1School of Life Sciences, University of Warwick, Coventry, UK
2De Novo Synthetic Biology Lab, I2SysBio, CSIC-University of Valencia, Paterna, Spain.
3Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
4Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Keele, UK.
| Received 25 Aug 2022 |
Accepted 25 Dec 2022 |
Published 07 Feb 2023 |
Genetic variations such as mutations and recombinations arise spontaneously in all cultured organisms. Although it is possible to identify nonneutral mutations by selection or counterselection, the identification of neutral mutations in a heterogeneous population usually requires expensive and time-consuming methods such as quantitative or droplet polymerase chain reaction and high-throughput sequencing. Neutral mutations could even become dominant under changing environmental conditions enforcing transitory selection or counterselection. We propose a novel method, which we called qSanger, to quantify DNA using amplitude ratios of aligned electropherogram peaks from mixed Sanger sequencing reads. Plasmids expressing enhanced green fluorescent protein and mCherry fluorescent markers were used to validate qSanger both in vitro and in cotransformed Escherichia coli via quantitative polymerase chain reaction and fluorescence quantifications. We show that qSanger allows the quantification of genetic variants, including single-base natural polymorphisms or de novo mutations, from mixed Sanger sequencing reads, with substantial reduction of labor and costs compared to canonical approaches.
