Chloroplast in Greegnenes 2 2022.10

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1

Hi @wasade
Thank you for the update. I have analysed my V4 dataset with the 2024.09.backbone.v4.nb.qza classifier (using q2-amplicon-2024.10 release) and found all putative chloroplast 16S reads annotated with
d__Bacteria; p__Cyanobacteriota; c__Chloroplast; o__; f__; g__; s__

This is also the lowest annotation in the taxonomy artifact 2024.09.backbone.tax.qza:
Does it mean that chloroplast sequences are annotated only to the 'class' level?
Best,

2

Hi @arwqiime,

Correct, we forced the taxonomy for Chloroplast. Further discussion related to that can be found here.

Best,
Daniel

3

Hi @wasade
Thank you for the link to the ongoing discussion about chloroplast and mitochondria within Greengenes2. It is for sure not an easy task to handle sequences of (phylogentically) prokaryotic origin such as chloroplast and mitochondria within a taxonomic system that consider these organelles as part of eukaryotes.
When working with sequences, however, I would prefer work with the phylogenetic origin of theses sequences and to place them into the taxonomy as described above ( d__Bacteria; p__Cyanobacteriota; c__Chloroplast;...), in particular as these sequences reside in a phylogenetic tree within the procaryotes.

Best,

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6

Thanks, @arwqiime. I agree there is high value in a phylogenetic expression of these records.

All the best,
Daniel

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7

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