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

Abstract

The genus Hosta, which has a native distribution in temperate East Asia and a number of species ranging from 23 to 40, represents a taxonomically important and ornamentally popular plant. Despite its taxonomic and horticultural importance, the genus Hosta has remained taxonomically challenging owing to insufficient diagnostic features, continuous morphological variation, and the process of hybridization and introgression, making species circumscription and phylogenetic inference difficult. In this study, we sequenced 11 accessions of Hosta plastomes, including members of three geographically defined subgenera, Hosta, Bryocles, and Giboshi, determined the characteristics of plastomes, and inferred their phylogenetic relationships. We found highly conserved plastomes among the three subgenera, identified several mutation hotspots that can be used as barcodes, and revealed the patterns of codon usage bias and RNA editing sites. Five positively selected plastome genes (rbcL, rpoB, rpoC2, rpl16, and rpl20) were identified. Phylogenetic analysis suggested (1) the earliest divergence of subg. Hosta, (2) non-monophyly of subg. Bryocles and its two sections (Lamellatae and Stoloniferae), (3) a sister relationship between H. sieboldiana (subg. Giboshi) and H. ventricosa (subg. Bryocles), and (4) reciprocally monophyletic and divergent lineages of H. capitata in Korea and Japan, requiring further studies of their taxonomic distinction.

Chloroplast Genomic Variation in Euonymus maackii Rupr. and Its Differentiation Time in Euonymus

“…In addition, it has relatively high genetic variation; therefore, it is often employed to infer the genetic relationships of species, estimate their differentiation time [12][13][14][15], and sometimes identify germplasm [16]. For example, Zeb et al compared the cp genomes of twenty-four Pinus species and identified a total of thirteen divergent hotspot regions.…”

Characterization of the Complete Chloroplast Genome Sequence of the Socotra Dragon`s Blood Tree (Dracaena cinnabari Balf.)

“…Chloroplast genome sequences are commonly used in various areas of biology, i.e., phylogenetics [37,38], DNA barcoding [39,40], taxonomy, evolution, and population genetics [41] of both angiosperms and gymnosperms. In the last five years, many genomic studies of various representatives of the genus Dracaena [25,26] and the family Asparagaceae [22,23,42,43] have also been published, but so far, none have included D. cinnabari. Taking into account the lack of genomic study on this iconic species, we decided to provide new and valuable omics data which enable the protection of its genetic resources as well as for further phylogenetic studies of the genus Dracaena.…”

“…We also found no major differences in the number of annotated genes in D. cinnabari and other Dracaena species. The complete chloroplast genome of D. cinnabari has a typical quadripartite structure, consisting of a pair of inverted repeats (IRs), separated by a large single-copy region (LSC) and a small single-copy region (SSC) that occurs in many other plant species [45][46][47], including those of the genus Dracaena [25,26] and the family Asparagaceae [23,24,42,43]. Our findings in this study regarding the organization of the D. cinnabari cp genome are very similar to those previously published for other members of the genus Dracaena [25,26].…”

Plastome-based backbone phylogeny of East Asian Phedimus (Subgenus Aizoon: Crassulaceae), with special emphasis on Korean endemics

“…The pairwise sequence divergence was calculated based on the Kimura 2-parameter method ( Kimura, 1980 ) using MEGA11 ( Tamura et al., 2021 ). According to earlier studies, we sequenced the entire plastome (e.g., Kim et al., 2019 ; Cho et al., 2020 ; Yang et al., 2021 ; Yun and Kim, 2022 ). An Illumina paired-end (PE) genomic library was constructed and sequenced using the Illumina HiSeq platform (Illumina, Inc., San Diego, CA, USA) at Macrogen Corporation (Seoul, Korea).…”

“…Therefore, as of today, we have very limited phylogenetic relationships among Phedimus species in East Asia, and phylogenomic analysis based on the complete plastome using broader sampling has never been conducted to gain insight into the origin of Korean endemic species. Plastome-based phylogenomic analysis has provided good resolutions and supports, demonstrating its importance in various plant groups (e.g., Xie et al., 2019 ; Cho et al., 2020 ; Xie et al., 2020 ; Yang et al., 2020 ; Yang et al., 2021 ). Since the plastome represents the evolutionary history of maternal lineages only, we employed nrDNA ITS sequences to complement the phylogenetic inferences from the plastome sequences.…”