HybSeq of Carex tomentosa L.
Baits were designed from transcriptomic data from Carex siderosticta and the relatively distantly related Cyperaceae species Cyperus papyrus L. (available through the 1KP initiative: www.onekp.com/public_data.html), using the MarkerMiner v.1 pipeline (Chamala et al., 2015). We identified orthologous low copy nuclear genes (LCNGs) using the proteome of Oryza sativa as reference. A total of 554 orthologous loci were selected to develop the gene target baits, which ranged from 802 to 7,445 bp, for a total exon length of 1,032,784 bp (Supplementary Information, Table S3 in Villaverde et al. 2019). The target enrichment kit was manufactured as 15,075 120-bp baits with in-solution biotinylated baits at Arbor Biosciences (Ann Arbor, Michigan, USA), tiling across our exon targets with 2 coverage. De-multiplexed sequences were quality trimmed (>Q20 in a 5-bp window) using Trimmomatic (Bolger et al., 2014).