Data from: 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, and
clarified previously ambiguous relationships of the
genera Bosea and Charpentiera. Gene tree
conflict analysis revealed mainly high levels of gene tree concordance
within the lineage, with a couple of notable exceptions. Discussion: The
Amaranthaceae1000 kit will provide the basis for an Amaranthaceae
s.s.-wide phylogenetic tree, facilitating future studies on systematics,
diversification, and genome evolution within in this economically
important lineage.