The nuclear genome of conifers is large and organized in complex gene families, and due primarily to a lack of comparative studies of protein coding nuclear genes across conifer families, very little is known about its evolutionary dynamics. In this study, we investigated the evolution of a low-copy nuclear gene encoding cinnamyl alcohol dehydrogenase (CAD), a key enzyme in the lignin biosynthetic pathway, in Pinaceae and Taxodiaceae. A portion of the CAD gene, including three exons and four introns, was PCR-amplified, cloned, and sequenced from all eleven genera of Pinaceae and five sampled genera from Taxodiaceae. Sequences of 627 nucleotides of the three exons were aligned among the sampled conifer species, as well as angiosperm species used as outgroups. Phylogenetic analysis of the aligned exon sequences yielded 862 most parsimonious trees, of which the strict consensus topology of the ingroup taxa is identical to that of the maximum likelihood tree. Surprisingly, a clade, which contains members of Taxodiaceae and species of Abies (Pinaceae), is nested within Pinaceae and has extremely short internal branches. The average synonymous and nonsynonymous divergences within this clade are 0.0149 + 0.0058 and 0.0074 + 0.0019, respectively. Given that Pinaceae and Taxodiaceae diverged as early as the Triassic Era, it is striking that such similar CAD sequences were found. Herein, three hypotheses explaining the remarkably similar CAD sequences are examined, DNA contamination, extremely slow rates of sequence divergence, and recent lateral gene transfer. Ultimately, we conclude that it is most likely that the CAD genes were recently transferred from Abies to members of Taxodiaceae. The lateral transfer of functionally important structural genes between reproductively isolated plants opens a new avenue for the exchange of genetic material, and may provide new insights into conifer evolution.

Key words: cinnamyl alcohol dehydrogenase, lateral gene transfer, Pinaceae, Taxodiaceae