Over time, many parts of the chloroplast genome were transferred to the nuclear genome of the host, a process called endosymbiotic gene transfer.
As a result, the chloroplast genome is heavily reduced compared to that of free-living cyanobacteria. Chloroplasts may contain 60–100 genes whereas cyanobacteria often have more than 1500 genes in their genome. Contrarily, there are only a few known instances where genes have been transferred to the chloroplast from various donors, including bacteria.
Endosymbiotic gene transfer is how we know about the lost chloroplasts in many chromalveolate lineages. Even if a chloroplast is eventually lost, the genes it donated to the former hosts nucleus persist, providing evidence for the lost chloroplasts existence. For example, while diatoms (a heterokontophyte) now have a red algal derived chloroplast, the presence of many green algal genes in the diatom nucleus provide evidence that the diatom ancestor (probably the ancestor of all chromalveolates too) had a green algal derived chloroplast at some point, which was subsequently replaced by the red chloroplast.
In land plants, some 11–14% of the DNA in their nuclei can be traced back to the chloroplast, up to 18% in Arabidopsis, corresponding to about 4,500 protein-coding genes. There have been a few recent transfers of genes from the chloroplast DNA to the nuclear genome in land plants.