Using molecular hooks (‘baits’), the capture of genes within total DNA will technically increase the concentration of these targeted genes. Then, the enriched matrix will be sequenced in the same way as for whole genome sequencing. Bioinformatics analysis has demonstrated that the raw sequencing data, obtained through targeted sequencing, effectively captures the gene sequences, which is essential for population genetics. Furthermore, it has been established that these sequences include not only exons but also introns and flanking regions. Additionally, the analysis has revealed the presence of repeated DNA sequences in the genomes, such as mitochondrial, plastid, and ribosomal genes. Targeted sequencing thus offers the possibility of uncovering diverse genetic information from various genomic regions. It does so with good robustness and at a lower cost than whole genome sequencing, and without the need for a reference genome.
Quattrini, A. M., Faircloth, B. C., Dueñas, L. F., Bridge, T. C., Brugler, M. R., Calixto‐Botía, I. F., … & McFadden, C. S. (2018). Universal target‐enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long‐standing problems. Molecular ecology resources, 18(2), 281-295
Johnson, M. G., Pokorny, L., Dodsworth, S., Botigué, L. R., Cowan, R. S., Devault, A., … & Wickett, N. J. (2019). A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering. Systematic biology, 68(4), 594-606.