Additional file 9: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

Plant transcripts in fasta format. Transcript-ids in the fasta file correspond to those described in Additional file 8. Compressed .tar.gz text file. (GZ 8552 kb

Additional file 12: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

Microbial-assigned transcripts, full results table, annotation and DESeq2 analysis. Description of File: The table includes information on expressed microbial transcripts. 1) Phylogenetic annotation of each transcript; 2) Whether significantly expressed in root acid bog soil (RA), root limestone soil (RL), shoot acid bog soil (SA) and/or shoot limestone soil (SL). Significantly expressed transcripts is defined as the number of microbial annotated transcripts that obtained ≥5 aligned reads in at least 3 samples in each of the treatments RA (total 8 samples), RL (total 9 samples), SA (total 10 samples), SL (total 9 samples); 3) two columns indicating whether the transcript is “upregulated in acid or limestone ecotype in acid bog soil” and/or “upregulated in acid or limestone ecotype in limestone soil” 4) KOG functional annotation (KOG ID, KOG definition, KOG class, KOG group) and best BLAST match (sequence length, database that contained the best match, accession number, gene description, best match organism, e-value, percentage ID, BLAST score, percentage sequence coverage); 5) The full DESeq2 result for each pairwise comparison in shoot (list 1-4) and root (list 5-8): these columns contain the log2foldchange and adjusted P value (FDR) for pairwise comparisons. Pairwise comparisons are coded as follows: soil (A = acid bog soil, L = limestone quarry soil), plant ecotype (a = acid bog plant ecotype, l = limestone quarry plant ecotype), shoots and roots (Shoot, Root), see sheet “DESeq2 pairwise comparisons” for further explanation of the 8 pairwise comparisons; 6) The count table. (XLSX 6498 kb

Additional file 7: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

Additional references cited in Additional file 6 and Additional file 11. (DOCX 32 kb

Additional file 14: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

Significantly expressed and KOG annotated Glomeromycotina transcripts in root and shoot in each soil. The number of significantly expressed and KOG annotated Glomeromycotina transcripts (All) is defined as the number of transcripts that obtained ≥5 aligned reads in at least 3 samples from each of the following treatments: root acid bog soil (RA), root lime soil (RL), shoot acid bog soil (SA) and shoot lime soil (SL). Significant ecotype effects (absolute log2FC ≥ 1 or ≤ − 1, FDR <  0.05) as identified by DESeq2 analysis are reported in subsequent columns for each treatment group, under the heading plant effect. (DOCX 27 kb

Additional file 16: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

Colonization percentages of AM hyphae, non-AM hyphae, arbuscules and vesicles, in acid bog and limestone quarry ecotypes of H. lanatus, grown in a reciprocal soil transplantation design. (A = acid bog soil, L = limestone quarry soil), plant ecotype (a = acid bog plant ecotype, l = limestone quarry plant ecotype). (DOCX 18 kb

Additional file 15: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

Microbial transcripts in fasta format. Transcript-ids in the fasta file correspond to those described in Additional file 12. Compressed .tar.gz text file. (GZ 2398 kb

Additional file 17: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

AM and non-AM fungal structures of stained H. lanatus roots of (a, b) acid bog ecotype on acid bog soil; (c, d) limestone quarry ecotype on acid bog soil; (e, f) acid bog ecotype on limestone quarry soil; (g, h) limestone quarry ecotype on limestone quarry soil. (DOCX 93871 kb

Additional file 11: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

Selected fungal annotated transcript results, including those discussed in the text. The table contains the following information for selected microbial assigned transcripts that are expressed in Holcus lanatus roots, many of which discussed in the text: 1) Transcript ID; 2) Best BLAST match (taxonomic division, genus and gene description); 3) KOG annotations (KOG ID, KOG group, KOG class, KOG definition); 4) possible role; 5) relevant reference (citations for relevant references are contained in Additional file 7); 6) two columns to indicate whether the transcript was significantly upregulated in acid or limestone soil, acid or limestone ecotype; 7) The full DESeq2 result for each root pairwise comparison: these columns contain the log2foldchange and adjusted P value (FDR) for root pairwise comparisons. Pairwise comparisons are coded as follows: soil (A = acid bog soil, L = limestone quarry soil), plant ecotype (a = acid bog plant ecotype, l = limestone quarry plant ecotype): Root Aa-v-La = Acid bog soil acid ecotype versus Limestone soil acid ecotype, Root Al-v-Ll = Acid bog soil limestone ecotype versus Limestone soil limestone ecotype, Root Aa-v-Al = Acid bog soil acid ecotype versus Acid bog soil limestone ecotype, Root La-v-Ll = Limestone soil acid ecotype versus Limestone soil limestone ecotype. (XLSX 35 kb

Additional file 8: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

Plant-assigned transcripts, full results table, annotation and DESeq2 analysis. The table contains the following information for each expressed plant-assigned transcript: 1) The annotation of transcripts: this includes functional annotation (KOG class, KOG group, KOG definition) and best BLAST match against plant-refseq (match accession number, match description, percentage ID, BLAST score, length of alignment and percentage sequence coverage); 2) The full DESeq2 result for each pairwise comparison in shoot (list 1-4) and root (list 5-8): these columns contain the log2foldchange and adjusted P value (FDR) for pairwise comparisons. Pairwise comparisons are coded as follows: soil (A = acid bog soil, L = limestone quarry soil), plant ecotype (a = acid bog plant ecotype, l = limestone quarry plant ecotype) in shoots and roots: Shoot Aa-v-La = Acid bog soil acid ecotype versus Limestone soil acid ecotype, Shoot Al-v-Ll = Acid bog soil limestone ecotype versus Limestone soil limestone ecotype, Shoot Aa-v-Al = Acid bog soil acid ecotype versus Acid bog soil limestone ecotype, Shoot La-v-Ll = Limestone soil acid ecotype versus Limestone soil limestone ecotype, Root Aa-v-La = Acid bog soil acid ecotype versus Limestone soil acid ecotype, Root Al-v-Ll = Acid bog soil limestone ecotype versus Limestone soil limestone ecotype, Root Aa-v-Al = Acid bog soil acid ecotype versus Acid bog soil limestone ecotype, Root La-v-Ll = Limestone soil acid ecotype versus Limestone soil limestone ecotype; 3) The count table; 4) Additional BLAST annotations showing the best BLAST match against Arabidopsis lyrata, Arabidopsis thaliana and Brachypodium distachyon databases (sequence length, match accession number, e-value, percentage ID, BLAST score and length of alignment). (XLSX 18037 kb

Additional file 10: of Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

Additional qPCR information. Targets and primers used for qPCR and comparison of results obtained with RNA-Seq and qPCR. (DOCX 22 kb