, !These!elements!may!lack!a!few!components!of!an!active! conjugation!system,!but!still!be!regarded!as!valid!systems!by!CONJscan!because!they!fit!the! minimal!conditions!of!the!model.!Degenerate!elements!may!also!complicate!the! identification!of!the!ICEs!because!the!gene!families!of!the!element!are!present!at!different! 420! frequencies!in!the!pan:genome.!It!is!difficult!to!distinguish!mildly!degenerate!elements!from! atypical!functional!ones!, Mobile!genetic!elements!may!endure!inactivating!mutations!:!including!large!deletions:!that! result!in!degenerate!elements

, Intermingled!components!of!conjugative!elements!can!occur!in!a!number!of!cases

, !leading!to!a!series!of! 425! components!from!different!MPFs!and!thus!to!an!apparent!intermingled!set!of!conjugative! elements.!Some!cases!of!true!intermingled!elements!occur!when!an!element!integrates! inside!another!element.!These!cases!may!be!hard!to!disentangle!without!experimental! evidence, MPF!types!are!close!and!their!protein!profiles!cross:match

, !If!the!MGE!of!interest! has!many!such!elements!after!annotation!with!standard!tools!(generic!tools!like!Prokka)! then!specific!curation!may!be!necessary,!e.g.,!by!using!broader!databases!of!protein!profiles! like!EggNOG!or!using!iterative!searches!with!PSI:BLAST!or!jackhmmer!(Table!2).!It!is!not! unusual!that!several!genes!remain!of!unknown!function!after!all!these!analyses, Many!genes!in!mobile!genetic!elements!have!their!function!unknown

, This!work!was!supported!by!the!ANR!MAGISBAC!project,!the!CNRS!and!the!Institut!Pasteur

!. Fernando, . Cruz, !. Chris, . Smillie, . Marie!touchon et al., We!thank!the!collaborators!who!have!worked!with!us!on!this!topic!in!the!last!decade

!. !grohmann, !. Muth, and !. Espinosa!m!, Conjugative!plasmid!transfer!in!gram:positive! bacteria, !Microbiol!Mol!Biol!Rev!, vol.67, p.301, 2003.

!. Smillie, !. Pilar!garcillan, ;. Barcia, !. Victoria, !. Francia et al., ! Mobility!of!Plasmids.!Microbiol!Mol!Biol!Rev!, vol.74, 2010.

!. Cruz, !. Frost, . Ls, !. Meyer, !. Rj et al., The!diversity!of!conjugative!relaxases! and!its!application!in!plasmid!classification, !FEMS!Microbiol!Rev!, vol.34, p.687, 2009.

!. Guglielmini, !. Cruz, !. , !. Rocha, and !. Epc!, Evolution!of!Conjugation!and!Type!IV! 450! Secretion!Systems, !Mol!Biol!Evol!, vol.30, 2013.

!. Abby, !. Ss, !. Neron, !. Menager, !. Touchon et al., MacSyFinder:!A!Program!to! Mine!Genomes!for!Molecular!Systems!with!an!Application!to!CRISPR:Cas!Systems, PLoS!One!, vol.9, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01080418

!. Guglielmini, !. Neron, !. Abby, !. Ss, !. Garcillan et al., Key! 455! components!of!the!eight!classes!of!type!IV!secretion!systems!involved!in!bacterial! conjugation!or!protein!secretion, !Nucleic!Acids!Res!, vol.42, p.5727, 2014.

!. Abby, !. Ss, !. Cury, !. Guglielmini, !. Neron et al., !Identification!of! protein!secretion!systems!in!bacterial!genomes, !Sci!Rep!, vol.6, p.23080, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01677379

!. Coluzzi, !. Guedon, !. Devignes, !. Md, !. Ambroset et al., A!Glimpse!into!the!World!of!Integrative!and!Mobilizable!Elements!in! Streptococci!Reveals!an!Unexpected!Diversity!and!Novel!Families!of!Mobilization!Proteins, ! Front!Microbiol!, vol.8, p.443, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01580789

!. Camacho, !. Coulouris, !. Avagyan, !. Ma, !. Papadopoulos et al., !Parallelization!of!the!MAFFT!multiple!sequence!alignment! program, BLAST+:!architecture!and!applications.!BMC!Bioinformatics!10:421.! 465! 11.!Eddy!SR!(2011)!Accelerated!Profile!HMM!Searches, vol.7, 1899.

!. Gouy, !. Guindon, !. , !. Gascuel, !. O!-;-!miele et al., SeaView!version!4:!A!multiplatform!graphical!user! interface!for!sequence!alignment!and!phylogenetic!tree!building, !BMC!Bioinformatics, vol.27, p.116, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511794

!. Edgar and !. Rc!, Search!and!clustering!orders!of!magnitude!faster!than!BLAST, ! Bioinformatics!, vol.26, 2010.

!. White, !. Ep, !. Baldridge, !. Brym, . Zt et al., Nine!simple!ways! 475! to!make!it!easier!to!(re)!use!your!data, !Ideas!in!Ecology!and!Evolution!, vol.6, issue.1, p.10, 2013.

!. Keane, . Ja, and !. Parkhill, Roary:!rapid!large:scale!prokaryote!pan!genome!analysis, ! Bioinformatics!, vol.31, 2015.

!. Seemann, !. Bellanger, !. Morel, !. Gonot, !. Puymege et al., Site:specific! accretion!of!an!integrative!conjugative!element!together!with!a!related!genomic!island!leads! to!cis!mobilization!and!gene!capture, Prokka:!rapid!prokaryotic!genome!annotation.!Bioinformatics! 480! 30:2068:2069.! 19, vol.81, 2009.

!. Thomas, !. Bc, !. Banfield, !. Jf!-;-!abby, !. Ss et al., Identification!of!Protein!Secretion!Systems!in!Bacterial! 490! Genomes!Using!MacSyFinder.!In:!Cascales!E!(ed)!Bacterial!protein!secretion!systems, ! Methods!in!Molecular!Biology, 2016.

!. Database,

, IntegronFinder! Integrons! Detects!integrons!in!genomes!

. Rfam!-rna!-database!of!covariance, Models!to!find! many!types!of!RNA! http://rfam.xfam.org/! Infernal! RNA! Searches!for!RNAs!using!covariance!models,! notably!for!RFAM

, Clustering!method!to!build!protein!families! from!"blast!all!against!all, SiLiX: .html?lang=en! Prokka! Annotation! Rapid!annotation!of!bacterial!genomes

, Database!of!antibiotic!resistance!genes!

!. Victors!-virulence!factor!-database and . Virulent,