Data from: 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.

多种生物中的大量基因已被证实处于正向选择压力之下，其中尤以参与生殖、不同环境适应性、杂种不育以及宿主-病原体互作的基因为甚。在病原体中筛选处于正向选择压力下的基因，是研究协同进化动态、开发疫苗与药物的核心方向之一。为阐明宿主特化相关的分子功能，本研究旨在从不同宿主专化的近缘病原体中，筛选出可能经正向选择演化的候选序列。为此，我们对4种黑粉菌属（Microbotryum）物种分别进行了约17000~32000条表达序列标签（Expressed Sequence Tags, ESTs）的测序，该属真菌为引发石竹科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种黑粉菌属物种中的16个上述基因进行测序后证实，这些基因在不同宿主专化的病原体类群中确实经历了快速演化。呈现显著正向选择信号的基因，其推定功能涵盖从宿主获取营养、次生代谢产物的合成与分泌、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。其中多数基因携带跨膜结构域，因此也可能参与宿主对病原体的识别过程。综上，本研究方法取得了丰硕成果，且对于亟需获取趋异选择候选基因的诸多非模式生物而言，该方法具备可推广性。