TrichOME: a comparative omics database for plant trichomes

Abstract

Plant secretory trichomes have a unique capacity for chemical synthesis and secretion and have been described as biofactories for the production of natural products. However, until recently, most trichome-specific metabolic pathways and genes involved in various trichome developmental stages have remained unknown. Furthermore, only a very limited amount of plant trichome genomics information is available in scattered databases. We present an integrated "omics" database, TrichOME, to facilitate the study of plant trichomes. The database hosts a large volume of functional omics data, including expressed sequence tag/unigene sequences, microarray hybridizations from both trichome and control tissues, mass spectrometry-based trichome metabolite profiles, and trichome-related genes curated from published literature. The expressed sequence tag/unigene sequences have been annotated based upon sequence similarity with popular databases (e.g. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Transporter Classification Database). The unigenes, metabolites, curated genes, and probe sets have been mapped against each other to enable comparative analysis. The database also integrates bioinformatics tools with a focus on the mining of trichome-specific genes in unigenes and microarray-based gene expression profiles. TrichOME is a valuable and unique resource for plant trichome research, since the genes and metabolites expressed in trichomes are often underrepresented in regular non-tissue-targeted cDNA libraries. TrichOME is freely available at http://www.planttrichome.org/.

Figure 1.

Representative scanning electron microscopy images of trichomes on plants. A, Erect glandular trichome on the stem of M. sativa. B, Nonglandular trichome on a rosette leaf of Arabidopsis. C, Procumbent trichome on the petiole of M. truncatula. D, Field of glandular trichomes on a female bract of Cannabis sativa. E, Glandular trichomes on a bract of H. lupulus. F, Nonglandular trichome on a leaf of M. truncatula. G, Types VI (small arrow) and I (large arrow) trichomes on a leaf of S. lycopersicum. All the scanning electron microscopy images were generated as described previously (Ahlstrand, 1996; Esch et al., 2004) using an Emitech Technologies (www.emitech.co.uk) K1150 cyropreparation system and a Hitachi High Technologies (www.hitachi-hhta.com) S3500N scanning electron microscope. Bars = 100 μm.

Figure 2.

The interface for metabolite profiles by GC-MS in TrichOME. [See online article for color version of this figure.]

Figure 3.

The interface for searching trichome-related ESTs/unigenes. A, List of species with trichome-related ESTs/unigenes and links for batch downloading. Acc., Accession number. B, Trichome-related unigenes classified by KEGG metabolic pathways. [See online article for color version of this figure.]

Figure 4.

The interface for in silico gene expression analysis. The function calculates R values for the identification of trichome-specific or highly expressed unigenes by comparing with EST members of unigenes expressed in the trichome library and nontrichome control libraries.