Journal article

Publication year: 2009

Journal: BMC Genomics

Volume number: 10

ISSN: 1471-2164

Open access status: Gold

DOI Link: https://doi.org/10.1186/1471-2164-10-295

Publisher: BioMed Central

Abstract: 
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.\nTranscripts 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.\nThis 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.\nBACKGROUND\nRESULTS\nCONCLUSION

Harvard Citation style: Obermeier, C., Hosseini, B., Friedt, W. and Snowdon, R. (2009) Gene expression profiling via LongSAGE in a non-model plant species: a case study in seeds of Brassica napus, BMC Genomics, 10, Article 295. https://doi.org/10.1186/1471-2164-10-295

APA Citation style: Obermeier, C., Hosseini, B., Friedt, W., & Snowdon, R. (2009). Gene expression profiling via LongSAGE in a non-model plant species: a case study in seeds of Brassica napus. BMC Genomics. 10, Article 295. https://doi.org/10.1186/1471-2164-10-295