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

Premise: Current phylogenies of Amaranthaceae 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 sub-lineages. To overcome these challenges when reconstructing a phylogeny, we designed a new target enrichment bait set and demonstrated its applicability to the entire Amaranthaceae s.s. lineage. Methods: 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 1,000 orthologous exons for phylogenomic analyses. Results: Our in vivo application showed a high locus recovery rate across all major clades of Amaranthaceae s.s., generated a robust phylogenetic tree,..., , # Data from: Advancing phylogenomics in Amaranthaceae sensu stricto: Development and application of a new nuclear target enrichment bait set Dataset DOI: [10.5061/dryad.k3j9kd5m6](10.5061/dryad.k3j9kd5m6) ## Description of the data and file structure We analyzed a total of 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 1,000 orthologous exons for phylogenomic analyses. The final bait set targets a total of 1.29 Mbp. ### Files and variables #### File: Amaranthaceae1000_Design_Files_input-seq.fasta **Description:** 2,000 target sequences with a total target size of 2,571,494nt and an average GC content of 42.6%. Targets were softmasked for simple and low complexity repeats against the dicot plant database. Strings of Ns 1-10nt were replaced with T. #### File: Amaranthaceae1000_Design_..., ,