Monophyletic Origin and Evolution of the Largest Crucifer Genomes

Abstract

Clade E, or the clade, is one of the major Brassicaceae (Crucifereae) clades, comprising some 48 genera and 351 species classified into seven tribes and is distributed predominantly across arid and montane regions of Asia. Several taxa have socioeconomic significance, being important ornamental but also weedy and invasive species. From the comparative genomic perspective, the clade is noteworthy as it harbors species with the largest crucifer genomes but low numbers of chromosomes ( = 5-7). By applying comparative cytogenetic analysis and whole-chloroplast phylogenetics, we constructed, to our knowledge, the first partial and complete cytogenetic maps for selected representatives of clade E tribes and investigated their relationships in a family-wide context. The clade is a well-supported monophyletic lineage comprising seven tribes: Anchonieae, Buniadeae, Chorisporeae, Dontostemoneae, Euclidieae, Hesperideae, and Shehbazieae. The clade diverged from other Brassicaceae crown-group clades during the Oligocene, followed by subsequent Miocene tribal diversifications in central/southwestern Asia. The inferred ancestral karyotype of clade E (CEK; = 7) originated from an older = 8 genome, which also was the purported progenitor of tribe Arabideae (KAA genome). In most taxa of clade E, the seven linkage groups of CEK either remained conserved (Chorisporeae) or were reshuffled by chromosomal translocations (Euclidieae). In 50% of Anchonieae and Hesperideae species, the CEK genome has undergone descending dysploidy toward = 6 (-5). These genomic data elucidate early genome evolution in Brassicaceae and pave the way for future whole-genome sequencing and assembly efforts in this as yet genomically neglected group of crucifer plants.

Brassicales phylogeny inferred from 72 plastid genes: A reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses

“…Importantly, these estimates are congruent with the topology reported in our previous phylotranscriptomic study (Edger et al., ) with the exception of the addition of the three new families. This consistency suggests that future studies could utilize plastid genomes as markers for resolving relationships within some notoriously difficult clades across Brassicales, as was previously demonstrated within Brassicaceae (Hohmann et al., ; Mandáková et al., ). The sequencing and assembly of plastid genomes has remained an easier and more cost‐effective approach compared to phylotranscriptomics (Wysocki et al., ; Honaas et al., ).…”

“…Phylogenomic analyses utilizing coding sequences from the plastid genome have obtained strongly supported phylogenetic estimates for some notoriously difficult plant clades at various taxonomic levels, including angiosperms (Jansen et al., ), basal angiosperms (Leebens‐Mack et al., ), eudicots (Moore et al., ), grasses (Cotton et al., ; Saarela et al., ), and Brassicaceae (Hohmann et al., ; Mandáková et al., ). Here, we report a phylogenetic estimate of the relationships among all 17 Brassicales families based on 72 plastid coding regions assembled from Illumina next‐generation sequencing (NGS) data.…”

Exploring the History of Chloroplast Capture in Arabis Using Whole Chloroplast Genome Sequencing

“…The complete chloroplast genomes of the Arabis species had total lengths of 152,866–153,758 base pairs, which included 82,338 to 82,811 base pair long single copy (LSC) regions and 17,938 to 18,156 base pair short single copy (SSC) regions, which were separated by a pair of 26,421 to 26,933 base pair inverted repeat (IR) regions. The structure and length are conserved, and are similar to other Brassicaceae species’ chloroplast genome sequences [ 19 , 20 , 21 , 22 ]. The complete genomes contain 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes.…”

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

“…Since its description, the release of additional whole genome sequences as well as comparative cytogenetic analyses have led to the family-wide expansion of the genomic-block concept and reduction to 22 conserved GBs (Lysak et al, 2016). The PCK (Proto-Calepineae Karyotype, n = 7) was described as the ancestral karyotype for clades of lineage II/B (Mandáková and Lysak, 2008), and the CEK (Clade E Karyotype, n = 7) as the ancestral karyotype of lineage III/E (Mandáková et al, 2017a). The CEK genome bears some resemblance to the organization of GBs in the A. alpina genome (Willing et al, 2015).…”