Fields of Biology
Plants & Agricultural Biotechnology
Overview
Traditionally, the complexity and size of plant genomes has limited the ability of plant researchers to obtain comprehensive sequence information. With conventional Sanger sequencing technology, many plant sequencing projects have been cost prohibitive or technically unfeasible, confining projects to large scale sequencing centers. The Genome Sequencer FLX System delivers outstanding data quality with long, highly accurate reads at a speed and price point that puts plant sequencing in the hands of the entire plant research community.
Download the Plant and Agricultural Biotechnology Flyer
Applications
Whole plant genome sequencing
Use the GS FLX System to perform either a BAC-to-BAC or a whole genome shotgun approach to sequence the complete genome of your plant of interest.
Transcriptome sequencing
With its highly accurate long reads, the GS FLX system is ideal for the de novo assembly of whole plant transcriptomes. Obtain quick, unbiased transcriptome surveys of unknown genomes in order to assess new gene functions and to find novel genes, polymorphisms for genotyping, alternative splice variants, and other sequence motifs.
Allele specific gene expression profiling
The GS FLX System's long reads have been proven to resolve the challenges of polyploidy in allele specific gene expression, such as resolving expression of closely-related genes.
Rhizosphere and soil Metagenomics
With long reads and high throughput, the GS FLX system provides the necessary sequence depth to reveal the presence and quantity of culturable and non-culturable microbes in the complex rhizosphere.
Pathogenic viruses, fungi & bacteria
The long read lengths and high throughput provided by the GS FLX system, in combination with the assembly and alignment software enables the identification and genomic analysis of this group of mostly non-sequenced microorganisms.
Targeted region sequencing
The combination of NimbleGen Sequence Capture and the GS FLX System's long reads ensures comprehensive detection of all types of variations: SNPs; small insertions and deletions; and copy number variations.
Expression profiling (including SuperSAGE, and other ditag based methods)
Obtain an unbiased, high-quality gene expression profile by performing SuperSAGE ditag sequencing (2x26 nucleotides) on the GS FLX System.
Identification and analysis of non coding RNA such as microRNA, development of genotyping assays and many more.
Publications
- Weber et al. Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiology 144: 32-42. May 2007.)
- Novaes et al. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 9: 312. June 30, 2008.
- Bekal et al. Genomic DNA sequence comparison between two inbred soybean cyst nematode biotypes facilitated by massively parallel 454 micro-bead sequencing. Molecular Genetic and Genomics 279: 535-543. May 2008.
Click here to see a full list of Plant & Agricultural Biotechnology publications.
User Experience
"Together with Roche, we have extensively tested the use of the GS FLX in our BAC-by-BAC sequencing approach of the potato and tomato genomes, which we are pursuing in the international collaborations of the Potato Genome Sequencing Consortium and the International Solanaceae Genome Project. We were thrilled with the results, which were comparable or sometimes better than what we obtained by conventional sequencing. We obtained high-quality and entirely unbiased coverage of the BACs, and we got these fast and cheap. We were also very impressed by the power and quality of the software that comes with the platform, which made the assembly of the sequences a straightforward and robust procedure. We are convinced that the Roche 454 GS FLX will enable us to complete our sequencing effort in these genomes ahead of schedule."
Dr. Roeland Van Ham, Ph.D.
Associate Professor, Wageningen University