Hybridization capture using short PCR products enriches small genomes by Capturing Flanking sequences (CapFlank), which is the title of the manuscript is detail description and proof of principle of how you can enrich and sequence small genomes using

During hybridization capture huge amount of sequencing was considered to be of target. We demonstrate that during capture, the bait-hybridized library molecules add additional flanking library sequences iteratively, such that baits limited to targeting relatively short regions (e.g. few hundred nucleotides) can result in enrichment across entire mitochondrial and bacterial genomes