The characterization of in vitro xylogenic cultures of zinnia (Zinnia elegans) has led to major discoveries in the understanding of xylem formation in plants. We have constructed and characterized a subtractive library from zinnia cultures enriched in genes that are specifically expressed at the onset of secondary wall deposition and tracheary element (TE) programmed cell death. This Late Xylogenesis Library (LXL) consisted of 236 nonredundant cDNAs, 77% of which encoded novel sequences in comparison with the 17,622 expressed sequence tag sequences publicly available. cDNA arrays were constructed to examine dynamic global gene expression during the course of TE formation. As a first step in dissecting auxin and cytokinin signaling during TE differentiation, macroarrays were probed with cDNAs from cells cultured in different hormonal conditions. Fiftyone percent of the LXL genes were induced by either auxin or cytokinin individually, the large majority by auxin. To determine the potential involvement of these categories of genes in TE differentiation, multiplex in situ-reverse transcription-PCR was performed on cells for two genes encoding putative cell wall proteins: Gibberellin stimulated transcript-1, induced by auxin alone, and expansin 5, induced by cytokinin alone. All transcriptionally active TEs expressed both genes, indicating that, although these genes may not be considered as specific markers for TE differentiation per se, they are nevertheless an integral part of TE differentiation program. Among the non-TE population, four different gene expression-based cell types could be distinguished. Together, these results demonstrate the underlying complexity of hormonal perception and the existence of several different cell types in in vitro TE cell cultures.The formation of xylem, or xylogenesis, constitutes one of the most spectacular forms of cell differentiation in plants. Xylem, initiating from meristematic procambial or cambial cells, is a heterogeneous tissue composed of nonconducting cells including parenchyma and fibers, and conducting cells or tracheary elements (TEs; for recent review, see Ye, 2002). In angiosperms, TEs are essential for the transport and storage of water and nutrients in land plants. Although it is clear that TE function is of prime importance in plant development, our knowledge of the cascade of cellular and molecular events from procambium and cambium formation to the initiation of xylem differentiation, cell elongation, secondary wall deposition, and programmed cell death (PCD), is at best fragmentary. Our lack of knowledge is due to the high degree of organizational complexity of vascular tissues throughout the plant and the limited number of cells actually undergoing differentiation at a given time. As a result, the accessibility of vascular cells is limited and makes experimentation difficult in planta.To gain a more in-depth knowledge of xylem formation, two approaches have been largely exploited. The genetic dissection of Arabidopsis (Arabidopsis thaliana) mutants with alt...