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Table 2 NBS sequences obtained by PCR

From: TIR-NBS-LRR genes are rare in monocots: evidence from diverse monocot orders

Species Number of fragments successfully cloned and sequenced by primer specificity Number of fragments that resulted in TIR vs. non-TIR NBS sequences Number of unique NBS sequences obtained
  TIR primers Non-TIR primers General primers TIR Non-TIR  
Carex blanda 11 5 8 0 3 5
Cycas revoluta 3 1 2 3 0 1
Dracaena marginata 2 1 5 0 3 3
Sansevieria trifasciata 8 1 1 0 2 2
Spathiphyllum sp. 1 1 4 0 4 9
Coffea canephora 2 0 4 1 3 4
*Arabidopsis thaliana 5 0 2 3 0 3
Total (excluding A. thaliana) 27 9 24 4 15 24
  1. For each species tested, the table shows the number of fragments successfully cloned and sequenced for each type of primer set, the number of these fragments that produced TIR and non-TIR sequences, and the number of unique NBS sequences found. Based on previous work, we expected PCR products of approximately 700-900 base pairs [8, 9]. In general, we cloned fragments of approximately 600-1000 bp, but we also cloned some fragments as small as 300 bp and as large as 1.5 kb to allow for the possibility that the NBS domain of TIR-type sequences in monocots differs significantly from those observed previously. At least five fragments smaller than expected and five larger than expected were cloned and sequenced, none of which contained identifiable NBS sequence. We cloned a total of 62 fragments and successfully obtained 105 sequences from 60 of those fragments. The BLASTP algorithm was used to compare the translations to the Genbank non-redundant database. A conserved domain search identified 30 sequences from 19 fragments that showed homology to an NB-ARC domain. We excluded six sequences that did not contain an open reading frame, were redundant, or were fragments identical to longer sequences, resulting in a total of 24 unique sequences.
  2. * A. thaliana was used only to confirm that TIR-specific primers would amplify TIR-type NBS sequences. No non-TIR fragments were cloned from A. thaliana. The table only shows A. thaliana sequences obtained that included an open-reading frame from 5' to 3' primer. Additional sequences obtained that included introns were not included in the table.