TARGETED ENRICHMENT STRATEGIES FOR NEXT-GENERATION PLANT BIOLOGY
TARGETED ENRICHMENT STRATEGIES FOR NEXT-GENERATION PLANT BIOLOGY
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DOI：
10.3732/ajb.1100356
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发表时间：
2012-02-01
影响因子：
3
通讯作者：
Udall, Joshua
中科院分区：
文献类型：
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作者：
Cronn, Richard;Knaus, Brian J.;Udall, Joshua
研究前提：现代DNA测序仪带来的巨大进步继续重新定义比较植物生物学的极限。然而，即使有了最近的成就，植物基因组也存在障碍，这使得在下一代测序平台上进行大规模种群和系统发育研究变得困难。诸如大的基因组大小、细胞器DNA在总DNA中所占比例的广泛变化、多倍体和基因数量/冗余等因素都导致了这些挑战，它们需要灵活的靶向富集策略来实现预期的目标。方法：在本文中，我们总结了许多可用的靶向富集策略，可用于靶向部分到完整的细胞体基因组，以及已知和匿名的核靶标。这些方法可分为四类：基于pcr的富集、基于杂交的富集、基于限制性内切酶的富集和表达基因序列的富集。关键结果：几乎所有描述的方法都存在植物特异性应用的例子。虽然一些方法已经建立良好（例如转录组测序），但其他有前途的方法还处于起步阶段（杂交富集）。两种方法的直接比较表明，基于pcr的富集可能是获取小基因组靶点(例如，
Premise of the study: 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.Methods: 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.Key results: 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 (e.g.,