An amplicon sequence variant (ASV) is any one of the inferred single DNA sequences recovered from a high-throughput analysis of marker genes. Because these analyses, also called "amplicon reads," are created following the removal of erroneous sequences generated during PCR and sequencing, using ASVs makes it possible to distinguish sequence variation by a single nucleotide change. The uses of ASVs include classifying groups of species based on DNA sequences, finding biological and environmental variation, and determining ecological patterns.
ASVs were first described in 2013, by Eren and colleagues.[1] Before that, for many years the standard unit for marker-gene analysis was the operational taxonomic unit (OTU), which is generated by clustering sequences based on a threshold of similarity.
Compared to ASVs, OTUs reflect a coarser notion of similarity. Though there is no single threshold, the most commonly chosen value is 3%, which means these units share 97% of the DNA sequence. ASV methods on the other hand are able to resolve sequence differences by as little as a single nucleotide change, thus avoiding similarity-based operational clustering units altogether. Therefore, ASVs represent a finer distinction between sequences.
ASVs are also referred to as exact sequence variants (ESVs), zero-radius OTUs (ZOTUs), sub-OTUs (sOTUs), haplotypes, or oligotypes.[2][3]
^Eren AM, Maignien L, Sul WJ, Murphy LG, Grim SL, Morrison HG, Sogin ML (December 2013). "Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data". Methods in Ecology and Evolution. 4 (12): 1111–1119. Bibcode:2013MEcEv...4.1111E. doi:10.1111/2041-210X.12114. hdl:1912/6377. PMC 3864673. PMID 24358444.
^Porter TM, Hajibabaei M (January 2018). "Scaling up: A guide to high-throughput genomic approaches for biodiversity analysis". Molecular Ecology. 27 (2): 313–338. Bibcode:2018MolEc..27..313P. doi:10.1111/mec.14478. PMID 29292539.
^Callahan BJ, McMurdie PJ, Holmes SP (December 2017). "Exact sequence variants should replace operational taxonomic units in marker-gene data analysis". The ISME Journal. 11 (12): 2639–2643. Bibcode:2017ISMEJ..11.2639C. doi:10.1038/ismej.2017.119. PMC 5702726. PMID 28731476.
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