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-根瘤菌共生（legume-rhizobia mutualism）体系中，共生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。为从分子层面解析宿主层面的基因组-基因组互作（genome × genome）范围，并明确导致表型差异的潜在机制，本研究对4种基因型蒺藜苜蓿（Medicago truncatula）分别与苜蓿中华根瘤菌（Ensifer meliloti）或E. medicae共生体进行共培养，进而检测其根瘤（nodule，共生发生的植物器官）内的宿主基因表达情况。此类宿主-共生体互作（host × symbiont）组合在根瘤与生物量表型上存在显著差异；同理，各组合的转录组（transcriptome）亦存在分化：宿主因子、共生体因子以及宿主-共生体互作分别调控根瘤中约27000个表达的宿主基因的70%、27%与21%。高表达基因往往因宿主和/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（leghemoglobins），以及数百个参与共生体分化与根瘤内存活力维持的根瘤富含半胱氨酸肽（Nodule Cysteine-Rich, NCR）。受宿主-共生体互作调控的表达基因，其功能富集于双方资源交换相关通路（糖/硫酸盐/铁/氨基酸转运以及二羧酸/氨基酸合成）。此类功能富集现象揭示了宿主调控共生体系交换因子的潜在机制。蒺藜苜蓿品系HM101（A17）是多数分子研究采用的参考基因组，其转录组受共生体遗传特征的影响程度低于其余宿主基因型。本研究结果凸显了在多种遗传背景下，解析生态重要性状（尤其是参与生物互作的性状）差异的分子基础的重要性。