GTDB Forum

16S gene copy nrs

Dear all,
I was wondering whether the information regarding 16S gene copy nrs is already present in the FTP-files: bac120_ssu_reps_r95.fna & ar122_ssu_reps_r95.fna
Wether the locus tag # refers to 16S gene copy nr?
example: s__Faecalibaculum rodentium [locus_tag=NZ_CP011391.1-#8] has 8 copies?
Or should this be determined manually?

Many thanks,
Hugo.

Hi Hugo,

No - the # number is not a reliable indication of 16S rRNA copy number. The files bac120_ssu_reps_r95.fna and ar122_ssu_reps_r95.fna contain one 16S rRNA gene per genome, even if the genome contains multiple 16S rRNA genes. The FILE_DESCRIPTIONS file has useful information for understanding the contents of each of the provided GTDB files:
https://data.gtdb.ecogenomic.org/releases/latest/FILE_DESCRIPTIONS

Cheers,
Donovan

Thank you Donovan,

I will then stringsearch the 16S sequences against the full genomes to get this information.

Kind regards,
Hugo.