 In addition to repairing DNA , homologous recombination also helps produce genetic diversity when cells divide in meiosis to become specialized gamete cells — sperm or egg cells in animals , pollen or ovules in plants , and spores in fungi . It does so by facilitating chromosomal crossover , in which regions of similar but not identical DNA are exchanged between homologous chromosomes . This creates new , possibly beneficial combinations of genes , which can give offspring an evolutionary advantage . Chromosomal crossover often begins when a protein called Spo11 makes a targeted double @-@ strand break in DNA . These sites are non @-@ randomly located on the chromosomes ; usually in intergenic promoter regions and preferentially in GC @-@ rich domains These double @-@ strand break sites often occur at recombination hotspots , regions in chromosomes that are about 1 @,@ 000 – 2 @,@ 000 base pairs in length and have high rates of recombination . The absence of a recombination hotspot between two genes on the same chromosome often means that those genes will be inherited by future generations in equal proportion . This represents linkage between the two genes greater than would be expected from genes that independently assort during meiosis . 
