Background The human oocyte transmits one set of haploid genome into female pronucleus (FPN) while discards the remaining genome into the first polar body (PB1) and the second polar body (PB2). The FPN genome carries an assembly of maternal and paternal genome that resulted from homologous recombination during the prophase of the first meiosis. However, how parental genome has been shuffled and transmitted is difficult to assess by analysing only the progeny’s genome.

Objective To assess meiotic chromatid recombination and segregation in human oocytes.

Methods Single cell genome sequencing data of PB1, PB2 and FPN that originated from the same oocyte were used to analyse the human oocyte homologous chromosome interaction and segregation. To analyse whether chromosomes were non-randomly segregated into polar bodies or pronucleus, we analysed the ratio of crossover in PB2 and FPN, and constructed a model to detect the randomness of oocyte chromosome segregation.

Results We found that during oocyte meiosis, in addition to homologous chromosome recombination, there was also a genome conversion phenomenon which generated a non-reciprocal genetic information transmission between homologous chromosomes. We also inferred that during meiosis, DNA breaks and repairs frequently occurred at centromere-adjacent regions. From our data we did not find obvious evidence supporting the crossover number-based or SNP-based meiotic drive in oocytes.

Conclusion In addition to the crossover-based recombination, during human oocyte meiosis, a direct genome conversion between homologous chromosomes is used in some oocytes. Our findings are helpful in understanding the specific features of meiotic chromatid recombination and segregation in human oocytes.