Pinus rbcL Primers

rbcL primers that work in Pinus

  Primer name sequence 5prime to 3prime length Position in
Pinus thunbergii		 Reference  
  atpB45359 gct aca gct cta acc tta tga ttt cc 26 45359 Gernandt unpublished  
  atpBrbcL44777 tct ctt ctc ttc ata cgc aca tc 23 44777 Gernandt unpublished  
  atpBrbcL44652 gca acc caa tct ttg ctc tt 20 44652 Gernandt unpublished  
  rbcL1a atg tca cca caa aca gar act aaa gc 26 44448 Olmstead et al. 1992  
  rbcL44369 ctc gga atg ctg cca aga ta 20 44369 Gernandt unpublished  
  rbcL3F acc caa ttt tgg ttt gat ag 20 43937 Wang et al. 1999  
  rbcL43856 gca tga atg gtt ggg aat tt 20 43856 Gernandt unpublished  
  rbcL2F gga cat acg caa tgc ttt ag 20 43511 Wang et al. 1999  
  rbcL1F cag cag cta gtt cag gac tc 20 43102 Wang et al. 1999  
  rbcL1R aca atg gcc tac ttc ttc ac 20 43598 Wang et al. 1999  
  rbcL2R ccc tgc tta ttc caa aac tt 20 44032 Wang et al. 1999  
  rbcL3R atg tca cca aaa aca gag act 21 44453 Wang et al. 1999  
  rbcL12 ctt tta gta aaa gat tgg gcc gag 24 43017 Olmstead et al. 1992  
  rbcL42977 cca tat ctc cgc tca cga tt 20 42977 Gernandt et al. 2003  

rbcL is coded on the antisense strand; Wang et al. (1999) use "F" and "R" to refer to the positive strand rather than the rbcL open reading frame.

We are currently amplifing the atpB-rbcL spacer and rbcL in three separate reactions 1) atpB45359 & rbcL44369 (often difficult because of a poly A/T run near atpB; when we have trouble, we amplify atpBrbcL44777 & rbcL44369 separately from atpB45359 & atpBrbcL44652 ) 2) rbcL3R & rbcL2F (942 bp), and 3) rbcL2R & rbcL42977 (1055 bp).

Primer mismatches in Pinaceae are known. Two primers (rbcL1R and rbcL2R) even have mismatches in pines. The atpBrbcL primers probably do not work in most Pinaceae nor in other families.

© 2012 DS Gernandt