More than 5000 chloroplast genomes have been sequenced and are accessible via the NCBI organelle genome database. The first chloroplast genomes were sequenced in 1986, from tobacco (Nicotiana tabacum) and liverwort (Marchantia polymorpha). Comparison of the gene sequences of the cyanobacteria Synechocystis to those of the chloroplast genome of Arabidopsis provided confirmation of the endosymbiotic origin of the chloroplast. It also demonstrated the significant extent of gene transfer from the cyanobacterial ancestor to the nuclear genome.
In most plant species, the chloroplast genome encodes approximately 120 genes. The genes primarily encode core components of the photosynthetic machinery and factors involved in their expression and assembly. Across species of land plants, the set of genes encoded by the chloroplast genome is fairly conserved. This includes four ribosomal RNAs, approximately 30 tRNAs, 21 ribosomal proteins, and 4 subunits of the plastid-encoded RNA polymerase complex that are involved in plastid gene expression. The large Rubisco subunit and 28 photosynthetic thylakoid proteins are encoded within the chloroplast genome.