HybSeq of Carex stipata Muhl. ex Willd.
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).