gRNA alignments on Mongo edited mRNAs of maxicircle-encoded cryptogenes

Prior identification of gRNA cassettes based on the semi-conserved, inverted 18-bp repeats had detected three cassettes in 73 minicircles and four cassettes in 48 minicircles (a total of 411 cassettes) (Figure 11). Alignment allowing no gaps between gRNA and edited mRNA identified two maxicircle-encoded gRNA genes and 532 candidate minicircle-encoded gRNA genes. The vast majority of gRNA genes (523 or 98.7%) are located in 323 cassettes flanked by the 18-bp inverted repeats reported before in <i>T. brucei </i>and <i>T. congolense </i>{Nasir, 1987 #13;Pollard, 1990 #30;Hong, 2003 #255;Jasmer, 1986 #288;Read, 1993 #70} (Figure 12 ). The seven gRNAs whose genes were not bound within cassettes were termed ‘orphan gRNAs’ {Riley, 1994 #294;Hong, 2003 #255}{Cooper, 2019 #21}. Not all cassettes contain gRNA genes, and a cassette may encode multiple gRNAs. If we only considered the gRNAs that edited the differentiated regions over alternatively edited mRNAs, the annotation yielded 347 unique gRNA genes, of which 338 (97.4%) were encoded on cassettes. Only 15 cassettes truly contained multiple gRNA genes