Analysis of the NAC gene family in Triticum aestivum employing novel bioinformatics tools

A novel pipeline was created to sift through large Expressed Sequence Tag (EST) data sets of Triticum aestivum, and assemble only sequences identified as being of the NAC gene family. This approach bypassed the bottleneck of assembly of large EST data sets, enabling the full cycle of sequence quality trimming and assembly to take place on a Personal Computer (PC) in a matter of a few hours. An iterative sequencing conjoined with assembly approach was employed to fully sequence full length cDNA clones. Sequences were then reduced to a unigene set using both CAP3 assembly and MegaBLAST. A software prototype designed to find protein coding regions, particularly in EST assemblies, was built and used to automatically identify full length NAC cDNA clones for sequencing, and create NAC nucleic and amino acid sequences trimmed to the protein coding regions and conserved domains. A total of 130 NAC gene sequences were identified, 41 of which contained the entire protein coding region. Sequences containing the entire NAC conserved domain were used for conserved domain analysis, and a phylogenetic tree was built with previously identified NAC gene families in Orzya sativa, and Arabidopsis thaliana. At least one wheat NAC gene could be found in every phylogenetic group in which a rice NAC was present. Interestingly, a number of wheat NAC clusters without any definitive rice orthologs were found