Skip to Main Content
Targeted enrichment strategies for next-generation plant biologyAuthor(s): Richard Cronn; Brian J. Knaus; Aaron Liston; Peter J. Maughan; Matthew Parks; John V. Syring; Joshua Udall
Source: American Journal of Botany. 99(2): 291-311
Publication Series: Scientific Journal (JRNL)
Station: Pacific Northwest Research Station
PDF: Download Publication (1.78 MB)
DescriptionThe dramatic advances offered by modem 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-based enrichment may be a reasonable strategy for accessing small genomic targets, but that hybridization and transcriptome sequencing scale more efficiently if larger targets are desired. While the benefits of targeted sequencing are greatest in plants with large genomes, nearly all comparative projects can benefit from the improved throughput offered by targeted multiplex DNA sequencing, particularly as the amount of data produced from a single instrument approaches a trillion bases per run.
- Visit PNW's Publication Request Page to request a hard copy of this publication.
- We recommend that you also print this page and attach it to the printout of the article, to retain the full citation information.
- This article was written and prepared by U.S. Government employees on official time, and is therefore in the public domain.
CitationCronn, Richard; Knaus, Brian J.; Liston, Aaron; Maughan, Peter J.; Parks, Matthew; Syring, John V.; Udall, Joshua. 2012. Targeted enrichment strategies for next-generation plant biology. American Journal of Botany. 99(2): 291-311.
Keywordstarget enrichment, genome reduction, hybridization, genotyping-by-sequencing, microfluidic PCR, multiplex PCR, transcriptome sequencing
- Hyb-Seq: combining target enrichment and genome skimming for plant phylogenomics
- Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae)
- Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology
XML: View XML