Genomic Blocks in Aethionema arabicum Support Arabideae as Next Diverging Clade in Brassicaceae

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.

Linked by Ancestral Bonds: Multiple Whole-Genome Duplications and Reticulate Evolution in a Brassicaceae Tribe

“…The fact that ancPCK genome was most likely an ancestral genome of both Lineage I (ancPKC → ACK) and expanded Lineage II (ancPCK → PCK) ( Geiser et al. 2016 ; Walden et al 2020b ), and that ancPCK × PCK recurrent hybridization preceded the origin of Lunaria and Ricotia genomes, explains not only the incongruence between phylogenetic trees, inferred with plastid ( Mandáková et al. 2018 ) and nuclear genes (this study) but also occasionally recovered polyphyletic relationships of Biscutelleae ( Warwick et al.…”

“…2016 ; Nikolov et al. 2019 ; Walden et al 2020b ) consisting of monophyletic clades, classified as tribes ( Al-Shehbaz 2012 ). Whereas genomes of some lineages and tribes essentially retained their paleotetraploid character ( Vision et al.…”

Whole-genome microsynteny-based phylogeny of angiosperms

“…We note that the phylogenetic position of Arabis has also been controversial 62 , 63 . A recent study identified shared genomic block associations between Arabis and Aethionema (which is sister to all other Brassicaceae) 64 . Based on macrosynteny, the study of Walden et al 2020 supports Arabideae as the clade diverging after the the divergence of Aethionema within Brassicaceae 64 , which is consistent with our synteny tree (Fig.…”

Arabis alpina: a perennial model plant for ecological genomics and life-history evolution

“…It is a monophyletic assemblage with roughly 545 species distributed among 18 accepted genera, and convergence of morphological traits and trait complexes is found in all main lineages (Walden, German, et al, 2020). Based on recent cytogenetic evidence, Arabideae has been considered one of the early emerging tribes among the evolutionary lineages described in Brassicaceae, that is likely basal to all lineages except Aethionemeae (Walden, Nguyen, Mandáková, Lysak, & Schranz, 2020). However, this finding contradicts phylogenomic analyses (e.g.…”

“…FIGURE A (A) Different phylogenetic positioning of tribe Arabideae within Brassicaceae core groups depending on the marker set used, indicating a biological phenomenon rather than an analytical artifact (following Walden, Nguyen, et al, 2020). (B) Summary of present-day phylogenetic knowledge on clade relationships in Arabideae (species number given).…”