Comparative serial analysis of gene expression of transcript profiles of tomato roots infected with cyst nematode

We analyzed global transcripts for tomato roots infected with the cyst nematode Globodera rostochiensis using serial analysis of gene expression (SAGE). SAGE libraries were made from nematode-infected roots and uninfected roots at 14 days after inoculation, and the clones including SAGE tags were sequenced. Genes were identified by matching the SAGE tags to tomato expressed sequence tags and cDNA databases. We then compiled a list of numerous genes according to the mRNA levels that were altered after cyst nematode infection. Our SAGE results showed significant changes in expression of many unreported genes involved in nematode infection. Of these, for discussion we selected five SAGE tags of RSI-1, BURP domain-containing protein, hexose transporter, P-rich protein, and PHAP2A that were activated by cyst nematode infection. Over 20% of the tags that were upregulated in the infected root have unknown functions (non-annotated), suggesting that we can obtain information on previously unreported and uncharacterized genes by SAGE. We can also obtain information on previously reported genes involved in nematode infection (e.g., multicystatin, peroxidase, catalase, pectin esterase, and S-adenosylmethionine transferase). To evaluate the validity of our SAGE results, seven genes were further analyzed by semiquantitative reverse transcriptase-polymerase chain reaction and Northern blot hybridization; the results agreed well with the SAGE data.