PtHSP02 aligned to a single scaffold, PgtSC7. A second haplotype was not detected as the Pgt assembly represents most loci with a single sequence. Nine Pt ORFs could be aligned to homologs on PgtSC7. As with the other BAC clones, gene order was kinase inhibitor Bicalutamide generally maintained. However, PtHSP02 1 and PtHSP02 2 were found embedded between retroele ments and LTRs. While PtHSP02 1 aligned to two fragments on PgtSC7, PtHSP02 2 was 48% homologous to a gene on PgtSC15 elsewhere in the genome. The remaining genes in PtHSP02 were in the same order as on PgtSC7, except a large insertion of approximately 70 kB of DNA, including sequence similar to mobile elements, was found between PGTG 03709 and PGTG 03708 on PgtSC7. Additional PgtSC7 DNA insertions were evident within this gene cluster whereas the Pt homologs were packed in a tighter arrangement.

Across this region, a higher number of retrotransposon elements were found on PtHSP02. PtHSP04 aligned to at least six regions within the Pgt genome and represents the least syntenic sequence amongst the three BAC clones. PtHSP04 1 and 2 were found on PgtSC84, however, there were several repeat elements within both the Pt and Pgt regions. PtHSP04 3 appeared to be a fragmented ORF because a single homologous ORF was found on PgtSC35. PtHSP04 4 and 5 were found on two separate scaffolds, PgtSC4 and PgtSC48, respectively. PtHSP 6, 7, 8, and 9 have homologs on Pgt SC89 in the same order and similar gene distance. PtHSP04 10, flanked by an LTR and Harbinger element, does not have a homolog on PgtSC89, but on PgtSC13. Microsynteny of PtHSP04 11, 12, and 13 to Pgt is main tained.

PtHSP04 14 is a single copy gene in Pt but is repeated in Pgt. between BAC positions 60,000 and 125,000 there are a high number repeat elements. One of the most interesting sets of sequences were Pt ORFs for which numerous homologous copies were found in the Pgt genome but were not classified as typical mobile elements. Cilengitide Twenty of these ORFs had repeats in the Pgt genome numbering from 19 to 474. Table 2 lists the conserved amino acid domains, if present, in each of the ORFs and the percent identity, which. ranged from 34 74%. Each ORF was compared to an RNAseq cDNA library of Pt infected leaf tissue and nine aligned to the experimental cDNA sequences. The predicted proteins were analyzed for peptide content and most had an abundance of Lys, which is suggestive of helical structures. Each of the proteins was also compared to the PHYRE 2. 0 structural data base resulting in seven that revealed regions that aligned, with confidence, to known structures. The first 191 peptides of PtHSP04 j had a structure similar to RAD54, with 99. 7% confidence. Of note, PtHSP04 e was expressed and was 51% identical to a protein in Mlp.