title: Species Delimitation and Interspecific Relationships of the GenusOrychophragmus(Brassicaceae) Inferred from Whole Chloroplast Genomes.
abstract: Genetic variations from few chloroplast DNA fragments show lower discriminatory power in the delimitation of closely related species and less resolution ability in discerning interspecific relationships than from nrITS. Here we useOrychophragmus(Brassicaceae) as a model system to test the hypothesis that the whole chloroplast genomes (plastomes), with accumulation of more variations despite the slow evolution, can overcome these weaknesses. We used Illumina sequencing technology via a reference-guided assembly to construct complete plastomes of 17 individuals from six putatively assumed species in the genus. All plastomes are highly conserved in genome structure, gene order, and orientation, and they are around 153 kb in length and contain 113 unique genes. However, nucleotide variations are quite substantial to support the delimitation of all sampled species and to resolve interspecific relationships with high statistical supports. As expected, the estimated divergences between major clades and species are lower than those estimated from nrITS probably due to the slow substitution rate of the plastomes. However, the plastome and nrITS phylogenies were contradictory in the placements of most species, thus suggesting that these species may have experienced complex non-bifurcating evolutions with incomplete lineage sorting and/or hybrid introgressions. Overall, our case study highlights the importance of using plastomes to examine species boundaries and establish an independent phylogeny to infer the speciation history of plants.
authors.affiliation: MOE Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University Chengdu, China.
authors.forename: Huan
authors.initials: H
authors.lastname: Hu
authors.affiliation: MOE Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University Chengdu, China.
authors.forename: Quanjun
authors.initials: Q
authors.lastname: Hu
authors.affiliation: Missouri Botanical Garden St. Louis, MO, USA.
authors.forename: Ihsan A
authors.initials: IA
authors.lastname: Al-Shehbaz
authors.affiliation: MOE Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University Chengdu, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Luo
authors.affiliation: MOE Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University Chengdu, China.
authors.forename: Tingting
authors.initials: T
authors.lastname: Zeng
authors.affiliation: MOE Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University Chengdu, China.
authors.forename: Xinyi
authors.initials: X
authors.lastname: Guo
authors.affiliation: MOE Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University Chengdu, China.
authors.forename: Jianquan
authors.initials: J
authors.lastname: Liu
keywords: Brassicaceae; Orychophragmus; chloroplast genome; phylogenetic relationship; species delimitation