Advancing phylogenomics in Amaranthaceae sensu stricto: Development and application of a new nuclear target enrichment bait set

<h4>Premise</h4>Current phylogenies of Amaranthaceae sensu stricto (s.s.) are inadequately sampled and resolved to reflect the entire evolutionary history of the lineage, which is likely complex due to at least three whole-genome duplication events, occasionally followed by subsequent additional polyploidization events and rapid diversification of individual sublineages. We designed a new target enrichment bait set to overcome these challenges when reconstructing a phylogeny and demonstrated its applicability to the entire Amaranthaceae s.s. lineage.<h4>Methods</h4>We analyzed 12,775 orthologous and low-copy genes from a previous comprehensive transcriptomic study for marker selection. Following a newly developed approach that allows the selection of long exons and thus avoids the assembly of chimeric loci, we selected 1000 orthologous exons for phylogenomic analyses.<h4>Results</h4>Our in vivo application showed a high locus recovery rate across all major clades of Amaranthaceae s.s., generated a robust phylogenetic tree, and clarified previously ambiguous relationships of the genera <i>Bosea</i> and <i>Charpentiera</i>. Gene tree conflict analysis revealed mainly high levels of gene tree concordance within the lineage, with a few notable exceptions.<h4>Discussion</h4>The Amaranthaceae1000 kit will provide the basis for a phylogenetic tree across the Amaranthaceae s.s., facilitating future studies on systematics, diversification, and genome evolution within this economically important lineage.