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Analyzing complex plant genomes with the newest next-generation DNA sequencing techniques
Date:2/27/2012

ect genome sequencing is less tractable for many plants, whose simple appearance belies their genomic complexity. As complex as we are, humans possess about as many genes (22,000) as diminutive mosses, and less than half the number of genes found in alfalfa or apple. Moreover, our genome of 3.2 billion nucleotides is dwarfed by many plants, such as pines and coastal redwood (which are 10 times larger). Finally, plants have an additional genome within each cell that encodes the genes required to carry out photosynthesis inside the chloroplast.

"At the moment, these sequencers are less than optimal for comparative plant biologists who focus on select regions of the genome from hundreds of samples," adds David Spooner, one of the editors for the special issue.

The enrichment methods described by the authors fill this much-needed gap, and are based on time-tested methodologies, including: (1) PCR-based enrichment, (2) hybridization-based enrichment, (3) restriction enzyme-based enrichment, and (4) enrichment of expressed gene sequences. The advantages and disadvantages of each technique are explored, and suggestions are offered for their optimal use.

In their study, the authors conclude that traditional PCR-based methods offer a cost-effective strategy for accessing small genomic targets in the range of 50,000 nucleotides or less. Larger genomic targets are most efficiently enriched using hybridization- and transcriptome-based methods. The article is accompanied by open-access electronic appendices that provide example protocols for hybridization-enrichment techniques, and detailed cost estimates for each targeted sequencing method.

"The use of these methods is sure to hasten the pace of discovery in all aspects of plant biologycrop production, ecosystem health, and our understanding of plant diversity in the present and the distant evolutionary past," adds Cronn.


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Contact: Richard Hund
rhund@botany.org
314-577-9557
American Journal of Botany
Source:Eurekalert  

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