Numerical simulations have been carried out to study and compare the mechanisms of the formations of the topside and bottomside ionospheric irregularities. As is well-known, the topside ionospheric irregularities have always originated from the bottomside ionosphere due to Gravitational Rayleigh-Taylor (GRT) instability. From the penetration process we found that the primary bubble with a horizontal scale of tens of kilometers always has a smooth shape in the bottomside ionosphere and breaks into much smaller-scale structures after penetrating into deep topside ionosphere. Since the plasma bubble is unlikely to break into irregularities in the bottomside ionosphere, the bottomside irregularities probably result from the turbulence in the neutral atmosphere. Examples of simulations are presented to demonstrate that bottomside irregularities may exist in a region with a strong neutral wind jet and seeding gravity wave motion. A strong neutral jet stream always has a strong vertical wind shear, which provides a broad height range of dynamic instability. When the atmospheric gravity wave approaches its critical level, its amplitude will continually grow to break into smaller-scale waves and turbulence. Then all the waves of different scales as well as the turbulence will become the seeds of the bottomside irregularities.