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383 lab 3 intro

Submitted by liamharvey on Sun, 04/22/2018 - 15:30

Using the gene sequence from Sanger sequencing, we compared our gene sequence with several related species. Five species were used, including B. distachyon, and well explored genomes such as O. sativa, which like B. distachyon is a grass species. We also compared our gene with the eudicots A. thaliana and S. lycopersicum.  A. thaliana’s genome is very well studied, and its genes are closely related to B. distahcyon’s. A. trichopoda is considered a sister of flowering plants and was also used. Once again, we used NCBI to align these species; a PSI-BLAST compared our genes amino acid sequence with genes in these five species.  We then used a program called MAFFTA. We took the PSI-BLAST results and used the MAFFTA software to create a phylogenetic tree of our gene and related genes from those five species.  Here we could explore our genes evolutionary relationship with similar species’ genes and using closely related genes, find further clues about our genes function. Finally, we will use two histochemical stains, T-blue and Ph-HCL to observe the polysaccharide and lignin content of our mutant and wildtype stems. We will select regions of the stem which have been predicted to be of high expression in our gene of interest to find if the mutant histology differs from that of wild type.