Exploring the History of Chloroplast Capture in Arabis Using Whole Chloroplast Genome Sequencing

Abstract

Chloroplast capture occurs when the chloroplast of one plant species is introgressed into another plant species. The phylogenies of nuclear and chloroplast markers from East Asian Arabis species are incongruent, which indicates hybrid origin and shows chloroplast capture. In the present study, the complete chloroplast genomes of A. hirsuta, A. nipponica, and A. flagellosa were sequenced in order to analyze their divergence and their relationships. The chloroplast genomes of A. nipponica and A. flagellosa were similar, which indicates chloroplast replacement. If hybridization causing chloroplast capture occurred once, divergence between recipient species would be lower than between donor species. However, the chloroplast genomes of species with possible hybrid origins, A. nipponica and A. stelleri, differ at similar levels to possible maternal donor species A. flagellosa, which suggests that multiple hybridization events have occurred in their respective histories. The mitochondrial genomes exhibited similar patterns, while A. nipponica and A. flagellosa were more similar to each other than to A. hirsuta. This suggests that the two organellar genomes were co-transferred during the hybridization history of the East Asian Arabis species.

Characteristics of the Completed Chloroplast Genome Sequence of Xanthium Spinosum: Comparative Analyses, Identification of Mutational Hotspots and Phylogenetic Implications

“…An earlier study reported that the variation in number and variety of repeats play a major role in the plastome organization, but we could not found any correlation between these large repeat regions and rearrangement endpoints [29]. Microsatellite repeats are predominantly present in the chloroplast genome, which displays a high level of polymorphism and used as a genetic marker in genetic investigations [30,31]. A total of 701 and 705 simple sequence repeats (SSR) were discovered in the X. spinosum and X. sibiricum cp genomes, respectively.…”

Phylogenetic lineages and the role of hybridization as driving force of evolution in grass supertribe Poodae

“…7). The examples of discordant grouping are best explained by ancient processes of hybridization or introgression resulting in "chloroplast capture", which means establishment of a new combination of nuclear and plastid genomes encountered in many groups of angio-and gymnosperms (Rieseberg & Soltis, 1991;Seehausen, 2004;Kawabe & al., 2018). It was recently discussed also as significant process in the origin of major phylogenetic lineages (Sun & al., 2015;García & al., 2017).…”

Two-Step Contractions of Inverted Repeat Region and <em>Psa</em>i Gene Duplication from the Plastome of <em>Croton Tiglium</em> (Euphorbiaceae)

“…The presence of dispersed repeat sequences in plant DNA has been widely used in comparative analysis between inter-or infra-specific species [34][35][36][37][38][39][40][41]. To identify dispersed large repeats, which are at least 26 bp long and with similarity of 100%, the REPuter program [42] and the find repeats of Geneious were used.…”