The chloroplast is the plant compartment in which light energy is captured and transformed into chemical energy, ultimately making life on Earth possible. They are descendants of free-living photosynthetic bacteria and maintain a small but essential genome. Most genes are transcribed into polycistrons that are then heavily processed by a combination of RNA-binding proteins and ribonucleases to produce the functional RNA population. One poorly understood aspect of chloroplast gene expression and regulation is the functions of asRNAs and more globally double-stranded RNA-related processes. One of the key enzymes in these processes is RNase J, whose characteristic is to be both a 5’-3’ exoribonuclease and an endoribonuclease. It trims RNA termini 5’ ends and eliminate deleterious antisense RNA that could harm translation. The goal of the JOAQUIN project is to gain a better understanding of chloroplast RNA quality control by (i) identifying the full set of chloroplast RNA isoforms and RNA-RNA duplexes and (ii) and understand how this transcriptome is shaped by RNase J. The substrate specificity of RNase J will be deciphered focusing on the land plant’s specific C-terminal GT-1 domain and by the identification of the protein and nucleic acids that co-purify with the enzyme.