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We collected 175 maize transcripts with NAC domains.
Maize transcripts with expression patterns matching a model with a PCC value of 0.7 or greater were considered to have a circadian rhythm.
Transcripts represented on the Affymetrix GeneChip® Maize array were mapped to maize transcripts with a custom Perl script that used the DNA sequences provided by Affymetrix and BLASTn to query the ZmB73 4.53a filtered CDS sequences [ 31].
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We estimate that 5.67% (86,069 sequences) do not align with public ESTs or annotated genes, potentially representing new maize transcripts.
We estimate that 5.67% (86,069 sequences) do not align with public ESTs or annotated genes and potentially represent new maize transcripts.
Due to the limited functional annotation currently available for maize transcripts, functional classification of differentially expressed transcripts was carried out using the MapMan hierarchical ontology software [30] and BioMaps at the Virtual-Plant site (www.virtual plant.org) as described in Materials and Methods with similar results.
The identification of maize transcripts was done in the maize transcriptome database available in our laboratory.
However, nucleotide compositions of the nrFLcDNA was more AT-rich than those of maize transcripts [ 27].
To determine whether the maize circadian transcriptome was similarly organized, the cycling maize transcripts were sorted into six phase bins based on expression waveform.
The Palomero sequences covered over 50% of all reported maize unigenes, and an estimated of 5.67% of the reads potentially represent new maize transcripts.
In their analysis of the maize shoot apical meristem, Emrich and colleagues [ 16] discovered 261,000 ESTs, annotated more than 25,000 maize genomic sequences, and identified ~400 maize transcripts for which homologs have not been identified in any other species.
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