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
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.

Daniel Vaulot
NTU, Singapore

Focusing on marine (pico)phytoplankton .