Targeted Enrichment of Large Gene Families for Phylogenetic Inference: Phylogeny and Molecular Evolution of Photosynthesis Genes in the Portullugo Clade (Caryophyllales)
Targeted Enrichment of Large Gene Families for Phylogenetic Inference: Phylogeny and Molecular Evolution of Photosynthesis Genes in the Portullugo Clade (Caryophyllales)
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DOI：
10.1093/sysbio/syx078
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发表时间：
2018-05
影响因子：
6.5
通讯作者：
A. Moore;J. D. de Vos;L. Hancock;Eric W. Goolsby;E. Edwards
中科院分区：
文献类型：
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作者：
A. Moore;J. D. de Vos;L. Hancock;Eric W. Goolsby;E. Edwards
杂交浓缩是一种越来越受欢迎的方法，可以快速而廉价地获得数百个基因座，用于跨许多分类群的系统发育分析。测序的目标基因通常是单拷贝基因座，这有助于更直接的序列组装和同源性分配过程。然而，这种方法限制了大多数功能感兴趣的基因的包含，这些基因通常属于多基因家族。在这里，我们证明了在杂交浓缩协议中包括大基因家族的可行性，用于系统发育重建和后续的分子进化分析，使用一组新的诱饵序列设计的“portullugo”(石竹目)，一个中等大小的开花植物谱系(CAM2200种)，包括仙人掌，并包含许多进化过渡到C4和˜光合作用。包括多基因家族使我们能够同时推断强大的系统发育和构建C4和CAM光合作用的主要酶序列的密集样本，这揭示了与C4和CAM起源相关的适应性氨基酸替代的积累，特别是近海相思。我们最后一组用于系统发育分析的矩阵包括74个分类群的75-218个基因座，其中˜在所有数据集上的矩阵完备率为50%。整个树的系统发育分辨率大大提高，无论是在浅层还是深层。串联和基于合并的方法都在强有力的支持下解决了仙人掌的姐妹谱系：水仙子科+马齿苋科，这两个谱系大多是温暖、干旱地区微小的肉质草本植物。尽管有这种一致性，巴基一致性分析显示了基因树上强烈而相互矛盾的信号。我们的结果增加了越来越多的例子，说明了基因组规模数据中系统发育信号的复杂性。
&NA; Hybrid enrichment is an increasingly popular approach for obtaining hundreds of loci for phylogenetic analysis across many taxa quickly and cheaply. The genes targeted for sequencing are typically single‐copy loci, which facilitate a more straightforward sequence assembly and homology assignment process. However, this approach limits the inclusion of most genes of functional interest, which often belong to multi‐gene families. Here, we demonstrate the feasibility of including large gene families in hybrid enrichment protocols for phylogeny reconstruction and subsequent analyses of molecular evolution, using a new set of bait sequences designed for the “portullugo” (Caryophyllales), a moderately sized lineage of flowering plants (˜ 2200 species) that includes the cacti and harbors many evolutionary transitions to C4 and CAM photosynthesis. Including multi‐gene families allowed us to simultaneously infer a robust phylogeny and construct a dense sampling of sequences for a major enzyme of C4 and CAM photosynthesis, which revealed the accumulation of adaptive amino acid substitutions associated with C4 and CAM origins in particular paralogs. Our final set of matrices for phylogenetic analyses included 75‐218 loci across 74 taxa, with ˜ 50% matrix completeness across data sets. Phylogenetic resolution was greatly improved across the tree, at both shallow and deep levels. Concatenation and coalescent‐based approaches both resolve the sister lineage of the cacti with strong support: Anacampserotaceae + Portulacaceae, two lineages of mostly diminutive succulent herbs of warm, arid regions. In spite of this congruence, BUCKy concordance analyses demonstrated strong and conflicting signals across gene trees. Our results add to the growing number of examples illustrating the complexity of phylogenetic signals in genomic‐scale data.