大规模核基因的系统基因组学分析为蔷薇科植物内部的进化关系提供了新的见解
Phylogenomic Analyses of Large-scale Nuclear Genes Provide New Insights into the Evolutionary Relationships within the Rosids
摘要：
蔷薇科植物是开花植物中最大的类群之一，有140科，约70，000种。以前的蔷薇科植物系统发育研究主要利用细胞器基因，可能不同的进化历史，从核基因。为了更好地了解蔷薇科植物的进化历史，有必要利用核基因研究它们的系统发育关系。在这里，我们采用了由核基因组成的大规模基因组数据集，包括891个推定的正向同源基因簇。结合全面的分类单元采样，涵盖63种代表14的17个目，我们重建了蔷薇科植物的系统发育与合并和连接的方法，从所有数据集产生类似的树拓扑结构。然而，这些拓扑结构并不同意的Zygophyllales的位置。通过综合分析发现，缺失数据和基因树异质性是可能误导拼接方法的潜在因素，尤其是在基因树异质性较高的情况下存在大量的缺失数据。我们的研究结果为深入了解蔷薇科植物的系统发育关系提供了新的见解，并表明聚结方法可以有效地解决高基因树异质性下缺失数据的蔷薇科植物的系统发育关系。
英文摘要：
The Rosids is one of the largest groups of flowering plants, with 140 families and ~70,000 species. Previous phylogenetic studies of the rosids have primarily utilized organelle genes that likely differ in evolutionary histories from nuclear genes. To better understand the evolutionary history of rosids, it is necessary to investigate their phylogenetic relationships using nuclear genes. Here, we employed large-scale phylogenomic datasets composed of nuclear genes, including 891 clusters of putative orthologous genes. Combined with comprehensive taxon sampling covering 63 species representing 14 out of the 17 orders, we reconstructed the rosids phylogeny with coalescence and concatenation methods, yielding similar tree topologies from all datasets. However, these topologies did not agree on the placement of Zygophyllales. Through comprehensive analyses, we found that missing data and gene tree heterogeneity were potential factors that may mislead concatenation methods, in particular, large amounts of missing data under high gene tree heterogeneity. Our results provided new insights into the deep phylogenetic relationships of the rosids, and demonstrated that coalescence methods may effectively resolve the phylogenetic relationships of the rosids with missing data under high gene tree heterogeneity.
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