Editing Plasmid (section)

=== Plasmid collections ===
Many plasmids have been created over the years and researchers have given out plasmids to plasmid databases such as the non-profit organisations [https://www.addgene.org Addgene] and [https://bccm.belspo.be/about-GeneCorner BCCM/GeneCorner]. One can find and request plasmids from those databases for research.
Researchers also often upload plasmid sequences to the [https://www.ncbi.nlm.nih.gov/nuccore/ NCBI database], from which sequences of specific plasmids can be retrieved. There have been multiple efforts to create curated and quality controlled databases from these uploaded sequences; an early example is by Orlek ''et al'',<ref>{{cite journal |last1=Orlek |first1=Alex |last2=Phan |first2=Hang |last3=Sheppard |first3=Anna E. |last4=Doumith |first4=Michel |last5=Ellington |first5=Matthew |last6=Peto |first6=Tim |last7=Crook |first7=Derrick |last8=Walker |first8=A. Sarah |last9=Woodford |first9=Neil |last10=Anjum |first10=Muna F. |last11=Stoesser |first11=Nicole |title=A curated dataset of complete Enterobacteriaceae plasmids compiled from the NCBI nucleotide database |journal=Data in Brief |date=June 2017 |volume=12 |pages=423–426 |doi=10.1016/j.dib.2017.04.024 |pmc=5426034 |pmid=28516137 |bibcode=2017DIB....12..423O }}</ref> which limited itself to ''[[Enterobacteriaceae]]'' plasmids, while COMPASS also encompassed plasmids from other bacteria. More recently, PLSDB<ref>{{cite journal |last1=Schmartz |first1=Georges P |last2=Hartung |first2=Anna |last3=Hirsch |first3=Pascal |last4=Kern |first4=Fabian |last5=Fehlmann |first5=Tobias |last6=Müller |first6=Rolf |last7=Keller |first7=Andreas |title=PLSDB: advancing a comprehensive database of bacterial plasmids |journal=Nucleic Acids Research |date=7 January 2022 |volume=50 |issue=D1 |pages=D273–D278 |doi=10.1093/nar/gkab1111 |pmc=8728149 |pmid=34850116 }}</ref> was made as a more up to date curated database of NCBI plasmids, and as of 2024 contains over 72,000 entries.<ref>{{cite journal |last1=Molano |first1=Leidy-Alejandra G |last2=Hirsch |first2=Pascal |last3=Hannig |first3=Matthias |last4=Müller |first4=Rolf |last5=Keller |first5=Andreas |title=The PLSDB 2025 update: enhanced annotations and improved functionality for comprehensive plasmid research |journal=Nucleic Acids Research |date=6 January 2025 |volume=53 |issue=D1 |pages=D189–D196 |doi=10.1093/nar/gkae1095 |pmc=11701622 |pmid=39565221 }}</ref> A similar database is pATLAS, which additionally includes visual analytics tools to show relationships between plasmids.<ref>{{cite journal |last1=Jesus |first1=Tiago F |last2=Ribeiro-Gonçalves |first2=Bruno |last3=Silva |first3=Diogo N |last4=Bortolaia |first4=Valeria |last5=Ramirez |first5=Mário |last6=Carriço |first6=João A |title=Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data |journal=Nucleic Acids Research |date=8 January 2019 |volume=47 |issue=D1 |pages=D188–D194 |doi=10.1093/nar/gky1073 |pmc=6323984 |pmid=30395323 }}</ref> The largest plasmid database made from publicly available data is IMG/PR, which not only contains full plasmid sequences retrieved from NCBI, but novel plasmid genomes found from [[Metagenomics|metagenomes]] and metatranscriptomes.<ref>{{cite journal |last1=Camargo |first1=Antonio Pedro |last2=Call |first2=Lee |last3=Roux |first3=Simon |last4=Nayfach |first4=Stephen |last5=Huntemann |first5=Marcel |last6=Palaniappan |first6=Krishnaveni |last7=Ratner |first7=Anna |last8=Chu |first8=Ken |last9=Mukherjeep |first9=Supratim |last10=Reddy |first10=T B K |last11=Chen |first11=I-Min A |last12=Ivanova |first12=Natalia N |last13=Eloe-Fadrosh |first13=Emiley A |last14=Woyke |first14=Tanja |last15=Baltrus |first15=David A |last16=Castañeda-Barba |first16=Salvador |last17=de la Cruz |first17=Fernando |last18=Funnell |first18=Barbara E |last19=Hall |first19=James P J |last20=Mukhopadhyay |first20=Aindrila |last21=Rocha |first21=Eduardo P C |last22=Stalder |first22=Thibault |last23=Top |first23=Eva |last24=Kyrpides |first24=Nikos C |title=IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata |journal=Nucleic Acids Research |date=5 January 2024 |volume=52 |issue=D1 |pages=D164–D173 |doi=10.1093/nar/gkad964 |pmc=10767988 |pmid=37930866 }}</ref>

Other datasets have been created by sequencing and computing plasmid genomes from pre-existing bacterial collections, e.g. the NORM collection<ref>{{Cite journal |last1=Gladstone |first1=Rebecca A. |last2=McNally |first2=Alan |last3=Pöntinen |first3=Anna K. |last4=Tonkin-Hill |first4=Gerry |last5=Lees |first5=John A. |last6=Skytén |first6=Kusti |last7=Cléon |first7=François |last8=Christensen |first8=Martin O. K. |last9=Haldorsen |first9=Bjørg C. |last10=Bye |first10=Kristina K. |last11=Gammelsrud |first11=Karianne W. |last12=Hjetland |first12=Reidar |last13=Kümmel |first13=Angela |last14=Larsen |first14=Hege E. |last15=Lindemann |first15=Paul Christoffer |date=2021-07-01 |title=Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002–17: a nationwide, longitudinal, microbial population genomic study |journal=The Lancet Microbe |language=English |volume=2 |issue=7 |pages=e331–e341 |doi=10.1016/S2666-5247(21)00031-8 |pmc=7614948 |pmid=35544167}}</ref><ref>{{cite report |type=Preprint |doi=10.1101/2023.10.14.562336 |title=Plasmid-driven strategies for clone success in ''Escherichia coli'' |date=2024 |last1=Arredondo-Alonso |first1=Sergio |last2=Pöntinen |first2=Anna K. |last3=Gama |first3=João Alves |last4=Gladstone |first4=Rebecca A. |last5=Harms |first5=Klaus |last6=Tonkin-Hill |first6=Gerry |last7=Thorpe |first7=Harry A. |last8=Simonsen |first8=Gunnar S. |last9=Samuelsen |first9=Ørjan |last10=Johnsen |first10=Pål J. |last11=Corander |first11=Jukka }}</ref> and the Murray Collection.<ref>{{cite journal |last1=Baker |first1=Kate S. |last2=Burnett |first2=Edward |last3=McGregor |first3=Hannah |last4=Deheer-Graham |first4=Ana |last5=Boinett |first5=Christine |last6=Langridge |first6=Gemma C. |last7=Wailan |first7=Alexander M. |last8=Cain |first8=Amy K. |last9=Thomson |first9=Nicholas R. |last10=Russell |first10=Julie E. |last11=Parkhill |first11=Julian |title=The Murray collection of pre-antibiotic era Enterobacteriacae: a unique research resource |journal=Genome Medicine |date=December 2015 |volume=7 |issue=1 |page=97 |doi=10.1186/s13073-015-0222-7 |doi-broken-date=10 March 2025 |doi-access=free |pmc=4584482 |pmid=26411565 }}</ref><ref>{{cite report |type=Preprint |doi=10.1101/2024.09.03.610986 |title=Pre and Post antibiotic epoch: Insights into the historical spread of antimicrobial resistance |date=2024 |last1=Cazares |first1=Adrian |last2=Figueroa |first2=Wendy |last3=Cazares |first3=Daniel |last4=Lima |first4=Leandro |last5=Turnbull |first5=Jake D. |last6=McGregor |first6=Hannah |last7=Dicks |first7=Jo |last8=Alexander |first8=Sarah |last9=Iqbal |first9=Zamin |last10=Thomson |first10=Nicholas R. }}</ref>