6. Screening of the structural variant nearCYP6P5/CYP6P9b from whole-genome sequences from different regions
of Africa
Based on the previous observations of the likely presence of an SV in
the intergenic region between CYP6P9b and CYP6P5 (Mugenzi
et al., 2019) due to the lack of amplification of the 1kb fragment, SV
was searched using PoolSeq data from An. funestus populations
available under European Nucleotide bioprojects PRJEB24384, PRJEB13485,
PRJEB35040, PRJEB35040, PRJEB24351 and PRJEB10294 (Weedall et al., 2019,
2020) for 12 populations of An. funestus sampled across Africa
from 2002 to 2016. These were aligned to the An. funestus F3
genome (Ghurye et al., 2019) using BWA (v0.7.17-r1188) (Li et al.,
2009). Reads were coordinate sorted, and duplicates were marked with
Picard (v2.18.15) (”Picard Toolkit,” 2019). The subsequent alignments
were visually inspected for evidence of an insertion in the intergenic
region of CYP6P5 and CYP6P9b in IGV. In addition,
non-reference transposon insertions were searched for computationally
using TranSurVeyor (v1.0) (Rajaby & Sung, 2018).