A plastome primer set for comprehensive quantitative real time RT-PCR analysis of Zea mays: a starter primer set for other Poaceae species

Additional File 1:

q2(RT)PCR primer pairs with their corresponding genes, category, and optimal elongation time, and annealing temperatures. All primers were initially designed to produce amplicons between 75 and 150 base pairs from specific maize RNAs. Primer pair "category" is based on the specificity of the reaction conditions required to produce a single amplicon. Category 1 pairs produce a single product within a range of conditions, category 2 pairs require more stringent annealing or elongation times, and category 3 are genes with intercellular homologs (see text for full descriptions).

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Additional File 2:

in silico comparison of maize primers to other plastome sequences. Primer sequences were compared to representative plastomes from the BEP and PACCAD clades, as well as Arabidopsis. Success was gauged by overall percent homology and the presence of mismatched bases at the 3' end of the primers. These data are summarized in Figure 3.

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