BMC Genomics Research article Gene expression profiling via LongSAGE in a non-model plant species: a case study in seeds of Brassica napus Christian Obermeier*, Bashir Hosseini, Wolfgang Friedt and Rod Snowdon BioMed Central Open Access Address: Justus Liebig University Giessen, Department of Plant Breeding, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany Email: Christian Obermeier* - christian.obermeier@agrar.uni-giessen.de; Bashir Hosseini - bashir.hosseini@agrar.uni-giessen.de; Wolfgang Friedt - wolfgang.friedt@agrar.uni-giessen.de; Rod Snowdon - rod.snowdon@agrar.uni-giessen.de * Corresponding author Published: 3 July 2009 BMC Genomics 2009, 10:295 doi:10.1186/1471-2164-10-295 This article is available from: http://www.biomedcentral.com/1471-2164/10/295 Received: 16 February 2009 Accepted: 3 July 2009 © 2009 Obermeier et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Serial analysis of gene expression (LongSAGE) was applied for gene expression profiling in seeds of oilseed rape (Brassica napus ssp. napus). The usefulness of this technique for detailed expression profiling in a non-model organism was demonstrated for the highly complex, neither fully sequenced nor annotated genome of B. napus by applying a tag-to-gene matching strategy based on Brassica ESTs and the annotated proteome of the closely related model crucifer A. thaliana. Results: Transcripts from 3,094 genes were detected at two time-points of seed development, 23 days and 35 days after pollination (DAP). Differential expression showed a shift from gene expression involved in diverse developmental processes including cell proliferation and seed coat formation at 23 DAP to more focussed metabolic processes including storage protein accumulation and lipid deposition at 35 DAP. The most abundant transcripts at 23 DAP were coding for diverse protease inhibitor proteins and proteases, including cysteine proteases involved in seed coat formation and a number of lipid transfer proteins involved in embryo pattern formation. At 35 DAP, transcripts encoding napin, cruciferin and oleosin storage proteins were most abundant. Over both time-points, 18.6% of the detected genes were matched by Brassica ESTs identified by LongSAGE tags in antisense orientation. This suggests a strong involvement of antisense transcript expression in regulatory processes during B. napus seed development. Conclusion: This study underlines the potential of transcript tagging approaches for gene expression profiling in Brassica crop species via EST matching to annotated A. thaliana genes. Limits of tag detection for low-abundance transcripts can today be overcome by ultra-high throughput sequencing approaches, so that tag-based gene expression profiling may soon become the method of choice for global expression profiling in non-model species. Background Seed developmental processes of plants are complex and follow coordinated gene expression programs. Some genes are exclusively expressed during seed development [1]. Understanding the genetics of developmental proc- esses and regulatory networks involved in embryogenesis and seed development is crucial for improvement of seed quality in crop plants. Gene expression during seed devel- opment has been studied intensively in the model plant Arabidopsis thaliana using mutagenesis [2,3] and microar- Page 1 of 16 (page number not for citation purposes)