TABLE CONTENTS

Novel Approaches to Analyze Gene Expression during Pathogenesis: The
Second Generation Comes of Age
Schaff, J.E. (1), N. Deighton (1), D. Bird (2) & C.H. Opperman (2)
(1) Genomic Sciences Laboratory, NC State University, Raleigh, NC 27606; (2) Centre for the Biology of
Nematode Parasitism, NC State University, Raleigh, NC, 27606
Rapid advances in genomic technologies and our ability to analyze and interpret the data are
revolutionizing detailed studies of parasitic nematodes. There are at least 10 whole genome
sequencing projects currently ongoing, and countless laboratories are performing expression
analysis. Metabolomic and proteomic approaches can be applied to these systems as well, and
this combination provides a powerful platform for cell biology. Also during this period, a
number of key host species have been/are being sequenced. Recently, we completed a
comprehensive transcriptional analysis of the tomato-root-knot nematode parasitic interaction
using microarray approaches. We performed these studies on both the susceptible and
resistant interactions. In the susceptible interactions, large suites of genes had altered
expression patterns over time, mostly up-regulated. In some cases, however, specific genes or
groups of genes were substantially repressed, suggesting a role in the alteration of the normal
plant developmental patterns. In the resistant response, many typical resistance response
genes were activated, but the data also revealed a role for a glycosyltransferase in the
response to nematodes. Although conditioned by the classical R-gene Mi, resistance to
nematodes appears to be manifested slightly differently than to other pathogens. New secondgeneration
DNA sequencers, such as the Roche 454 FLX platform and the Solexa platforms,
have revolutionized our abilities to both sequence and perform transcriptional analysis. These
platforms enable extremely high-throughput analyses at a fraction of the cost of the first
generation technologies, and in a much shorter time-period. We have begun applying these
approaches at the Genomic Sciences Laboratory at NC State, to great success. These new
technologies promise to rapidly expand our abilities to analyze many host nematode
interactions. With the advent of fully sequenced reference genomes, it becomes possible to
perform 2X skims of related parasite genomes, and to assemble these.
5 th International Congress of Nematology, 2008 147