Qiime2 taxonomy

I did taxonomy analysis of ASV using qiime2 and imported data into phyloseq but in my phyloseq object, the chloroplast is present as class whereas mitochondria present as family: Is it ok or there is some issue with taxonomy assignment?

I have also seen the same taxa assignment in taxonomy file using qiime2view so there no issue with phyloseq import.

[1] 67405
physeq0 <- subset_taxa(physeq, (Class!=“Chloroplast”) | is.na(Class))
[1] 66946
physeq1 <- subset_taxa(physeq0, (Class!=“mitochondria”) | is.na(Class))
[1] 66946
physeq1 <- subset_taxa(physeq0, (Family!=“mitochondria”) | is.na(Class))
[1] 64545


There is not any such thing as a “QIIME 2 taxonomy”.

Reference databases, such as greengenes, SILVA, unite, etc, are external resources. So what you are describing is a characteristic of the database you used, not an artifact of any QIIME 2 analysis.

I just checked the greengenes taxonomy and, sure enough, mitochondria is listed as a family and chloroplast is listed as a class.

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