Feb 9, 2012

Targeted enrichment strategies for next-generation plant biology

American Journal of Botany
Richard CronnJoshua A Udall

Abstract

The dramatic advances offered by modern DNA sequencers continue to redefine the limits of what can be accomplished in comparative plant biology. Even with recent achievements, however, plant genomes present obstacles that can make it difficult to execute large-scale population and phylogenetic studies on next-generation sequencing platforms. Factors like large genome size, extensive variation in the proportion of organellar DNA in total DNA, polyploidy, and gene number/redundancy contribute to these challenges, and they demand flexible targeted enrichment strategies to achieve the desired goals. In this article, we summarize the many available targeted enrichment strategies that can be used to target partial-to-complete organellar genomes, as well as known and anonymous nuclear targets. These methods fall under four categories: PCR-based enrichment, hybridization-based enrichment, restriction enzyme-based enrichment, and enrichment of expressed gene sequences. Examples of plant-specific applications exist for nearly all methods described. While some methods are well established (e.g., transcriptome sequencing), other promising methods are in their infancy (hybridization enrichment). A direct comparison of methods shows that PCR...Continue Reading

  • References121
  • Citations54

References

  • References121
  • Citations54

Citations

Mentioned in this Paper

Genome
Nucleic Acid Hybridization Procedure
Cell Nucleus
Phylogeny
Genomics
Sequencing
Massively-Parallel Sequencing
Sequence Determinations, DNA
Etioplasts
DNA Restriction Enzymes

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