Plastome phylogeny and early diversification of Brassicaceae

Xinyi Guo,Ihsan A Al-Shehbaz,Quanjun Hu,Guoqian Hao,Xiaojuan Wang,Kangshan Mao,Lei Zhang,Dan Zhang,Tao Ma,Jianquan Liu,Marcus A Koch

doi:10.1186/s12864-017-3555-3

Xinyi Guo, Ihsan A Al-Shehbaz + Show 9 more

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https://doi.org/10.1186/s12864-017-3555-3

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Abstract

BackgroundThe 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.ResultsBayesian 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.ConclusionsPlastome 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.

Highlights

The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance
We aimed to examine whether the plastome dataset could: (1) significantly support the previously shown deep splits; (2) resolve the disputed interrelationships between lineages or clades; and (3) reveal any previously overlooked structural evolution within Brassicaceae plastomes
Basic characteristics of Brassicaceae chloroplast genomes The average length of the plastomes from 53 species of Brassicales (Additional file 1: Table S1) is 154 kb, ranging from 152,659 bp in Lobularia maritima to 160,100 bp in Carica papaya (Additional file 1: Table S2)

Summary

Introduction

The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Diversifications and phylogenetic relationships between major lineages or clades remain unclear. 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. DNAs or ITS, identified four major lineages, with the basal lineage (tribe Aethionemeae) sister to the remaining three lineages (I, II, and III, i.e., core Brassicaceae) [2,3,4,5, 11,12,13,14,15,16]. The clade E (lineage III) was sister to the remaining core Brassicaceae species (clades A + B + C or lineages I + II), but the relationship within the core were unsolved in the previous study [5]. Phylogenetic conflicts between different datasets, especially between nuclear and cytoplasmic genomes in plants, were found [18, 19], possibly suggesting complex evolutionary history

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