Orchidaceae963 bait set page

HOT OFF THE PRESS

Our newly published research on the Orchidaceae963 bait set

By Lauren Eserman, PhD - Research Scientist, Genetics

With over 27,000 species, the orchid family is one of the largest and most diverse of the flowering plants. Humans have been captivated by orchids for thousands of years. In the wild, orchids face enormous pressures from poaching, habitat loss and climate change. Currently, over half of all orchid species assessed by the IUCN Red List have been shown to be threatened. While orchid conservation is critical, it has thus far been difficult to perform conservation genetic studies on orchids for lack of a reliable, orchid-specific toolkit.

In collaboration with researchers from the University of Georgia and the University of Missouri, we used available genomic data to develop the Orchidaceae963 target capture bait set1. ‘Baits’ are small nucleotide molecules that can be manufactured to retrieve and isolate specific gene fragments of interest for sequencing. In this study, we tested our newly developed bait set on 28 species from across the orchid family tree. We demonstrated that this toolkit can recover an average of 812 genes per sample for orchid species in the subfamily Epidendroideae and an average of 501 genes for species in the Orchidoideae and Cypripedioideae. Furthermore, samples contained on average 107 of the 254 genes that are also included in the widely-used Angiosperms353 bait set (a general bait set for flowering plants that can target up to 353 genes), which would allow for direct comparison across studies using either bait set. Orchidaceae963 allows the user to sequence up to 963 genes from any single orchid sample, with the potential to improve the accessibility and use of nextgeneration sequencing for orchid systematics, population genetics and identification.

1. Eserman, L. A., Thomas, S. K., Coffey, E. E. D. & Leebens-Mack, J. H. (2021) Target sequence capture in orchids: Developing a kit to sequence hundreds of single-copy loci. Applications in Plant Sciences 9 (7): e11416. Lycaste xytriophora

UP FOR THE BAIT – This summer, we used the new Orchidaceae963 bait set to study the genetic structure of a Georgia population of pink slipper orchid (Cypripedium acaule, pictured life-sized).