Due to low sequence coverage and small scaffold size, the 17 mitochondrial scaffolds of ICPB 2039 line only covered 15 protein and 11 tRNA genes between them (Supplementary Table S5).
Apparent absence could also be a technical artifact from low sequence coverage, consistent with the observation that the genome assemblies for these taxa largely comprise small contigs.
For very small inversions, deep sequence coverage would be required to obtain several DNA fragments spanning one breakpoint.
However, at this stage, we do not rule out the possibility that canonical miRNAs could be identified in response to other environmental cues and/or through a more important small RNA sequencing coverage than the one used in the present study.
Statistical power is limited for smaller CNVs but increasing sequence coverage can in some instances improve sensitivity (Chiang et al., 2009).
Briefly, two genes were considered orthologs if each gene identified the other as its best hit in the bi-directional blasts satisfying two conditions: the e-values of both hits were equal to or smaller than 10-15 and sequence coverage was at least 60%.
Developed expressly for use on a bacterial genome, CSDeconv and programs like it may represent an excellent choice for microbial ChIP-seq experiments with only a few binding sites, small genome size and high sequence coverage.
As Figure 6 depicts, on average 99.87% (SD = 0.23%) of the mtGenome was covered by at least 2 sequences, and 99.07% (SD = 0.67%) of the mtGenome had both forward and reverse sequence coverage when small regions with unidirectional coverage due to length heteroplasmy in hypervariable regions 1 and 2 were ignored.
During the initial random-sequencing phase, 8-fold sequence coverage was achieved with the small- and medium-size libraries sequenced to yield 5-fold and 3-fold coverage, respectively.
Of the chaotropes, guanidine was preferable, especially for increasing the number of hydrophobic peptides and average sequence coverage of smaller proteins.
