Whole-genome sequencing reveals highly specific gene targeting by in vitro assembled Cas9-ribonucleoprotein complexes in Aspergillus fumigatus

Table 2 Cas9-mediated gene deletion is not associated with increased genomic mutations in A. fumigatus

	NC1	NC2	NC3	HC4	HC5	HC6	LC7	LC8	LC9
Average coverage	53×	62×	60×	58×	54×	61×	56×	49×	38×
Total mutations	396	342	385	345	326	307	345	366	474
Average total mutations	373 ± 28 SD			326 ± 19 SD (p > 0.05)			395 ± 69 SD (p > 0.05)
Analysis based on type of mutation identified
SNPs	371	318	363	321	314	292	326	347	439
Indels	25	24	22	24	12	15	19	19	35
Analysis based on location of mutation
Intergenic	380 (96%)	331 (97%)	379 (98%)	331 (96%)	320 (98%)	301 (98%)	339 (98%)	359 (98%)	446 (94%)
Average intergenic	363 ± 28 SD			317 ± 15 SD (p = 0.04)			381 ± 57 SD (p > 0.05)
Coding region	16 (4%)	11 (3%)	6 (2%)	14 (4%)	6 (2%)	6 (2%)	6 (2%)	7 (2%)	28 (6%)
Average coding region	11 ± 5 SD			9 ± 5 SD (p > 0.05)			14 ± 12 SD (p > 0.05)

Displayed are the total and average number of mutations among the three experimental groups: no (“NC”—0 µg/µl), low (“LC”—0.5 µg/µl) and high (“HC”—1 µg/µl) levels of Cas9. For the intergenic and coding region mutation rows, the numbers in parentheses represent the percent (%) of total mutations. For the average mutations per group, the mean ± standard deviation (SD) is provided. The Student’s t test assuming unequal variance was used for statistical comparisons of the Cas9 (HC or LC) and the no-Cas9 (NC) groups and p values are presented

ISSN: 2054-3085