<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>Hybridization of labelled cDNA from various cell types with high-density arrays of expressed sequence tags is a powerful technique for investigating gene expression. Few
conifer cDNA libraries have been sequenced. Because of the high level of sequence
conservation between <italic>Pinus</italic> and <italic>Picea</italic> we have investigated the use of arrays from
one genus for studies of gene expression in the other. The partial cDNAs from 384
identifiable genes expressed in differentiating xylem of <italic>Pinus taeda</italic> were printed on
nylon membranes in randomized replicates. These were hybridized with labelled
cDNA from needles or embryogenic cultures of <italic>Pinus taeda</italic>, P. <italic>sylvestris</italic> and <italic>Picea abies</italic>, and with labelled cDNA from leaves of <italic>Nicotiana tabacum</italic>. The Spearman
correlation of gene expression for pairs of conifer species was high for needles
(r<sup>2</sup> = 0.78 − 0.86), and somewhat lower for embryogenic cultures (r<sup>2</sup> = 0.68 − 0.83).
The correlation of gene expression for tobacco leaves and needles of each of the three
conifer species was lower but sufficiently high (r<sup>2</sup> = 0.52 − 0.63) to suggest that many
partial gene sequences are conserved in angiosperms and gymnosperms. Heterologous
probing was further used to identify tissue-specific gene expression over species
boundaries. To evaluate the significance of differences in gene expression, conventional
parametric tests were compared with permutation tests after four methods of
normalization. Permutation tests after Z-normalization provide the highest degree
of discrimination but may enhance the probability of type I errors. It is concluded
that arrays of cDNA from loblolly pine are useful for studies of gene expression in
other pines or spruces.</p>
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Comp Funct Genomics. 2002 Aug; 3(4):306-318