Department of Biology, Texas A&M University.
Department of Nuclear Engineering, Texas A&M University.
Genome Biol Evol. 2017 Dec 1;9(12):3478-3494. doi: 10.1093/gbe/evx259.
Plants on serpentine soils provide extreme examples of adaptation to environment, and thus offer excellent models for the study of evolution at the molecular and genomic level. Serpentine outcrops are derived from ultramafic rock and have extremely low levels of essential plant nutrients (e.g., N, P, K, and Ca), as well as toxic levels of heavy metals (e.g., Ni, Cr, and Co) and low moisture availability. These outcrops provide habitat to a number of endemic plant species, including the annual mustard Caulanthus amplexicaulis var. barbarae (Cab) (Brassicaceae). Its sister taxon, C. amplexicaulis var. amplexicaulis (Caa), is intolerant to serpentine soils. Here, we assembled and annotated comprehensive reference transcriptomes of both Caa and Cab for use in protein coding sequence comparisons. A set of 29,443 reciprocal best Blast hit (RBH) orthologs between Caa and Cab was compared with identify coding sequence variants, revealing a high genome-wide dN/dS ratio between the two taxa (mean = 0.346). We show that elevated dN/dS likely results from the composite effects of genetic drift, positive selection, and the relaxation of negative selection. Further, analysis of paralogs within each taxon revealed the signature of a period of elevated gene duplication (∼10 Ma) that is shared with other species of the tribe Thelypodieae, and may have played a role in the striking morphological and ecological diversity of this tribe. In addition, distribution of the synonymous substitution rate, dS, is strongly bimodal, indicating a history of reticulate evolution that may have contributed to serpentine adaptation.
蛇纹岩土上的植物提供了适应环境的极端范例，因此为在分子和基因组水平上研究进化提供了极好的模型。蛇纹岩露头源自超镁铁质岩石，基本植物养分（如 N、P、K 和 Ca）含量极低，同时重金属（如 Ni、Cr 和 Co）含量过高且水分可用性低。这些露头为许多特有植物物种提供了栖息地，包括一年生芥菜 Caulanthus amplexicaulis var. barbarae（Cab）（十字花科）。它的姊妹类群 C. amplexicaulis var. amplexicaulis（Caa）不能耐受蛇纹岩土。在这里，我们组装并注释了 Caa 和 Cab 的综合参考转录组，用于比较蛋白质编码序列。将 Caa 和 Cab 之间的 29443 对相互最佳 Blast 命中（RBH）直系同源物进行比较，以识别编码序列变体，结果表明两个分类群之间存在高基因组范围内的 dN/dS 比值（平均值为 0.346）。我们表明，dN/dS 的升高可能是遗传漂变、正选择和负选择放松的综合作用的结果。此外，对每个分类群内的旁系同源物的分析显示出基因倍增（约 10 Ma）的一个时期的特征，这与 Thelypodieae 族的其他物种共享，并且可能在该族显著的形态和生态多样性中发挥了作用。此外，同义替换率 dS 的分布呈双峰模式，表明存在网状进化的历史，这可能有助于对蛇纹岩的适应。
