Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays

Lei Li^*¹^,8 , Hang He^*¹^,2^,3 , Juan Zhang⁴ , Xiangfeng Wang¹^,2^,3 , Sulan Bai⁵ , Viktor Stolc⁶ , Waraporn Tongprasit⁶ , Nevin D Young⁷ , Oliver Yu⁴ and Xing-Wang Deng¹

¹Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA

²National Institute of Biological Sciences, Beijing 102206, China

³Peking-Yale Joint Research Center of Plant Molecular Genetics and Agrobiotechnology, Peking University, Beijing 100871, China

⁴Donald Danforth Plant Science Center, St Louis, MO 63132, USA

⁵College of Life Sciences, Capital Normal University, Beijing 100037, China

⁶Genome Research Facility, NASA Ames Research Center, Moffett Field, CA 94035, USA

⁷Department of Plant Pathology, University of Minnesota, St Paul, MN 55108, USA

⁸Current address: Department of Biology, University of Virginia, Charlottesville, VA 22904, USA

author email corresponding author email* Contributed equally

Genome Biology 2008, 9:R57doi:10.1186/gb-2008-9-3-r57


Published:	19 March 2008

Subject areas: Plant biology, Genome studies, Model organisms

Abstract

Background

Legumes are the third largest family of flowering plants and are unique among crop species in their ability to fix atmospheric nitrogen. As a result of recent genome sequencing efforts, legumes are now one of a few plant families with extensive genomic and transcriptomic data available in multiple species. The unprecedented complexity and impending completeness of these data create opportunities for new approaches to discovery.

Results

We report here a transcriptional analysis in six different organ types of syntenic regions totaling approximately 1 Mb between the legume plants barrel medic (Medicago truncatula) and soybean (Glycine max) using oligonucleotide tiling microarrays. This analysis detected transcription of over 80% of the predicted genes in both species. We also identified 499 and 660 transcriptionally active regions from barrel medic and soybean, respectively, over half of which locate outside of the predicted exons. We used the tiling array data to detect differential gene expression in the six examined organ types and found several genes that are preferentially expressed in the nodule. Further investigation revealed that some collinear genes exhibit different expression patterns between the two species.

Conclusion

These results demonstrate the utility of genome tiling microarrays in generating transcriptomic data to complement computational annotation of the newly available legume genome sequences. The tiling microarray data was further used to quantify gene expression levels in multiple organ types of two related legume species. Further development of this method should provide a new approach to comparative genomics aimed at elucidating genome organization and transcriptional regulation.