Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes.
Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes.
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DOI：
10.1186/1741-7007-7-84
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发表时间：
2009-12-02
期刊：
影响因子：
5.4
通讯作者：
Liston A
中科院分区：
文献类型：
--
作者：
Parks M;Cronn R;Liston A
分子进化研究有着阐明历史关系的共同目标，以及充分采样分类群和性状的共同挑战。特别是在低分类水平上，最近的分歧、快速辐射和保守的基因组进化产生了有限的序列变异，并且密集的分类单元采样通常是可取的。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，而多重分析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？我们利用多重大规模并行测序生成的 37 个几乎完整的叶绿体基因组（大约 120 kb 基因组中每个平均 109 kb）重建了松树的属下系统发育。 30/33 个组内节点通过 ≥ 95% 的引导程序支持得到解决；相对于之前的研究，这是一个实质性的改进，并且表明基于大规模并行测序的策略可以产生足够的高质量序列，以达到最初为系统发育引导提出的支持水平。重采样模拟表明，至少整个质体对于完全解析松属是必要的，特别是在快速辐射的分支中。对 99 个已发表的属下系统发育的荟萃分析表明，整个质体分析应该在一系列植物属中提供类似的增益。不成比例的系统发育信息存在于两个基因座（ycf1、ycf2）中，突出了它们不寻常的进化特性。现在，质体测序是在植物系统发育和群体遗传分析中提高较低分类水平的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，例如系统发育分析和物种级 DNA 条形码。
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 ≥ 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.
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影响因子：
48
作者：
Craig, David W.;Pearson, John V.;Szelinger, Szabolcs;Sekar, Aswin;Redman, Margot;Corneveaux, Jason J.;Pawlowski, Traci L.;Laub, Trisha;Nunn, Gary;Stephan, Dietrich A.;Homer, Nils;Huentelman, Matthew J.
通讯作者：
Huentelman, Matthew J.
影响因子：
3.4
作者：
Gernandt, DS;López, GG;Liston, A
通讯作者：
Liston, A
影响因子：
48
作者：
Herman, Daniel S.;Hovingh, G. Kees;Seidman, Christine E.
通讯作者：
Seidman, Christine E.
影响因子：
1
作者：
Gernandt, David S.;Hernandez-Leon, Sergio;Perez de la Rosa, Jorge A.
通讯作者：
Perez de la Rosa, Jorge A.
DOI：
10.1073/pnas.0812297106
发表时间：
2009-02-24
影响因子：
11.1
作者：
Awano, Tomoyuki;Johnson, Gary S.;Coates, Joan R.
通讯作者：
Coates, Joan R.