KBell_plant_rbcL_2021-07

    Database citation :
    Bell, Karen; Brosi, Berry (2016): rbcL reference library. figshare. Collection. https://doi.org/10.6084/m9.figshare.c.3466311.v1 

    From Bell, Karen L., Virginia M. Loeffler, and Berry J. Brosi. "An rbcL reference library to aid in the identification of plant species mixtures by DNA metabarcoding." 
    Applications in plant sciences 5.3 (2017): 1600110.

    Files for DNA metabarcoding using rbcL. Includes sequence data in CSV and FASTA format, and trained database files for identification using RDP classifier or UTAX.

    Updated in July 2021, with sequences from North Queensland, and reformatted for use with DADA2. Please use the updated version available at: 10.6084/m9.figshare.c.5504193

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rbcL_BOLD databases : 

This databases contain the sequences of the Ribulose-1,5-bisphosphate 
carboxylase/oxygenase large subunit gene (rbcL and rbcLa)  of plants 
located in 
- rbcL_BOLD_Landes : the Landes de Gascogne Regional Nature Park (PNR des Landes 
de Gascogne).
- rbcL_BOLD_Arcachon : the Landes forest, located south of Arcachon Bay, France.

Sequences were extracted from the BOLD Public Record Barcode Database using 
the R package bold (Dubois S, Chamberlain S (2023), 
https://CRAN.R-project.org/package=bold, , v.1.3.0) based on species names.

Related taxonomy were extracted from NCBI using the R package taxize
(Scott Chamberlain and Eduard Szocs (2013), 
https://f1000research.com/articles/2-191/v2, v.0.9.1) considering only 
the "valid" plant names when available.
Ranks selected : Kingdom; Phylum; Class; Order; Family; Genus; Species

#    rbcL_BOLD_Landes

All plant species present in the region were considered. This included both 
"valid" and "invalid" species names recorded by the French National Natural 
Heritage Inventory (INPN) in the Landes de Gascogne Regional Nature Park.
Additonal species identified in the field by members of UMR BIOGECO using a 
quadrat protocol (2023) were added.
Species names of hybrid taxa (those containing the character " x ") were 
excluded.

Entries in rbcL_Landes :
            v.20240516      
Sequences   14465
Species     1345
Genera      671
Family      181

#    rbcL_BOLD_Arcachon

Plant species in the field were identified by members of UMR BIOGECO using a 
quadrat protocol (2023). In case of incomplete species identification 
(e.g., Rubus sp.), all plant species present in the region were considered 
for the considered genus . This included both "valid" and "invalid" species 
names recorded by the French National Natural Heritage Inventory (INPN) in 
the Landes de Gascogne Regional Nature Park (PNR des Landes de Gascogne). 
Species names of hybrid taxa (those containing the character " x ") were 
excluded.

Entries in rbcL_Arcachon :
            v.20240516      
Sequences   1508
Species     116
Genera      69
Family      35

contact : aloisberard@outlook.fr or alois.berard@inrae.fr, maxime.galan@inrae.fr