( Rodda and Niissalo, 2021 ). Phylogenetic analyses of 42 Hoya plastomes using exons larger than 90 bp erected a new clade Y, which was not captured by Rodda et al (2020b) demonstrating that any new data may return further insights.…”

“…The first sequenced complete plastomes of Hoya were as follows: Hoya carnosa ( H. carnosa ) reported by Wei et al (2020) , Hoya liangii ( H. liangii ) and Hoya pottsii ( H. pottsii ) reported by Tan et al (2018) . Additionally, Rodda and Niissalo (2021) reported 20 newly sequenced plastomes of species in the Hoya group. While plastomes usually contain ≈110–130 protein-coding genes, ≈30 transfer RNAs (tRNAs) genes, and ≈4 ribosomal RNAs (rRNA) ( Guisinger et al, 2010 ) organized in the LSC and small single copy (SSC), separated by the IR regions (including all rRNA gene), the Hoya plastomes have lost almost the entire SSC region due to the expansion of the two inverted repeats (IRs) ( Wei et al, 2020 ; Rodda and Niissalo, 2021 ).…”