Probe Design for Sequence Capture
One of the most cost-efficient ways to design probes for targeted sequencing is to use existing transcriptome data in combination with a relatively closely related genome. Homology between transcriptomes and genomes is detected using BLAST searches, or if several sources are available, using orthology searching software such as Orthofinder.
We have collaborated with several groups working on a variety of organisms, including angiosperms, mosses, and even birds. Probes can be designed to fit a variety of taxonomic depths (from species complexes to entire phyla) can include genes that are functionally relevant in addition to phylogenetically informative genes, and can incorporate sequence divergence by using multiple source species.
In collaboration with the Plant and Fungal Tree of Life (PAFTOL) team at Royal Botanical Gardens, Kew, we helped develop a probe kit that promises to reliably amplify up to 350 nuclear coding regions in any angiosperm species. You can read more about the probe design here.