Data download

Description	File link	Checksum (MD5)
MGE profile	mge_profile.tsv.gz	c90d47fc4f04d4dc2fa8b5125bf53db1
Nested MGE profile	mge_nested.tsv.gz	3b6cb29a068cdf1a7aa7f352a869ed8e
MGE clustering by 100% sequence identity (MGE100)	mge100_clusters.tsv.gz	aeb31f494eda0f0a4921864f701c12cb
Antibiotic resistance carrying MGEs	mge_antibiotic.tsv.gz	ed5fbbf8fe58a77c1e8a95534fb7dc36
Horizontal Gene Transfer data	hgt.tsv.gz	91ccd6e8eb50dc36fdc3b22eb1f5b0c1
Genomes quality	genomes_quality.tsv.gz	6686825565c34c8adecc31afa2c18e17
Genomes taxonomy	genomes_taxonomy.tsv.gz	caa07ce4b6658eaef0e8982293021ea4
Functional annotations for non-redundant MGEs (MGE100)	mge100.gff3.gz	03a52bfb5f09f757f89792f79c9f3513
Non-redundant MGE sequences (MGE100)	mge100.fna.gz	0f1e8fd3f12082f0f5f085fd34989b9e
Recombinase HMMs from proMGE (huh_y1, huh_y2, ser_tn, ser_ce, ser_lsr, cas1)	hmms.tgz	376b03ee2c4d19b9232da7c51cade8e9
README	README.md	1879911c74d39e66c61d77cfcee4619e

Annotations of Mobile Genetic Elements (MGEs) in isolate genomes from the proGenomes3 database and metagenome-assembled genomes (MAGs) from the SPIRE database

• MGEs were annotated in the context of the pangenome of a species (as given by a specI cluster). Core and accessory genomes were determined by co-clustering genes from MAGs and high-quality, complete isolate genomes assigned to the same species. Genes that were present in more than 95% (isolates) or 80% (MAGs) of all genomes of the same specI cluster were marked as core. specI clusters with fewer than 2 member genomes were excluded from the analysis.
• The profile HMMs used for recombinase annotations can be found in the SMART database by searching for the recombinase subfamily names (e.g. `ser_lsr`) in the keyword search.
• MGE identifiers (e.g., `MGE_SAMEA104467237.psa_megahit.psb_metabat2.00011_k141_144210:99994-101058`) are unique and descriptive, using the following pattern:

  MGE_<contig_id>:<start>-<end>

  • The identifier starts with `MGE_`
  • The <contig_id> is a composite of the NCBI/proGenomes3 genome id (GCA_<number>) in case of isolates or the <bin_id> in case of SPIRE MAGs. SPIRE MAG <bin_ids> start with their <sample_id> (e.g. SAMEA104467237), followed by a processing infix containing information about the assembly pipeline (e.g., psa_megahit.psb_metabat2: assembly with megahit, binning with metabat2), and the <within_sample_bin_id>, a 5 digit, left zero-padded integer
  • <start> and <end> are 1-based genomic coordinates
• MGE100 cluster IDs correspond to a 100% sequence identity, redundancy-reduced set of MGEs from MAGs and isolates, performed by comparing forward and reverse-complement MD5 sums of the corresponding nucleotide sequences. If available, MGEs discovered in isolate genomes were used as representatives, otherwise MGE100 representatives were metagenomic derived MGEs.
• MGE100 cluster IDs e.g. proMGE100_2.0_0000001_phage_48_1 are unique and descriptive, using the following pattern proMGE100_{version}_{id}_{mge_cat}_{n_members}_{n_species}
• The taxonomy was inferred from GTDB-based specI clusters taxonomy
• All the underlying data (contigs, genes, proteins, functional annotation) with the accessions used in this analysis can be found in the proGenomes3 or SPIRE databases by searching for the genome, specI cluster, or MAG ID respectively.
• For description of the content of the individual database tables refer to the README.