Essential genes for in vitro growth of the endophyte Herbaspirillum seropedicae SmR1 revealed by Tn-seq

To identify genes critical for growth of H. seropedicae, Tn mutant libraries were constructed under nutrient-rich conditions, i.e. in TY medium, using a biparental mating protocol. A total of six Tn mutant libraries were constructed with sizes ranging between 24,000 and 140,000 colony forming units (CFU). Tn insertion site sequencing (Tn-seq) was performed using Illumina sequencing. Tn-seq Illumina sequence reads were demultiplexed using the FastX toolkit barcode splitter and analysed using the ESSENTIALS pipeline.