title: A Phylogenetic Analysis of Chloroplast Genomes Elucidates the Relationships of the Six Economically ImportantBrassicaSpecies Comprising the Triangle of U.
abstract: TheBrassicagenus comprises many economically important worldwide cultivated crops. The well-established model of theBrassicagenus, U's triangle, consists of three basic diploid plant species (Brassica rapa,Brassica oleracea, andBrassica nigra) and three amphidiploid species (Brassica napus,Brassica juncea, andBrassica carinata) that arose through interspecific hybridizations. Despite being extensively studied because of its commercial relevance, several aspects of the origin of theBrassicaspecies and the relationships within and among these six species still remain open questions. Here, we successfullyde novoassembled 60 complete chloroplast genomes ofBrassicagenotypes of all six species. A complete map of the single nucleotide variants and insertions and deletions in the chloroplast genomes of differentBrassicaspecies was produced. The chloroplast genome consists of a Large and a Small Single Copy (LSC and SSC) region between two inverted repeats, and while these regions of chloroplast genomes have very different molecular evolutionary rates, phylogenetic analyses of different regions yielded no contradicting topologies and separated theBrassicagenus into four clades.B. carinataandB. junceashare their chloroplast genome with one of their hybridization donorsB. nigraandB. rapa, respectively, which fits the U model.B. rapa, surprisingly, shows evidence of two types of chloroplast genomes, with one type specific to some Italian broccoletto accessions.B. napusclearly has evidence for two independent hybridization events, as it contains eitherB. rapachloroplast genomes. The divergence estimation suggests thatB. nigraandB. carinatadiverged from the mainBrassicaclade 13.7 million years ago (Mya), whileB. rapaandB. oleraceadiverged at 2.18 Mya. The use of the complete chloroplast DNA sequence not only provides insights into comparative genome analysis but also paves the way for a better understanding of the phylogenetic relationships within theBrassicagenus.
authors.affiliation: Chinese Cabbage Department, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China; Plant Breeding, Wageningen University and ResearchWageningen, Netherlands.
authors.forename: Peirong
authors.initials: P
authors.lastname: Li
authors.affiliation: Chinese Cabbage Department, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences Beijing, China.
authors.forename: Shujiang
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Chinese Cabbage Department, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences Beijing, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Li
authors.affiliation: Chinese Cabbage Department, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences Beijing, China.
authors.forename: Shifan
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Chinese Cabbage Department, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences Beijing, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Chinese Cabbage Department, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences Beijing, China.
authors.forename: Xiaowu
authors.initials: X
authors.lastname: Wang
authors.affiliation: Chinese Cabbage Department, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences Beijing, China.
authors.forename: Rifei
authors.initials: R
authors.lastname: Sun
authors.affiliation: Plant Breeding, Wageningen University and Research Wageningen, Netherlands.
authors.forename: Guusje
authors.initials: G
authors.lastname: Bonnema
authors.affiliation: Plant Breeding, Wageningen University and Research Wageningen, Netherlands.
authors.forename: Theo J A
authors.initials: TJ
authors.lastname: Borm
keywords: Brassica; assembly; chloroplast genome; divergence; phylogeny; variation