The “universal target” region of the gene encoding the 60 kDa chaperonin protein (cpn60, also known as groEL or hsp60) is a proven sequence barcode for bacteria and a useful target for marker gene amplicon based studies of complex microbial communities.
This repository contains reference sequences and taxonomy table compatible with the QIIME2 q2-feature-classifier plugin (https://github.com/qiime2/q2-feature-classifier) for taxonomic assignment of cpn60 barcode sequences.
Sequence data and metadata for each record are provided to facilitate use of other classifiers and alignment based methods for sequence identification.
Ren, Q. and Hill, J.E. 2023. Rapid and accurate taxonomic classification of cpn60 amplicon sequence variants. ISME Communications 3:77 https://doi.org/10.1038/s43705-023-00283-z
Vancuren, S.J. and Hill, J.E. 2019. Update on cpnDB: a reference database of chaperonin sequences. Database, 2019, https://doi.org/10.1093/database/baz033
The classifier used in initial performance testing (Ren & Hill, 2023) is v10.1, which contains a non-redundant set of 11,001 cpn60 barcode sequences.
The latest release (v13.1) includes 18,520 cpn60 reference sequences.
(Releases prior to v13.1 included resources for use with the RDP Classifier, but will not be updated)