Generation of the Malaspina Gene Database (M-GeneDB)

All 3,872,410 predicted coding sequences larger than 100 bp from each assembled metagenome were pooled and clustered at 95% sequence similarity and 90% sequence overlap of the smaller sequence using cd-hit-est⁹⁷ v.4.6 using the following options: -c 0.95 -T 0 -M 0 -G 0 -aS 0.9 -g 1 -r 1 -d 0 to obtain 1,115,269 non-redundant gene clusters (from now on referred simply as genes). These gene clusters were aligned to UniRef100⁹⁸ (release 2019-10-16) with diamond blastx⁹⁹ (v0.9.22; e-value 0.0001). The least common ancestor taxonomic assignation of UniRef100 best matches was obtained from NCBI’s taxonomy database¹⁰⁰ (release 2020-01-30).

In order to explore the novelty of the M-GeneDB, we clustered it with the 46,775,154 non-redundant sequences from the Tara Oceans Microbial Reference Gene Catalog version 2 (OM-RGC.v2)³⁷ using cd-hit-est-2d⁹⁷ v.4.6 with the following options: -c 0.95 -T 48 -M 256000 -G 0 -aS 0.9 -g 1 -r 1 -d 0 to obtain a final catalog of 47,422,971 genes.