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.