Co-Enrichment of Divergent Organelle Genomes for Population Genomics Analysis

Natural animal and plant populations of conservation and management concern have benefited greatly from the application of molecular tools. With the advent of next-generation sequencing, complete organelle genomes can now be used to provide detailed haploid genealogical reconstructions, estimates of divergence and migration, and evidence for mutations that confer adaptive advantage or disease states. We designed short oligonucleotide hybridization baits to enrich two dissimilar organellar targets: the 16.5 kb mitochondrial (MT) genome of Westslope Cutthroat Trout (Oncorhynchus clarkii lewisi: Salmonidae) and the 125 kb chloroplast (CP) genome of Yellow Cedar (Callitropsis nootkatensis: Cupressaceae). Complete organelle genomes were isolated, sequenced on the Illumina HiSeq2000, and assembled from single hybridization reactions of 48 uniquely indexed and pooled samples for each taxon. Averaged across samples, targets were enriched to 55% of the sequence pool for MT genomes and 70% for CP genomes. Assembly depths for individual samples averaged 3,500X for MT genomes, to 250X for CP genomes. Remarkably, organelle genomes from 96 combined samples (48 trout, 48 trees) could be enriched in a single hybridization reaction with nearly equal efficiency. This ‘multi-kingdom’ probe pool should work with high efficiency on species sharing 90% or greater sequence similarity to our target organisms; this includes all salmonid fish (190) and cupressoid tree (140) species worldwide. Land and wildlife management agencies charged with the task of providing baseline data for diverse species in different kingdoms can take advantage of the flexibility of targeted capture bait pools that serve multiple purposes.