PR2 version 4.14.0
We are very pleased to announce the new PR2 version 4.14.0.
Very big thanks to all the contributors (Alex Schoenle, Miguel Sandin - Radiolaria, Raphael Morard, Frédéric Mahé, Anna Maria Fiore-Donno) and especially Javier del Campo who curated three important groups (Apicomplexa, Labyrinthulids and Excavata) …
A single SSU database
The most important change of this version is that we are now providing a single SSU database which contains sequences for:
- 18S rRNA from nuclear and nucleomorph
- 16S rRNA from plastid, apicoplast, chromatophore, mitochondrion
- 16S rRNA from a small selection of bacteria
We have added about 7,000 bacterial sequences so that the database can now be used to detect bacterial sequences that are amplified with either 18S or “universal” (i.e. amplifying both 18S and 16S) rRNA primers. These sequences can be further assigned with Silva or GTDB.
In order to allow correct assignation with software such as DECIPHER (IDTax), each taxonomy level is appended with 4 letters corresponding to the organelle (e.g. Chlorophyceae:plas for a sequence from the plastid assigned to Chlorophyceae).
| Organelle | Taxonomy suffix |
|---|---|
| nucleus | |
| nucleomorph | :nucl |
| plastid | :plas |
| apicoplast | :apic |
| chromatophore | :chrom |
| mitochondrion | :mito |
Taxonomy updates
The taxonomy of a number of major groups has been updated:
- Apicomplexa
- Labyrinthulids
- Radiolaria
- Foraminifera
- Radiolaria
The complete list of changes is available from here.
DECIPHER training set
DECIPHER is package that provides a function (IDTaxa) to assign metabarcodes. This function is quite fast once a training set has been created. We now provide a trained data set as well as a tutorial on how to create a training set and use it to assign metabarcodes.
Please let us know of any problem you encounter with this release on GitHub.
