MAUI-seq: Multiplexed, high-throughput amplicon diversity profiling using unique molecular identifiers

摘要: Correcting for sequencing and PCR errors is a major challenge when characterising genetic diversity using high-throughput amplicon (HTAS). Clustering amplicons by sequence similarity robust frequently used approach, but it reduces sensitivity makes more difficult to detect differences between closely related strains. We have developed multiplexed HTAS method, MAUI-seq, that incorporates unique molecular identifiers (UMIs) improve correction. profile Rhizobium leguminosarum biovar trifolii (Rlt) synthetic DNA mixes Rlt in white clover (Trifolium repens) root nodules of two plasmid-borne nodulation genes chromosomal genes. show the main advantages UMIs are efficient elimination chimeric reads ability confidently distinguish alleles differ at only single position. In addition, multi-amplicon profiling from different replicons enables increased resolution, allowing us demonstrate limited strain overlap geographically distinct locations. The method does not rely on commercial library preparation kits provides cost-effective, sensitive flexible intra-species diversity.