Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
BMC Biol. 2009 Dec 2;7:84. doi: 10.1186/1741-7007-7-84.
Molecular evolutionary studies share the common goal of elucidating historical relationships, and the common challenge of adequately sampling taxa and characters. Particularly at low taxonomic levels, recent divergence, rapid radiations, and conservative genome evolution yield limited sequence variation, and dense taxon sampling is often desirable. Recent advances in massively parallel sequencing make it possible to rapidly obtain large amounts of sequence data, and multiplexing makes extensive sampling of megabase sequences feasible. Is it possible to efficiently apply massively parallel sequencing to increase phylogenetic resolution at low taxonomic levels?
We reconstruct the infrageneric phylogeny of Pinus from 37 nearly-complete chloroplast genomes (average 109 kilobases each of an approximately 120 kilobase genome) generated using multiplexed massively parallel sequencing. 30/33 ingroup nodes resolved with > or = 95% bootstrap support; this is a substantial improvement relative to prior studies, and shows massively parallel sequencing-based strategies can produce sufficient high quality sequence to reach support levels originally proposed for the phylogenetic bootstrap. Resampling simulations show that at least the entire plastome is necessary to fully resolve Pinus, particularly in rapidly radiating clades. Meta-analysis of 99 published infrageneric phylogenies shows that whole plastome analysis should provide similar gains across a range of plant genera. A disproportionate amount of phylogenetic information resides in two loci (ycf1, ycf2), highlighting their unusual evolutionary properties.
Plastome sequencing is now an efficient option for increasing phylogenetic resolution at lower taxonomic levels in plant phylogenetic and population genetic analyses. With continuing improvements in sequencing capacity, the strategies herein should revolutionize efforts requiring dense taxon and character sampling, such as phylogeographic analyses and species-level DNA barcoding.
分子进化研究有一个共同的目标，即阐明历史关系，而共同的挑战是充分采样分类单元和特征。特别是在低分类水平上，最近的分化、快速辐射和保守的基因组进化产生了有限的序列变异，并且往往需要密集的分类单元采样。大规模并行测序的最新进展使得快速获得大量序列数据成为可能，而多重化使得对兆碱基序列的广泛采样成为可能。是否有可能有效地应用大规模并行测序来提高低分类水平的系统发育分辨率？
我们从 37 个近乎完整的叶绿体基因组（每个基因组约 120kb，平均长度为 109kb）中重建了松属的种下系统发育关系，这些基因组是使用多重大规模并行测序生成的。33 个/37 个内群节点的分辨率>或=95%bootstrap 支持；与之前的研究相比，这是一个实质性的改进，表明大规模并行测序策略可以产生足够高质量的序列，达到最初为系统发育 bootstrap 提出的支持水平。重采样模拟表明，至少整个质体基因组是必要的，以充分解决松属问题，特别是在快速辐射的分支中。对 99 个已发表的种下系统发育关系的元分析表明，整个质体基因组分析应该在一系列植物属中提供类似的增益。相当一部分系统发育信息位于两个基因座（ycf1、ycf2）中，突出了它们异常的进化特性。
在植物系统发育和群体遗传学分析中，质体测序现在是提高低分类水平系统发育分辨率的有效选择。随着测序能力的不断提高，本文中所提出的策略应该会彻底改变需要密集分类单元和特征采样的工作，如系统地理学分析和种级 DNA 条形码分析。
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