Abstract
The tribe Aethionemeae is sister to all other crucifers, making it a crucial group for unraveling genome evolution and phylogenetic relationships within the crown group Brassicaceae. In this study, we extend the analysis of Brassicaceae genomic blocks (GBs) to Aethionema whereby we identified unique block boundaries shared only with the tribe Arabideae. This was achieved using bioinformatic methods to analyze synteny between the recently updated genome sequence of Aethionema arabicum and other high-quality Brassicaceae genome sequences. We show that compared to the largely conserved genomic structure of most non-polyploid Brassicaceae lineages, GBs are highly rearranged in Aethionema. Furthermore, we detected similarities between the genomes of Aethionema and Arabis alpina, in which also a high number of genomic rearrangements compared to those of other Brassicaceae was found. These similarities suggest that tribe Arabideae, a clade showing conflicting phylogenetic position between studies, may have diverged before diversification of the other major lineages, and highlight the potential of synteny information for phylogenetic inference.
Highlights
The Brassicaceae is an economically important plant family, containing the Brassica crops, rapeseed and several ornamental taxa (e.g., Aubrieta, Iberis)
We present the syntenic blocks in the genome of Ae. arabicum and explore open questions concerning genome evolution and phylogenetics in Brassicaceae: Given the early divergence of Aethionema and its position as the species-poor sister group, is its genomic structure similar to the ACK and the largely conserved genomic structure of crown group Brassicaceae? Are the same breakpoints observed between Aethionema, Arabis and CEK genomes, and can synteny be used to obtain evidence for the phylogenetic position of early diverging lineages? We show that compared to the ACK, the syntenic blocks in the genome of Aethionema are broken into a high number of sub-blocks across its linkage groups
Our analysis revealed 13,719 syntenic genes between Aethionema and A. thaliana that are in syntenic blocks
Summary
The Brassicaceae is an economically important plant family, containing the Brassica crops, rapeseed and several ornamental taxa (e.g., Aubrieta, Iberis). The Brassicaceae family diverged from its sister-family, the Cleomaceae, ∼43 mya (million years ago) (Schranz and Mitchell-Olds, 2006; Edger et al, 2018). Divergence of tribe Aethionemeae, sister lineage to all other Brassicaceae, with its single genus Aethionema occurred ∼32 mya (Hohmann et al, 2015). The crown-group includes ∼3,900 species in 350 genera, grouped into 51 monophyletic tribes (BrassiBase; Koch et al, 2018). These tribes are further grouped into either three or five major lineages, termed I–III or A–E (Koch and Al-Shehbaz, 2009; Franzke et al, 2011; Huang et al, 2016; Nikolov et al, 2019)
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