Data from: Population genomics of a symbiont in the early stages of a pest invasion

Invasive species often depend on microbial symbionts, but few studies have examined the evolutionary dynamics of symbionts during the early stages of an invasion. The insect Megacopta cribraria and its bacterial nutritional symbiont Candidatus Ishikawaella capsulata invaded the southeastern US in 2009. While M. cribraria was initially discovered on wild kudzu plants, it was found as a pest on soybeans within 1 year of infestation. Because prior research suggests Ishikawaella confers the pest status—that is, the ability to thrive on soybeans—in some Megacopta species, we performed a genomic study on Ishikawaella from US. Megacopta cribraria populations to understand the role of the symbiont in driving host plant preferences. We included Ishikawaella samples collected in the first days of the invasion in 2009 and from 23 locations across the insect's 2011 US range. The 0.75 Mb symbiont genome revealed only 47 fixed differences from the pest-conferring Ishikawaella in Japan, with only one amino acid change in a nutrition-provisioning gene. This similarity, along with a lack of fixed substitutions in the US symbiont population, indicates that Ishikawella likely arrived in the US capable of being a soybean pest. Analyses of allele frequency changes between 2009 and 2011 uncover signatures of both positive and negative selection and suggest that symbionts on soybeans and kudzu experience differential selection for genes related to nutrient provisioning. Our data reveal the evolutionary trajectory of an important insect-bacteria symbiosis in the early stages of an invasion, highlighting the role microbial symbionts may play in the spread of invasive species.

入侵物种通常依赖微生物共生体，但目前鲜有研究探讨入侵初期共生体的演化动态。2009年，昆虫筛豆龟蝽（Megacopta cribraria）及其营养共生细菌候选石川氏菌（Candidatus Ishikawaella capsulata）入侵美国东南部地区。筛豆龟蝽最初在野生野葛上被发现，但在入侵后一年内就被报道为大豆害虫。鉴于已有研究表明，部分筛豆龟蝽物种体内的候选石川氏菌可赋予其害虫属性——即能够在大豆上存活繁殖的能力，本研究对美国本土筛豆龟蝽种群中的候选石川氏菌开展基因组学分析，以解析共生体在介导宿主植物偏好性中发挥的作用。本研究采集了2009年入侵初期的候选石川氏菌样本，以及2011年该昆虫美国分布区内23个采样点的样本。该共生体基因组大小为0.75 Mb，与日本可赋予害虫属性的候选石川氏菌仅存在47个固定差异位点，且仅在一个营养供给相关基因中存在1个氨基酸替换。这一相似性，加之美国共生体种群中未出现固定替换，表明候选石川氏菌入侵美国时就已具备成为大豆害虫的能力。对2009年至2011年等位基因频率变化的分析显示，同时存在正选择与负选择的信号，且取食大豆与野葛的共生体在营养供给相关基因上受到差异化选择压力。本研究数据揭示了入侵初期重要昆虫-细菌共生体系的演化轨迹，凸显了微生物共生体在入侵物种扩散过程中可能发挥的关键作用。