Comparing mitonerichment to targeted mitosequencing
The total number of reads was greater on the mitoenrichment method, however the proportion and number of sequences on target was greater for the targeted mitosequencing method (Table 3, S3, Fig. 2). On the other hand, the read depth was more evenly distributed across the mitogenome with the mitoenrichment method despite the average read depth being greater for the targeted mitosequencing approach. The use of liver increases the ratio of sequences on target for the mitoenrichmnent approach while also increasing the off-target number of sequences, which turns into a greater use of the flow cell. On the contrary, the heart does not perform better than skeletal muscle (Table 3, Fig.3). The more degraded the sample (low DIN) the lower the coverage and the shorter the reads were. Further enrichment was achieved for samples extracted from isolated mitochondria and treated with the Cas9 targeted sequencing method (Fig 3)
Figure 2. Overall representation of all runs and species for the proportion and number of sequences on-target and mean coverage by enrichment method. The targeted mitosequencing method has a greater proportion of sequences on target and deeper coverage overall.