Target sequence capture in orchids: Developing a kit to sequence hundreds of single-copy loci

Premise Understanding relationships among orchid species and populations is of critical importance for orchid conservation. Target sequence capture has become a standard method for extracting hundreds of orthologous loci for phylogenomics. Up-front cost and time associated with design of bait sets makes this method prohibitively expensive for many researchers. Therefore, we designed a target capture kit to reliably sequence hundreds of orthologous loci across orchid lineages. Methods We designed an Orchidaceae target capture bait set for 963 single-copy genes identified in published orchid genome sequences. The bait set was tested on 28 orchid species, with representatives of the subfamilies Cypripedioideae, Orchidoideae, and Epidendroideae. Results Between 1,518,041 and 87,946,590 paired-end 150-base reads were generated for target-enriched genomic libraries. We assembled an average of 812 genes per library for Epidendroideae species and a mean of 501 genes for species in the subfamilies Orchidoideae and Cypripedioideae. Furthermore, libraries had on average 107 of the 254 genes that are included in the Angiosperms353 bait set, allowing for direct comparison of studies using either bait set. Discussion The Orchidaceae963 kit will enable greater accessibility and utility of next-generation sequencing for orchid systematics, population genetics, and identification in the illegal orchid trade.