The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
Mol Phylogenet Evol. 2012 Sep;64(3):545-62. doi: 10.1016/j.ympev.2012.05.010. Epub 2012 May 27.
The complete nucleotide sequence of the chloroplast genome (cpDNA) of Smilax china L. (Smilacaceae) is reported. It is the first complete cp genome sequence in Liliales. Genomic analyses were conducted to examine the rate and pattern of cpDNA genome evolution in Smilax relative to other major lineages of monocots. The cpDNA genomic sequences were combined with those available for Lilium to evaluate the phylogenetic position of Liliales and to investigate the influence of taxon sampling, gene sampling, gene function, natural selection, and substitution rate on phylogenetic inference in monocots. Phylogenetic analyses using sequence data of gene groups partitioned according to gene function, selection force, and total substitution rate demonstrated evident impacts of these factors on phylogenetic inference of monocots and the placement of Liliales, suggesting potential evolutionary convergence or adaptation of some cpDNA genes in monocots. Our study also demonstrated that reduced taxon sampling reduced the bootstrap support for the placement of Liliales in the cpDNA phylogenomic analysis. Analyses of sequences of 77 protein genes with some missing data and sequences of 81 genes (all protein genes plus the rRNA genes) support a sister relationship of Liliales to the commelinids-Asparagales clade, consistent with the APG III system. Analyses of 63 cpDNA protein genes for 32 taxa with few missing data, however, support a sister relationship of Liliales (represented by Smilax and Lilium) to Dioscoreales-Pandanales. Topology tests indicated that these two alignments do not significantly differ given any of these three cpDNA genomic sequence data sets. Furthermore, we found no saturation effect of the data, suggesting that the cpDNA genomic sequence data used in the study are appropriate for monocot phylogenetic study and long-branch attraction is unlikely to be the cause to explain the result of two well-supported, conflict placements of Liliales. Further analyses using sufficient nuclear data remain necessary to evaluate these two phylogenetic hypotheses regarding the position of Liliales and to address the causes of signal conflict among genes and partitions.
中国菝葜（菝葜科）叶绿体基因组（cpDNA）的完整核苷酸序列已被报道。这是百合目植物中第一个完整的 cp 基因组序列。通过基因组分析，研究了 cpDNA 基因组在菝葜属植物中相对于单子叶植物其他主要谱系的进化速率和模式。将 cpDNA 基因组序列与百合属的序列相结合，评估了百合目在单子叶植物中的系统发育位置，并研究了分类群取样、基因取样、基因功能、自然选择和替代率对单子叶植物系统发育推断的影响。根据基因功能、选择力和总替代率对基因分组进行序列数据的系统发育分析表明，这些因素对单子叶植物的系统发育推断和百合目的位置有明显的影响，表明一些 cpDNA 基因在单子叶植物中可能存在进化趋同或适应。我们的研究还表明，减少分类群取样会降低 cpDNA 系统发育分析中百合目的支持率。对 77 个具有部分缺失数据的蛋白质基因序列和 81 个基因序列（所有蛋白质基因加 rRNA 基因）的分析支持百合目与鸭跖草目-百合目分支的姐妹关系，与 APG III 系统一致。然而，对 32 个具有少量缺失数据的 cpDNA 蛋白质基因的 63 个分析支持百合目（以菝葜属和百合属为代表）与薯蓣目-露兜树目分支的姐妹关系。拓扑学检验表明，在这三个 cpDNA 基因组序列数据集的任何一个中，这两种排列都没有显著差异。此外，我们没有发现数据的饱和效应，这表明在所研究的 cpDNA 基因组序列数据适用于单子叶植物的系统发育研究，并且长枝吸引不太可能是解释两个得到很好支持的、冲突的百合目位置的原因。需要进一步使用足够的核数据进行分析，以评估关于百合目位置的这两种系统发育假设，并解决基因和分区之间信号冲突的原因。
