The synaptonemal complex is a protein which forms between homolgous chromosomes. The synaptonemal complex begins to form during the zygotene phase of Prophase I in Meiosis and is complete in the pachytene phase. Acting like a 'zipper' it holds the homologous chromosomes together, aligning them perfectly. After complete synapsis, crossing over occurs and in the diplotene phase, where the chiasma is visible, the synaptonemal complex 'unzips' and disappears.
Hartl DL and Jones EW (2009) Genetics: Analysis of Genes and Genomes, Seventh Edition, USA, Jones and Bartlett Publishers