Plasmid Nomenclature in Officinae Bio

A guide to plasmid nomenclature in Officinae Bio based on the Standard European Vector Architecture (SEVA) standard.

Plasmid Nom Map

The SEVA format comprises a set of guidelines for physically assembling the three essential components of plasmid vectors - the origin of replication, selection marker, and the business cargo. In addition to the standard layout of constructs, the SEVA format mandates a specific nomenclature for designating each vector. The nomenclature follows a code that is explained in detail below.

All vectors must be designated with the prefix "pSEVA" followed by a four-digit code. The first digit indicates the antibiotic resistance marker, the second indicates the origin of replication, and the third represents the cargo module. In cases where multiple variants of the same cargo type exist, a capital letter is added to the numeral. The fourth digit is reserved for gadgets, which are designated by lowercase Greek letters.


List of SEVA modules and codes


Position 1: Antibiotic Resistance Marker

This module includes the structural gene for the antibiotic of choice with its own native promoter.
Marker code
Ap 1
K 2
Cm 3
Sm/Sp 4
Tet 5
Gm 6
Tmp 7
Apra 8
Km_G+ 2a
CG_G+ 3a

Position 2: Origin of Replication

This module comprises the oriV sequence and the replication proteins

ORI Cipher
R6K 1
RK2 2
pBBR1 3
pRO1600/ColE1  4
RSF1010 5
p15A 6
pSC101 7
pUC 8
pBR322-ROP  9
RK2-int-phiC31  2a
RK2-SCP2*  2b
pIJ101-RK2  2c
pSM19035-RK2 2d
pBBR1-int-phiC31  3a
pBBR1-SCP2*  3b
pUC-int-phiC31  8a
pUC-SCP2*  8b
pIJ101-pUC  8c


Position 3: Cargo

This DNA portion confers functionality to the vectors. 

Cargo Code Cargo Code
Cloning Multifunction
MCS 1 XylS-Pm —> I-Scel 8S
LacZalpha-pUC19  2 PEM7 —> I-SceI 13S
LacZalpha-pUC19-ISceI 2S PEM7 —> GFP 13G
LacZalpha-pUC18  3

PEM7 —> mCherry

LacZalpha-pUC18-IIs sites up 3X PPEM7 —> mTurquoise2 13T
LacZalpha-pUC18-IIs sites down  3Y XylS-Pm —> msfGFP 8M
Promoter - Probe LacIq-Ptrc —> GFP 4G
LacZ  5 AlkS-PalkB —> msfGFP 9M
LacZ  5T ChnR-PchnB —> msfGFP  11M
Lux 6 XylS-Pm —> msfGFP-Nt 8MN
GFP 7 XylS-Pm —> msfGFP-Ct 8MC
CFP 7C T7 —> msfGFP 25M
YFP 7Y PEM7 —> PHP 13P
DsRed2 7D Modular Cloning
mCherry 7R Golden Standard 19
msfGFP 7m Metagenomics
EcFbFP 7F cos-T7-ccdB-T3 15
mECFP 7B CRISPR array 16
Expression System
LacIq-Ptrc  4 PLiar_53 17
LacIq-Ptac 4R PLiar_15  17A
4E PLiar_17 17B
4F PLiar_51 17C
LacIq-Ptrc standard 4C PLiar_53 17D
XylS-Pm 8 PLiar_1 17E
AlkS-Palk  9 RhaRS-Prham 18
AraC-PBAD 10 PD_E20(T5 20
ChnR-PchnB  11 PLacIq 21
CprK1-PDB3  12 PR 21
PEM7 13 PRM 23
cI857-PL 14 PA1/04/03 24
    T7 25


Position 4: Gadget

A gadget is a dispensable DNA sequence that confers a new utility/property to the basic frame of the backbone plasmid.

CEN6-ARS209-URA3 beta



Deriving the Nomenclature


AntiBiotic Marker / Origin of Replications Cargo Gadget
# 1-9 9 Single Modules 1 -n Monofunction --
# >9 9A  
# <9 2A Doubles or Variants 8 M Variants or Multifunction
# >9 9AB 8MC


The table provides an outline of the expanded regulations for naming each of the four positions involved in creating a complete SEVA code. The first position indicates the antibiotic resistance, while the second position represents the origin of replication, which is identified by a single numeric code ranging from 1 to 9. If there are any variants or additions to either the antibiotic marker or a second replication origin, a lowercase letter is added next. The third position is for the cargo, which can be either mono-functional (designated by a number from 1 to n) or a variant/multi-functional thereof (designated by a number followed by a capital letter). Finally, the fourth position is reserved for gadgets, which are labeled with lowercase Greek letters ranging from α to ω.

For example, the code pSEVA237M signifies a plasmid for kanamycin (KmR) seletion and has a replication origin of pBBR1, with a mono-functional cargo of promoterless msfGFP reporter. Another example is pSEVA2313R, which indicates a KmR plasmid with a pBBR1 origin of replication and a bi-functional cargo of PEM7–>mCherry. Lastly, pSEVA2a2b8Rα means a KmR plasmid that can be selected in Gram-positive hosts, featuring a double RK2-SCP2* replication origin, a bi-functional cargo of xylS-Pm–> mCherry, and a gadget of hok-sok.