Conserved loci of leaf and stem rust fungi of wheat share synteny interrupted by lineage-specific influx of repeat elements

Table 2 Detailed analysis of non-transposable element, repeated sequences in three P. triticina BAC clones

ORF	Size bp	*Pgt* repeats	Conserved domain	% Ident	Exp*	Dominant peptide	Notes
1F16-a	757	35	194-443	51	no	9.2% Lys	216-252-40.3% CI Winged helix DNA/RNA binding
1F16-b	458	98	97-458	40	no	11.8% Lys	Highly helical
1F16-c	462	98	all	40	no	13.2% Lys	6-91-60.3% CI ubiquitin ligase
1F-16-d	489	44	344-485	48	no	10.8% Lys	3 alpha helices and 7 beta sheets in conserved domain
						13.0% Ser
1F16-f	651	80	51-245	74	yes	9.2% Lys	38-163-38.7% CI oxidoreductase
HSP02-a	658	19	all	31	no	9.7% Lys
HSP02-b	299	80	35-94	68	no	9.4% Lys	32-73-80% CI metal binding protein
						11.7% Ser	145-256-80% CI protease hydrolase inhibitor
HSP02-c	252	50	33-127	52	yes	11.1% Lys	33-95 53% CI DNA binding domain
						10.7% Glu
HSP02	243	35	all		yes	11.9% Ala	Alignment in Pgt are to DNA, not protein
						13.6% Ser
						11.5% Thr
HSP04-a	952	74	256-470	48	no	9.9% Ala
HSP04-b	484	76	300-454	74	no	none
HSP04-c	442	69	all	34	yes	9.0% Lys
HSP04-d	679	81	10-351	68	no	9.3% Lys	11 alpha helices in conserved region
HSP04-e	420	131	55-386	55	yes	9.5% ala	216-388-51% identical in Mlp
HSP04-f	262	474	20-189	44	no	11.5% ser	EST sequence hits
HSP04-g	543	96	all	69	yes	11.4% Lys	Highly helical
						9.0% ser
HSP04-h	262	66	199-258	65	yes	12.6% Lys	P-loop NTPase/DEAD box
HSP04-i	326	20	127-242	34	yes	12.8% Lys	Highly helical
						11.0% Glu
HSP04-j	309	69	191-303	35	no	9.7% Lys	2-191-99.7% CI Recombinant DNA binding/ RAD54 like
						10.7% Ser

Each was evaluated for number of repeated homologs in the Pgt genome, region of conservation, alignment identity, expression in infected tissue, the dominant peptides, and their best detected fit to a protein structural model.
* Exp - expression in infected tissue 6 dpi.
** PHYRE 2.0 confidence interval (CI) of protein segment matching a structural model with the listed function [35].

ISSN: 1471-2164