Data from: Transcriptomic basis of genome by genome variation in a legume-rhizobia mutualism

In the legume-rhizobia mutualism, the benefit each partner derives from the other depends on the genetic identity of both host and rhizobial symbiont. To gain insight into the extent of genome x genome interactions on hosts at the molecular level and to identify potential mechanisms responsible for the variation, we examined host gene expression within nodules (the plant organ where the symbiosis occurs) of four genotypes of Medicago truncatula grown with either Ensifer meliloti or E. medicae symbionts. These host x symbiont combinations show significant variation in nodule and biomass phenotypes. Likewise, combinations differ in their transcriptomes:  host, symbiont, and host x symbiont affected the expression of 70%, 27% and 21%, respectively, of the approximately 27,000 host genes expressed in nodules. Genes with the highest levels of expression often varied between hosts and/or symbiont strain and include leghemoglobins that modulate oxygen availability and hundreds of Nodule Cysteine-Rich (NCR) peptides involved in symbiont differentiation and viability in nodules. Genes with host x symbiont dependent expression were enriched for functions related to resource exchange between partners (sugar/sulfate/iron/amino acid transport and dicarboxylate/amino acid synthesis). These enrichments suggest mechanisms for host control of the currencies of the mutualism. The transcriptome of M. truncatula accession HM101 (A17), the reference genome used for most molecular research, was less affected by symbiont identity than the other hosts. These findings underscore the importance of assessing the molecular basis of variation in ecologically important traits, particularly those involved in biotic interactions, in multiple genetic contexts.

在豆科植物-根瘤菌互利共生体系中，双方从彼此获取的收益取决于宿主与根瘤菌共生体双方的遗传特征。为深入解析宿主层面基因组-基因组互作的分子范围与机制，并明确导致表型变异的潜在原因，本研究针对四种基因型的蒺藜苜蓿（*Medicago truncatula*）展开分析：这些宿主分别与苜蓿中华根瘤菌（*Ensifer meliloti*）或医研根瘤菌（*Ensifer medicae*，简称E. medicae）共生，研究人员检测了其根瘤（共生过程发生的植物器官）内的宿主基因表达情况。

上述宿主-共生体组合在根瘤与生物量表型上呈现显著差异。同理，各组合的转录组也存在明显分化：宿主、共生体以及宿主-共生体互作分别影响了根瘤中表达的约27000个宿主基因中的70%、27%和21%。

表达量最高的基因往往因宿主和/或共生体菌株而异，其中包括调控氧气可用性的豆血红蛋白，以及数百个参与共生体分化与根瘤内存活力的根瘤富半胱氨酸（Nodule Cysteine-Rich, NCR）肽。

受宿主-共生体互作依赖性调控表达的基因，其功能富集于互利双方资源交换相关的通路（包括糖/硫酸盐/铁/氨基酸转运以及二羧酸/氨基酸合成）。这些富集结果提示了宿主调控互利共生交换介质的潜在机制。

作为多数分子研究所用参考基因组的蒺藜苜蓿品系HM101（A17），其转录组受共生体遗传背景的影响程度低于其他宿主。

本研究结果凸显了在多种遗传背景下，评估生态重要性状（尤其是参与生物互作的性状）变异的分子基础的重要性。