Gtdb r207 archaea marker

Archaeal Taxonomy
1

Dear gtdb team,

I found that with new r207, marker for archaea is about 50 only and a majority of the 6000 archaea genomes contains only 1/3 of the 50 marker. With old version R202, 120+ archaea marker, majority of genomes contains 100+. how can you make sure that the overlap of those archaea marker in v207 is sufficient enough to have a significant concatenated marker set, worst case, nothing share between 2 archaea genome, one contains 1/3 and another contains a different 1/3.

2

The change in the number of markers (from 122 to 53) is explained in the release notes.

3

Hi,

You can find statistics regarding how often each of the 53 archaeal marker genes is identified across the archaeal GTDB representatives in ar53_msa_marker_info_r207.tsv:
https://data.gtdb.ecogenomic.org/releases/release207/207.0/auxillary_files/ar53_msa_marker_info_r207.tsv

Only 2 markers are identified in <50% of the archaeal GTDB representative genomes and the average is 82%.

Note that there are 3,412 archaeal representatives in GTDB R207. Many non-representatives genomes are partially complete MAGs which may account for the low ubiquity you are seeing.

Cheers,
Donovan