I found that the overexpression of gene in C. reinhardtii always use the non homologous random insertion. I just wonder is that OK to inserted a gene into the chromosome of C. reinhardtii with the homologous recombination.
Lots of people have tried many methods to promote homologous recombination in Chlamydomonas with little success (i.e., rates so low that you need a strong selection to find such an event). From many, many random insertions of various expresssion constructs, we find that some do shut down over time, but others continue to express at similar levels, without selection, for many years. We always select multiple different insertion events, and check them for expression level soon after growing and again after about 2 months. At that point, those that still express are usually stable. Some of these are coupled to selectable markers, so the selection can also be tested, but others are simple gene cassettes with selection on a separate plasmid, so that genetics can be used to separate the insertion of interest from the selection marker, and additional genes can then be transformed in using the same selection.