We provide here additional data obtained from our work: "Large-scale transcriptomics provides insights on the mycorrhizal symbiosis of the Mediterranean orchid Limodorum abortivum in nature".
**Description of content:**
***Trinity.fasta:***
raw transcriptome assembly obtained using trinity (default parameters, no filtering).
Be careful! The assembly, in addition to plant transcripts, contains quite a bit of fungal transcripts due to mychorriza. (We provide separated list later on).
***merged.gtf:***
assembled transcriptome obtained by remapping all the reads on the transcriptome using hisat2 and assembly the transcriptome using stringtie. This file also includes both plants and fungal transcripts.
***LM3.txt, LM4.txt, LM6.txt, LS2.txt, LS3.txt and LS6.txt:***
raw read counts on the transcripts assembled by stringtie (again, both plants and fungi present).
***AB_DE_raw_GO_KEGG_path_cazy.txt, plants_DE_raw_GO_KEGG_path_cazy.txt:***
results of differential expression, separated in fungal transcripts and plants transcripts (details on the separation process are provided in our paper).
Each of these files returns for each transcript the name (trinity_id=name in the original assembly, gene_id=names in the stringtie assembly), the result of DE analysis with DESeq2 for the gene (log2ratio, pvalue, etc. see DESeq2 manual for details), and annotation of the transcript according to several ontologies if available (GO, KEGG, Cazy).
Cazy pathways are scored on the dbcan web server using HMMER, Hotpep and DIAMOND (and the prediction tool signalP). These 4 columns are empty unless a match with a CAZYme has been identified.
