bioRxiv preprint doi: https://doi.org/10.1101/2020.03.30.017442; this version posted April 1, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Lessons and considerations for the creation of universal primers targeting non-conserved, horizontally 2 mobile genes 3 4 Damon C. Brown,a Raymond J. Turnera# 5 aDepartment of Biological Sciences, University of Calgary, Calgary, Alberta, Canada 6 7 Running Head: Primer design approaches for nonconserved mobile genes 8 #Address correspondence to Raymond J. Turner,
[email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.30.017442; this version posted April 1, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 9 Abstract 10 Effective and accurate primer design is an increasingly important skill as the use of PCR-based 11 diagnostics in clinical and environmental settings is on the rise. While universal primer sets have been 12 successfully designed for highly conserved core genes such as 16S rRNA and characteristic genes such as 13 dsrAB and dnaJ, primer sets for mobile, accessory genes such as multidrug resistance efflux pumps 14 (MDREP) have not been explored. Here, we describe an approach to create universal primer sets for 15 select MDREP genes chosen from five superfamilies (SMR, MFS, MATE, ABC and RND) identified in a 16 model community of six members (Acetobacterium woodii, Bacillus subtilis, Desulfovibrio vulgaris, 17 Geoalkalibacter subterraneus, Pseudomonas putida and Thauera aromatica).