Phylogenomics With Hyb-Seq Unravels Korean Hosta Evolution

Abstract

The genus Hosta (Agavoideae and Asparagaceae) is one of the most popular landscaping and ornamental plants native to temperate East Asia. Their popularity has led to extensive hybridization to develop various cultivars. However, their long history of hybridization, cultivation, and selection has brought about taxonomic confusion in the Hosta species delimitation along with their indistinguishable morphology. Here, we conducted the first broad phylogenetic analyses of Hosta species based on the most comprehensive genomic data set to date. To do so, we captured 246 nuclear gene sequences and plastomes from 55 accessions of Korean Hosta species using the Hyb-Seq method. As a result, this study provides the following novel and significant findings: (1) phylogenetic analyses of the captured sequences retrieved six species of Hosta in South Korea compared to five to eleven species based on the previous studies, (2) their phylogenetic relationships suggested that the large genome size was ancestral and the diversification of Korean Hosta species was accompanied by decreases in genome sizes, (3) comparison between nuclear genes and plastome revealed several introgressive hybridization events between Hosta species, and (4) divergence times estimated here showed that Hosta diverged 35.59 million years ago, while Korean Hosta species rapidly diversified during the late Miocene. Last, we explored whether these genomic data could be used to infer the origin of cultivars. In summary, this study provides the most comprehensive genomic resources to be used in phylogenetic, population, and conservation studies of Hosta, as well as for unraveling the origin of many cultivars.

Plastome Characterization and Phylogenomic Analysis Yield New Insights into the Evolutionary Relationships among the Species of the Subgenus Bryocles (Hosta; Asparagaceae) in East Asia

“…The positive selection of functional genes during plastome evolution is related to adaptation to environmental changes such as temperature, drought, carbon dioxide concentration, photosynthetic rate, and ecological niche or coevolutionary processes [ 52 , 55 ]. Therefore, we suggest that the selection patterns detected among Hosta species could be associated with adaptation to climate change in East Asia, especially in Korea and Japan, during the Miocene when rapid diversification of Hosta species occurred [ 24 ].…”

“…Two recent phylogenomic studies provided additional insights into the phylogenetic relationships among species in Korea [ 23 , 24 ]. First, complete plastome sequences were assembled for representative Korean Hosta species [ 23 ].…”

“…However, it is necessary to interpret these results cautiously, given the limited sampling to address species relationships rigorously. A more recent and rigorous phylogenomic study was conducted based on 246 nuclear genes and whole plastome sequences using 55 accessions of Korean Hosta species, including numerous cultivars [ 24 ]. A few important findings of this study include (1) the trend of genome size reduction during the diversification of Hosta species in Korea, (2) cases of introgressive hybridization events between species (especially between H. jonesii and H. yingeri and very rarely between H. jonesii and H. minor ), and (3) rapid diversification of Korean Hosta species during the late Miocene [ 24 ].…”

“…A more recent and rigorous phylogenomic study was conducted based on 246 nuclear genes and whole plastome sequences using 55 accessions of Korean Hosta species, including numerous cultivars [ 24 ]. A few important findings of this study include (1) the trend of genome size reduction during the diversification of Hosta species in Korea, (2) cases of introgressive hybridization events between species (especially between H. jonesii and H. yingeri and very rarely between H. jonesii and H. minor ), and (3) rapid diversification of Korean Hosta species during the late Miocene [ 24 ]. Although this study detected introgressive hybridization between species and inferred species relationships based on nuclear and chloroplast genomes, it was limited to assess overall phylogenetic relationships among species in three sections ( Bryocles , Stoloniferae , and Lamellatae ) of subg.…”

“…Bryocles in East Asia. In particular, as pointed out in the study, phylogenetic relationships of two Japanese endemics, H. tsushimensis and H. tibae , relative to species in Korea, remain to be determined [ 24 ].…”