DOI: 10.5061/dryad.348k2
title: Data from: Transcriptomic basis of genome by genome variation in a legume-rhizobia mutualism

description: 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.
description: HxSPhenotypingDataTab delimited raw symbiosis phenotype dataHxSPhenotypeAnalysisR code to analyze the raw symbiosis phenotypesExpressedNodGenesTableTab delimited file that summarizes expression category results and cluster membership for all the genes found to be expressed in nodulesExpressedGenesNodTableDryad.txtRNAseqcounts_allconditions_headA tab delimited file containing raw gene counts of all RNAseq samples and for all Mtv4 genesDESeq2codeR source code for the differential expression analysisDeSeq2code_Dryad.RFullModelHostSymResultsTab delimited file with DEseq2 output summarizing full model results for all genes expressed in nodules. Tabulated and compiled versions of the significance category results are in the ExpressedNodGenesTable.txt file which should be sufficient for most interested parties.FullModelRootResultsTab delimited file testing if host genotypes different in gene expression in roots. This is not emphasized in the paper but I included it in case anyone was interested.PairwiseResults.101.340Tab delimited file with pairwise test results and log fold changes in expression between HM101 and HM340 nodules containing E. medicae and E. melilotiPairwiseResults.101.056Tab delimited file with pairwise test results and log fold changes in expression between HM101 and HM056 nodules containing E. medicae and E. melilotiPairwiseResults.101.034Tab delimited file with pairwise test results and log fold changes in expression between HM101 and HM034 nodules containing E. medicae and E. melilotiPairwiseResults.056.340Tab delimited file with pairwise test results and log fold changes in expression between HM056 and HM340 nodules containing E. medicae and E. melilotiPairwiseResults.034.056Tab delimited file with pairwise test results and log fold changes in expression between HM034 and HM056 nodules containing E. medicae and E. melilotiPairwiseResults.034.340Tab delimited file with pairwise test results and log fold changes in expression between HM034 and HM340 nodules containing E. medicae and E. meliloti