qSanger: Quantification of Genetic Variants in Bacterial Cultures by Sanger Sequencing

Abstract

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.

Cytonuclear interplay in auto‐ and allopolyploids: a multifaceted perspective from the Festuca‐Lolium complex

“…Whole transcriptome data analysis was employed to determine the HEB of the genes involved in cytonuclear complexes. To confirm the RNA‐seq results determining HEB (Glombik et al., 2021), cDNA samples from both homoploids and allopolyploids were analyzed using quantitative Sanger sequencing (qSanger) (Liu et al., 2022; Prakash et al., 2023). Specific primers were designed to target nuclear genes encompassing regions containing SNPs (Table S6) and the resulting PCR products were subsequently sequenced as previously described.…”