title: Identification of conserved core xylem gene sets: conifer cDNA microarray development, transcript profiling and computational analyses.
abstract: One approach for investigating the molecular basis of wood formation is to integrate microarray profiling data sets and sequence analyses, comparing tree species with model plants such as Arabidopsis. Conifers may be included in comparative studies thanks to large-scale expressed sequence tag (EST) analyses, which enable the development of cDNA microarrays with very significant genome coverage. A microarray of 10,400 low-redundancy sequences was designed starting from white spruce (Picea glauca (Moench.) Voss) cDNAs. Computational procedures that were developed to ensure broad transcriptome coverage and efficient PCR amplification were used to select cDNA clones, which were re-sequenced in the microarray manufacture process. White spruce transcript profiling experiments that compared secondary xylem to phloem and needles identified 360 xylem-preferential gene sequences. The functional annotations of all differentially expressed sequences were highly consistent with the results of similar analyses carried out in angiosperm trees and herbaceous plants. Computational analyses comparing the spruce microarray sequences and core xylem gene sets from Arabidopsis identified 31 transcripts that were highly conserved in angiosperms and gymnosperms, in terms of both sequence and xylem expression. Several other spruce sequences have not previously been linked to xylem differentiation (including genes encoding TUBBY-like domain proteins (TLPs) and a gibberellin insensitive (gai) gene sequence) or were shown to encode proteins of unknown function encompassing diverse conserved domains of unknown function.
authors.affiliation: Centre d'Etude de la Forêt, 1030 rue de la Médecine, Université Laval, Québec, Québec, Canada, G1K 7P4.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Pavy
authors.forename: Brian
authors.initials: B
authors.lastname: Boyle
authors.forename: Colleen
authors.initials: C
authors.lastname: Nelson
authors.forename: Charles
authors.initials: C
authors.lastname: Paule
authors.forename: Isabelle
authors.initials: I
authors.lastname: Giguère
authors.forename: Sébastien
authors.initials: S
authors.lastname: Caron
authors.forename: Lee S
authors.initials: LS
authors.lastname: Parsons
authors.forename: Nancy
authors.initials: N
authors.lastname: Dallaire
authors.forename: Frank
authors.initials: F
authors.lastname: Bedon
authors.forename: Hugo
authors.initials: H
authors.lastname: Bérubé
authors.forename: Janice
authors.initials: J
authors.lastname: Cooke
authors.forename: John
authors.initials: J
authors.lastname: Mackay
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D046228:Microarray Analysis / Q000379:methods; D005810:Multigene Family; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D052585:Phloem / Q000235:genetics; D028222:Picea / Q000235:genetics*; D018515:Plant Leaves / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods; D017421:Sequence Analysis; D014158:Transcription, Genetic; D014197:Trees / Q000235:genetics; D052584:Xylem / Q000235:genetics*