Phylogeny and Multiple Independent Whole-Genome Duplication Events in the Brassicales

Abstract

Whole-genome duplications (WGDs) are prevalent throughout the evolutionary history of plants.For example, dozens of WGDs have been phylogenetically localized across the order Brassicales, specifically, within the family Brassicaceae. However, while its sister family, Cleomaceae, has also been characterized by a WGD, its placement, as well as that of other WGD events in other families in the order, remains unclear. Using phylo-transcriptomics from 74 taxa and genome survey sequencing for 66 of those taxa, we infer nuclear and chloroplast phylogenies to assess relationships among the major families of the Brassicales and within the Brassicaceae. We then use multiple methods of WGD inference to assess placement of WGD events. We not only present well-supported chloroplast and nuclear phylogenies for the Brassicales, but we also putatively place Th-ɑ and provide evidence for previously unknown events, including one shared by at least two members of the Resedaceae, which we name Rs-ɑ. Given its economic importance and many genomic resources, the Brassicales are an ideal group to continue assessing WGD inference methods. We add to the current conversation on WGD inference difficulties, by demonstrating that sampling is especially important for WGD identification. 5

Surprising amount of stasis in repetitive genome content across the Brassicales

“…For total TE abundance, we identified a shift toward a higher abundance in a clade of the Cleomaceae comprising the genus Polanisia and three species of Cleome. Surprisingly, this clade is sister to the clade recently characterized by the Cleomaceae specific WGD, Th -ɑ (Mabry et al 2020). For Gypsy elements alone, we identified a single shift in Lunaria annua; this was unsurprising, as in Figure 1, clear differences in the proportion of these elements can be seen.…”

“…Seeds were grown at the University of Missouri -Columbia or the University of Alberta in a sterile growth chamber environment. Leaf tissue from mature plants was collected for both RNA and DNA extraction followed by isolation and sequencing as in Mabry et al (2020).…”

“…Transcriptome assembly and alignment follow Mabry et al (2020), but in brief, reads were quality filtered and adapter-trimmed using Trimmomatic v 0.35 (Bolger et al 2014) and assembled using Trinity v 2.2 (Grabherr et al 2011) followed by translation to protein sequences using TransDecoder v 3.0 (github.com/TransDecoder/TransDecoder). Orthology was determermined using OrthoFinder v.2.2.6 (Emms and Kelly 2018) followed by filtering for taxon occupancy and alignment quality (github.com/MU-IRCF/filter_by_ortho_group, github.com/MU-IRCF/filter_by_gap_fraction).…”

“…The Brassicales is a particularly valuable order as a model in which to elucidate the connection between whole genome duplication and repetitive element proliferation. First, there are at least four major polyploid events in the Brassicales: "At -ɑ" at the base of the Brassicaceae, the Brassiceae whole-genome triplication ("WGT"), "Th -ɑ" in the Cleomaceae (Schranz and Mitchell-Olds 2006;Barker et al 2009;Mabry et al 2020), and "At -β" at the base of the order (Edger et al 2015;. Second, genomes within the Brassicales are typically small, less than 500 Mb.…”

Independent Recruitment of Duplicated β-Subunit-Coding NAD-ME Genes Aided the Evolution of C4 Photosynthesis in Cleomaceae

“…For species with entire genome information, NAD-ME coding sequences were extracted from primary gene models www.phytozome.net . Sequences from Cleomaceae species were acquired from transcriptome data ( Kulahoglu et al, 2014 ; Mabry et al, 2019 ); in case of Gynandropsis gynandra (C 4 ), Cleome angustifolia (C 4 ), and Tarenaya hassleriana (C 3 ) the sequences were verified and correctly assembled using cDNA-based sequencing as the transcriptomes showed misassembled transcripts for several NAD-ME genes. Sequences for Chara braunii, Azolla filiculoides, Salvinia cucullata, and Panicum miliaceum were identified from their respective genome publications ( Li et al, 2018 ; Nishiyama et al, 2018 ; Zou et al, 2019 ).…”