Data for "The mycorrhizal root-shoot axis elicits Coffea arabica growth under low phosphate conditions"

This folder contains relevant datasets generated in the study:Chialva M., Patono D.L, de Souza L.P., Novero M., Vercellino S., Maghrebi M., Morgante M., Lovisolo C., Vigani G., Fernie A., Fiorilli V., Lanfranco L., Bonfante P. (2023) The mycorrhizal root-shoot axis elicits <i>Coffea arabica</i> growth under low phosphate conditions.<i> The New Phytol.</i>, 239(1), 271-285.<br><b><i>RNA-seq dataset and annotations</i></b>RNAseq_raw_counts.tsv &gt; Raw mRNA-seq reads counts obtained by pseudo-aligning reads on the <i>C. arabica</i> reference transcriptome (NCBI reference genome accession GCF_003713225.1) using Salmon software in selective alignment mode and summarized using 'tximport' library in R.interproscan_proteins.local.tsv &gt; the parsed InterProScan analysis output run on known <i>Coffea arabica</i> proteins (NCBI reference genome accession GCF_003713225.1).gene2ko.tsv &gt; Protein IDs to Kegg Orthologs (KO) IDs obtained using KAAS server.<br><b><i>Orthogroups inference</i></b>Orthogroups predicted with Orthofinder (v.2.5.4) on <i>Coffea arabica, C. canephora, C. eugenioides, S. lycopersicum, P. trichocarpa, M. truncatula, </i>and<i> Vitis vinifera</i> proteomesHOGs_N0.tsv &gt; Phylogenetic Hierachical Orthogroups (HOGs) predicted by Orthofinder on proteomes at N0 hierachical levelOrthogroups.tsv &gt; Orthogroups predicted by Orthofinder (v.2.5.4) on proteomes (old-way)OGs.tsv &gt; refined OGs used in this study (manually integrating some missing genes)<br><b><i>Metabolomics</i></b>Metabolites_DB.xlsx &gt; An exhaustive list of detected coffee metabolites in previous studies used to enhance annotation of LC-MS spectra generated in this study.<br><i>Note: Sample names are coded by condition (M or MYC=mycorrhizal plants, C or NM=non-mycorrhized controls) and by organ type (s=leaves, r=roots)</i>