A novel non-protein-coding infection-specific gene family is clustered throughout the genome of Phytophthora infestans

Plant Pathology Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK Correspondence Paul R. J. Birch pbirch{at}scri.sari.ac.uk Phytophthora infestans is the cause of late blight, a devastating and re-emerging disease of potato. Significant advances have been made in understanding the biology of P. infestans , and in the development of molecular tools to study this oomycete. Nevertheless, little is known about the molecular bases of the establishment or development of disease in this hemibiotrophic pathogen. Suppression subtractive hybridization (SSH) was used to generate cDNA enriched for sequences upregulated during potato infection. To identify pathogen-derived cDNAs, and eliminate host sequences from further study, SSH cDNA was hybridized to a P. infestans bacterial artificial chromosome library. A new gene family was identified called Pinci 1, comprising more than 400 members arranged in clusters of up to nine copies throughout the P. infestans draft genome sequence. Real-time RT-PCR was used to quantify the expression of five classes of transcript within the family, relative to the constitutively expressed Piact A gene, and it revealed them to be significantly upregulated from 12 to 33 h post-inoculation, a period defining the biotrophic phase of infection. Computational analysis of sequences suggested that transcripts were non-protein coding, and this was confirmed by transient expression of FLAG-tagged ORFs in P. infestans . Abbreviations: BAC, bacterial artificial chromosome; hpi, h post-inoculation; HSP, high-scoring pair; LCR, locus control region; miRNA, microRNA; ncRNA, non-coding RNA; SSH, suppression subtractive hybridization The GenBank/EMBL/DDBJ accession numbers for the sequences reported in this paper are EF091715–EF091740. Supplementary Figs S1–S5 and Table S1 are available with the online version of this paper. Present address: Department of Botany and Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park, South Africa.