Oncorhynchus clarkii lewisi Raw sequence reads. Oncorhynchus clarkii lewisi

Mitochondrial genome variation in Westslope Cutthroat Trout (Oncorhynchus clarkii lewisi) inferred from targeted enrichment of mitochondrial genomes from samples representing the range of westslope cutthroat trout. The mitochondrial genome of Lahontan cutthroat trout (Oncorhynchus clarkii henshawi; genbank AY886762) was used to design hybridization-based target capture probes for trout mitochondrial genomes, and these probes were used to enrich mitogenomes from a panel of 96 westslope cutthroat trout (O. c. lewisi) representing the geographic range of the taxon. Genomic libraries were constructed using total genomic DNA and Illumina TruSeq version 2 chemistry, and individual samples were uniquely indexed. DNA sequencing was performed on two lanes of the HiSeq2000, with sample multiplexing set at 48×. The variation revealed from these genomes have been used to design taxon-specific quantitative PCR assays (see doi:10.1371/journal.pone.0142008), and for mitochondrion-based phylogeographic analysis.