Library construction and sequencing
Isolated RNA was separated into two fractions. The first fraction included eukaryotic mRNA that was extracted from total RNA by NEBNext® Poly(A) mRNA Magnetic Isolation Module (BioLabs) following manufacturers’ protocol. The second fraction (bacterial RNA and eukaryotic rRNA) was extracted from the supernatant after mRNA separation by RNAClean XP beads (Beckman Coulter). Both fractions were used for library constructions. cDNA libraries were built by Zymo-Seq RiboFree Total RNA-Seq Library Kit (Zymo Research) following manufacturers’ protocol. The quality of cDNA libraries was then visualized on Bioanalyzer by High Sensitivity DNA Kit (Agilent). Libraries were sequenced at CEITEC institute (Brno, Czechia) on the Illumina novaseq platform on a 2x 150 bp paired-end reads run.