Published October 18, 2021
| Version V1.0.0
Dataset
Open
The hsp65 metabarcoding DNA sequence database for taxonomic allocations using the Mothur (Version 1.0.0)
Creators
- 1. University of Lyon, UMR Ecologie Microbienne Lyon (LEM), CNRS 5557, INRAE 1418, Université Claude Bernard Lyon 1, VetAgro Sup, Research Team "Bacterial Opportunistic Pathogens and Environment" (BPOE), 69280 Marcy L'Etoile, France.
Contributors
Supervisor:
- 1. University of Lyon, UMR Ecologie Microbienne Lyon (LEM), CNRS 5557, INRAE 1418, Université Claude Bernard Lyon 1, VetAgro Sup, Research Team "Bacterial Opportunistic Pathogens and Environment" (BPOE), 69280 Marcy L'Etoile, France.
Description
- The hsp65 gene codes for an Heat Shock Protein (Telenti et al., 1993) and is widespread in the Actinobacteria phylum. It is well suited for the species allocation of the Nocardia genus (Rodriguez-Nava et al., 2006).
- The hsp65 database, named ACTIhsp65, was designed to apply the hsp65-metabarcoding analytical scheme published in Vautrin et al. (2021). It includes the full hsp65 identifiers, GenBank accession numbers, complete taxonomic records (domain down to strain code) of about 401 nucleotide-long hsp65 sequences of 1066 unique taxa belonging to 198 genera.
- Nucleotide sequences of hsp65 (range: 165-565 nucleotides) were either retrieved from public repositories (GenBank) or made available by Veronica Rodriguez-Nava.Vautrin et al. (2021) described the PCR and high throughput Illumina Miseq DNA sequencing procedures used to produce hsp65 sequences.
- ACTIhsp65 V1.0.0 (June 2018 release) is made available under the Creative Commons Attribution 4.0 International Licence. It can be used for the taxonomic allocations of hsp65 sequences down to the species.
Files
Files
(1.6 MB)
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md5:04839417ba37c2684f68a8fefcb76235
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Additional details
Funding
- Agence Nationale de la Recherche
- INFILTRON – INFILTRON package for assessing infiltration & filtration functions of urban soils in stormwater management ANR-17-CE04-0010
- Agence Nationale de la Recherche
- FROG – Functional Responses Of Groundwater ecosystems to managed aquifer recharge in urban areas ANR-16-CE32-0006
References
- Rodriguez-Nava et al. (2006) - Use of PCR-Restriction Enzyme Pattern Analysis and Sequencing Database for hsp65 Gene-Based Identification of Nocardia Species
- Telenti et al. (1993) - Rapid Identification of Mycobacteria to the Species Level by Polymerase Chain Reaction and Restriction Enzyme Analysis