title: Plastome phylogeny and early diversification of Brassicaceae.
abstract: The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies.
  
  
  
  Bayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades. All four lineages were well identified and interrelationships between them were resolved. The previously defined Clade C was found to be paraphyletic (the genus Megadenia formed a separate lineage), while the remaining clades were monophyletic. Clade E (lineage III) was sister to clades B + C rather than to all core Brassicaceae (clades A + B + C or lineages I + II), as suggested by a previous transcriptome study. Molecular dating based on plastome phylogeny supported the origin of major lineages or clades between late Oligocene and early Miocene, and the following radiative diversification across the family took place within a short timescale. In addition, gene losses in the plastomes occurred multiple times during the evolutionary diversification of the family.
  
  
  
  Plastome phylogeny illustrates the early diversification of cruciferous species. This phylogeny will facilitate our further understanding of evolution and adaptation of numerous species in the model family Brassicaceae.
authors.affiliation: MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China.
authors.forename: Xinyi
authors.initials: X
authors.lastname: Guo
authors.affiliation: MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China. liujq@nwipb.cas.cn.
authors.forename: Jianquan
authors.identifier: 0000-0001-5416-7787
authors.initials: J
authors.lastname: Liu
authors.affiliation: MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China.|Biodiversity Institute of Mount Emei, Mount Emei Scenic Area Management Committee, 614200, Leshan, Sichuan, People's Republic of China.
authors.forename: Guoqian
authors.initials: G
authors.lastname: Hao
authors.affiliation: MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China.
authors.forename: Lei
authors.initials: L
authors.lastname: Zhang
authors.affiliation: MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China.
authors.forename: Kangshan
authors.initials: K
authors.lastname: Mao
authors.affiliation: MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China.
authors.forename: Xiaojuan
authors.initials: X
authors.lastname: Wang
authors.affiliation: MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China.
authors.forename: Dan
authors.initials: D
authors.lastname: Zhang
authors.affiliation: MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China.
authors.forename: Tao
authors.initials: T
authors.lastname: Ma
authors.affiliation: MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, 610065, Chengdu, People's Republic of China.
authors.forename: Quanjun
authors.initials: Q
authors.lastname: Hu
authors.affiliation: Missouri Botanical Garden, PO Box 299, St. Louis, MO, 63166-0299, USA.
authors.forename: Ihsan A
authors.initials: IA
authors.lastname: Al-Shehbaz
authors.affiliation: Department of Biodiversity and Plant Systematics, Im Neuenheimer Feld 345, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, 69120, Heidelberg, Germany.
authors.forename: Marcus A
authors.initials: MA
authors.lastname: Koch
mesh_terms: D001499:Bayes Theorem; D019607:Brassicaceae / Q000145:classification / Q000235:genetics*; D002736:Chloroplasts / Q000235:genetics*; D017343:Genes, Plant / Q000235:genetics; D054628:Genome, Chloroplast / Q000235:genetics*; D016013:Likelihood Functions; D010802:Phylogeny; D016415:Sequence Alignment
keywords: Brassicaceae; Gene loss; Molecular dating; Phylogenomics; Plastome