Novel genes related to product synthesis  of Clostridium ljungdahlii were identified  by Tn-seq analysis
We optimized the mariner-based transposon system pYG3 to generate a new system, pCYG4, which exhibited a substantially increased plasmid loss rate. Using pCYG4, we achieved random insertions into the chromosome of *Clostridium ljungdahlii* and constructed a transposon mutant library. This library was subsequently subjected to high-throughput sequencing, yielding the datasets reported in this study.