Finding candidate genes under positive selection in non-model species: examples of genes involved in host specialization in pathogens

Numerous genes in diverse organisms have been shown to be under positive selection, especially genes involved in reproduction, adaptation to contrasting environments, hybrid inviability, and host-pathogen interactions. Looking for genes under positive selection in pathogens has been a priority in efforts to investigate coevolution dynamics and to develop vaccines or drugs. To elucidate the functions involved in host specialization, here we aimed at identifying candidate sequences that could have evolved under positive selection among closely related pathogens specialized on different hosts. For this goal, we sequenced ca. 17,000-32,000 ESTs from each of four Microbotryum species, which are fungal pathogens responsible for anther smut disease on host plants in the Caryophyllaceae. Forty-two of the 372 predicted orthologous genes showed significant signal of positive selection, which represents a good number of candidate genes for further investigation. Sequencing 16 of these genes in 9 additional Microbotryum species confirmed that they have indeed been rapidly evolving in the pathogen species specialized on different hosts. The genes showing significant signals of positive selection were putatively involved in nutrient uptake from the host, secondary metabolite synthesis and secretion, respiration under stressful conditions and stress response, hyphal growth and differentiation, and regulation of expression by other genes. Many of these genes had transmembrane domains and may therefore also be involved in pathogen recognition by the host. Our approach thus revealed fruitful and should be feasible for many non-model organisms for which candidate genes for diversifying selection are needed.

已有研究证实，诸多生物体内的众多基因均处于正向选择压力之下，其中与生殖过程、异质环境适应、杂种致死以及宿主-病原体互作相关的基因尤为典型。在病原体中筛选受正向选择的基因，是探究协同进化动力学、开发疫苗与药物的核心研究目标之一。为阐明宿主特化相关的功能机制，本研究旨在从寄生于不同宿主的近缘病原体类群中，筛选出可能经历正向选择进化的候选序列。为达成该研究目标，我们对4个Microbotryum（黑粉菌属）物种分别开展测序，每个物种获取约17000~32000条EST（Expressed Sequence Tags，表达序列标签）；该属真菌为引发石竹科（Caryophyllaceae）宿主植物花药黑粉病的致病菌。在预测得到的372个直系同源基因中，有42个呈现出显著的正向选择信号，这为后续研究提供了数量可观的候选基因。我们对另外9个Microbotryum（黑粉菌属）物种中的16个此类基因进行测序验证后证实，这些基因在寄生于不同宿主的病原体类群中确实处于快速进化状态。呈现显著正向选择信号的基因，其推定功能涵盖宿主营养摄取、次生代谢物合成与分泌、胁迫条件下的呼吸作用与应激响应、菌丝生长与分化，以及其他基因的表达调控。此类基因中多数含有跨膜结构域，因此可能还参与宿主对病原体的识别过程。综上，本研究方法成效斐然，且对于众多亟需获取趋异选择候选基因的非模式生物而言，该方案具备切实可行的推广价值。