Nomenclature of Gateway construct elements
The following abbreviations were chosen to name the different elements in the constructs.
- attR1, CmR, ccdB, attR2 orientation = m12GW or GW
- attR2, ccdB, CmR, attR1 orientation = m21GW or WG
- attR4, CmR, ccdB, attR2 orientation = m42GW
- attR2, ccdB, CmR, attR4 orientation = m24GW
- attR4, ccdB, CmR, attR3 orientation = m43GW
- attR3, CmR, ccdB, attR4 orientation = m34GW
- attR5, ccdB, CmR, attR6 orientation = m56GW
- attR6, CmR, ccdB, attR5 orientation = m65GW
The orientation of the cassette indicated by the order of the att sites is relative to the T-DNA left border when it is part of the vector.
Plasmids and plant selectable markers
- Plasmid (binary, high copy)= p
- Entry clones = pEN
- Donor vector = pDONR
- Modular vector = pM
- Expression clone = pX
- pNOS-KANR-tNOS = K
- pNOS-HYGR-tNOS = H
- pNOS-BASTAR-tNOS = B
Reporter genes and reporter expression units
- GUS =S
- Enhanced GFP = F
- Enhanced CFP = C
- Enhanced YPF = Y
- DsRed = R
- Luciferase = L
- Luciferase+ = L+
- GFP-GUS fusion = FS
- pROLD-GFP-t35S = D
- pNOS = 1
- p35S = 2
- pROLD = 3
- CsVMV = 4
- tNOS = 6
- t35S = 7
- tOCS = 8
- tG7 = 9
Other miscellaneous elements
- NLS signal = N
- ER signal = ER
- Stop codon = *
- Intron = I
Note that, in a binary T-DNA vector, the element's order is indicated relative to the left border.
Convention for entry clone names
The names of all entry clone are structured in the same way: the letters "pEN" are followed by the letter and number L4, L1 or R2 indicating which att site is placed at 5' end of the corresponding genetic element, the abbreviation of the element as listed above, and the letter and number R1, L2 or L3 indicating which att site is placed at its 3' end. For clarity, name parts are separated by hyphens.
Convention for MultiSite expression clone names
The name of expression clones created in a MultiSite LR clonase reaction starts with the letters "pX" followed by the letter K, H or B, indicating whether the plant selectable marker in the binary vector T-DNA codes for kanamycin, hygromycin or Basta resistance, respectively, then a succession of letters and numbers describing the newly assembled expression unit according to the element abbreviations listed in Table 1, and listed according to their order relative to the T-DNA left border.
Convention for modular destination vector names
The name of modular destination vectors created via reverse BP clonase reaction from an expression clone starts with the letters "pM" followed by the letter K, H or B, then the letters and numbers describing the expression unit (see above). The newly inserted ccdB cassette that replaced one or more of the elements in the original expression clone is specified by the letter "m" (for MultiSite), two numbers (1 and 2, or 3 and 4) indicating its flanking att sites, followed by the letters GW (short for Gateway), listed according to their order relative to the T-DNA left border.
Construct version number
The sequences of some vectors may be corrected or improved over time. The number placed after the coma at the end of a vector's name,tracks its successive versions: the initial version is numbered "0" (e.g. pJCGLOX,0), the second version "1" (e.g. pJCGLOX,1) and so on. For brevity's sake, the comma and version number are omitted when referring in general to a particular vector with a specific functionality (e.g. pJCGLOX).