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.
Highlights
The genus Arabis includes about 70 species that are distributed throughout the northern hemisphere
The complete chloroplast genomes of the Arabis species had total lengths of 152,866–153,758 base pairs, which included 82,338 to 82,811 base pair long single copy (LSC) regions and 17,938 to 18,156 base pair short single copy (SSC) regions, which were separated by a pair of 26,421 to 26,933 base pair inverted repeat (IR) regions
The rps16 gene became a pseudogene in A. flagellosa, A. hirsuta, and A. nipponica strain Midori, which was previously reported as a related species [23]
Summary
The genus Arabis includes about 70 species that are distributed throughout the northern hemisphere. The genus previously included many more species, but a large number of these were reclassified into other genera, including Arabidopsis, Turritis, and Boechera, Crucihimalaya, Scapiarabis, and Sinoarabis [1,2,3,4,5,6] Because of their highly variable morphology and life histories, Arabis species have been used for ecological and evolutionary studies of morphologic and phenotypic traits [7,8,9,10,11]. The evolutionary history and hybridization processes of A. nipponica and other East Asian Arabis species still need to be clarified Because these conclusions for incongruence between nuclear and chloroplast phylogenies came from analyzing a small number of short sequences, hybridized species, the divergence level, and the classification of species are somewhat ambiguous. The whole chloroplast genome sequences provide a basis for future marker development
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