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Title of supplement

A novel, non-protein-coding infection-specific gene family is clustered throughout the genome of Phytophthora infestans, by A. O. Avrova, S. C. Whisson, L. Pritchard, E. Venter, S. De Luca, I. Hein and P. R. J. Birch

Microbiology vol. 153, part 3, pp. 747&endash;759

The following are available as PDF files (Figs 2a, 3, 4 and 5; Table S1) or as JPEG files (Figs 1 and 2b).

Fig. S1. Analysis of P. infestans/potato interaction SSH using the following probes in Southern hybridizations: P.i. cDNA, P. infestans cDNA; P.i. gDNA, P. infestans genomic DNA; Binf_sub, SSH cDNA. All cDNAs used as hybridization probes were digested with RsaI and amplified with primer 1 from the Clontech PCR-Select cDNA subtraction kit following the ligation of both adaptors from the same kit. Lanes: M, 100 bp ladder (New England Biolabs); 1, uninfected potato cv Bintje (B0); 2, Bintje, 15 h post-infection (hpi) with P. infestans (B15); 3, Bintje 72 hpi with P. infestans (B72); 4, Bintje, 9 hpi with Pectobacterium atrosepticum (Ber); 5, Binf_sub.

Fig. S2a. UPGMA cluster analysis of BAC clones hybridizing to the Binf_sub probe. DNA from all BAC clones was digested with HindIII. Clusters were verified in all three instances by PCR from BAC end sequences; positive PCR amplification is marked by vertical lines, with the BAC end sequence marked on the right.

Fig. S2b. Fingerprints of 10 overlapping BAC clones (from left to right): 56N16, 66N16, 68C21, 29G21, 56A9, 65A8, 12L6, 30M17, 54K5 and 26M13 digested with HindIII, PstI and BamHI (A) and hybridized with a probe to Pinci1-1 (B). Restriction fragment sizes in kb are marked on the right.

Fig. S3. Alignment of Pinci1-1 to Pinci1-25 (accession numbers EF091715 to EF091740) cDNA sequences amplified by RT-PCR.

Fig. S4. Alignment of deduced protein sequences from ORF1 from 19 members of the Pinci1 family.

Fig. S5. Schematic diagram indicating the locations of blastn matches to Pinci1, blastn matches to unigene sequences from Randall et al. (2005) and predicted RXLR-containing ORFs on each of the 135 P. infestans draft genome supercontigs containing matches to Pinci1. Supercontigs are sorted in descending order of total length and are represented by three tracks, the topmost indicating locations of RXLR sequences (orange), the middle track representing matches to Pinci1 (full-length matches in green, 5' domain matches in red and 3' domain matches in blue), and the lower track indicating matches to unigenes (purple). Scale bars are marked at every tenth supercontig. The clustering of matches to Pinci1 sequences, and their co-location with unigenes are readily visible. The distribution of predicted RXLR sequences is also seen not to be associated with the distribution of Pinci1 matches.

Table S1. Oligonucleotide primers used in sequencing and PCR.

Reference

Randall, T. A., Dwyer, R. A., Huitema, E., Beyer, K., Cvitanich, C., Kelkar, H., Ah Fong, A., Gates, K., Roberts, S. & other authors (2005). Large-scale gene discovery in the oomycete Phytophthora infestans reveals likely components of phytopathogenicity shared with true fungi. Mol Plant Microbe Interact 18, 229-243.

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