Gene discovery in the wood-forming tissues of poplar: analysis of 5, 692 expressed sequence tags

Abstract

A rapidly growing area of genome research is the generation of expressed sequence tags (ESTs) in which large numbers of randomly selected cDNA clones are partially sequenced. The collection of ESTs reflects the level and complexity of gene expression in the sampled tissue. To date, the majority of plant ESTs are from nonwoody plants such as Arabidopsis, Brassica, maize, and rice. Here, we present a large-scale production of ESTs from the wood-forming tissues of two poplars, Populus tremula L. x tremuloides Michx. and Populus trichocarpa 'Trichobel.' The 5,692 ESTs analyzed represented a total of 3,719 unique transcripts for the two cDNA libraries. Putative functions could be assigned to 2,245 of these transcripts that corresponded to 820 protein functions. Of specific interest to forest biotechnology are the 4% of ESTs involved in various processes of cell wall formation, such as lignin and cellulose synthesis, 5% similar to developmental regulators and members of known signal transduction pathways, and 2% involved in hormone biosynthesis. An additional 12% of the ESTs showed no significant similarity to any other DNA or protein sequences in existing databases. The absence of these sequences from public databases may indicate a specific role for these proteins in wood formation. The cDNA libraries and the accompanying database are valuable resources for forest research directed toward understanding the genetic control of wood formation and future endeavors to modify wood and fiber properties for industrial use.

Figure 1

Transverse section of a poplar stem that shows the tissues used for the EST libraries. The cambial-region EST library was prepared from developing and mature phloem, the cambial meristem, and developing xylem. A separate library was prepared from the developing xylem only.

Figure 2

Classification of the 4,809 and 883 ESTs from the cambial-region (A) and developing-xylem (B) libraries, respectively. ESTs with blastx scores >100 were classified into functional categories: unknown, with similarity to uncharacterized DNA or protein sequences in existing databases; no hits, no sequence similarity found in existing databases; DNA-binding proteins; hormone synthesis-related proteins; protein synthesis; protein modification, degradation, and targeting; nucleotide and amino acid metabolism; cell wall formation; stress-related proteins; other proteins whose function does not fit into the other categories; cytoskeleton; cell cycle control; signal transduction; and general metabolism.