Samples for RNA-seq analysis (n = 3) were prepared as described in the TruSeq® RNA Sample Preparation Guide (Illumina). High-performance, paired-end (2 × 100 bp) sequencing was performed on an Illumina Hiseq 1500 apparatus by the Institute of Agrobiotechnology of Rosario (Rosario, Argentina). Low-quality RNA-Seq reads (QScore < Q30) detected using FastQC (Version 0.11.2) were discarded (Andrews 2010 ). De novo assembly was performed by merging the high-quality reads using Trinity software (Grabherr et al. 2011 (link)) with a minimum contig length of 200 bases and a k-mer size of 25 bp. Functional annotation of assembled transcripts was performed by homology search (BLAST/Uniprot and SwissProt), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and annotation databases search (eggnog/GO/Kegg) using Trinotate pipeline (Bryant et al. 2017 (link)).
The reads' FPKM (Fragments Per Kilobase Million) value was determined by the eXpress abundance estimation method (Roberts and Pachter 2013 (link)). Fold change for selected transcripts was estimated by FPKM of L. corniculatus / FPKM of L. tenuis.
The reads' FPKM (Fragments Per Kilobase Million) value was determined by the eXpress abundance estimation method (Roberts and Pachter 2013 (link)). Fold change for selected transcripts was estimated by FPKM of L. corniculatus / FPKM of L. tenuis.
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