zygotene

Zygotene is a substage of prophase I in meiosis, occurring after leptotene and before pachytene. During zygotene chromosomes condense further and homologous chromosomes begin to pair in a process called synapsis. The pairing is facilitated by the formation of the synaptonemal complex, a protein scaffold that holds homologs together along their lengths. Telomeres often cluster at the nuclear envelope in a bouquet arrangement, which is thought to promote homology search and pairing.

In this stage, homologous chromosomes start to align as bivalents, though full synapsis is not yet complete across all chromosomal regions. Recombination machinery becomes active, with programmed double-strand breaks initiating the process of genetic exchange. These breaks are processed by recombination proteins to facilitate strand invasion and the early steps of crossing over, which will be completed in later stages of meiosis.

By the end of zygotene, synapsis has begun along much of the chromosome length in many organisms, though the extent and timing of complete synapsis can vary among species. The stage transitions into pachytene, where synapsis is more extensive and crossing over becomes more evident as chiasmata form.

The name zygotene derives from Greek roots referring to pairing or yoked together, reflecting the key feature of this stage: the initial pairing of homologous chromosomes. Zygotene is thus a transitional phase that links chromosome condensation and early pairing with the more complete synapsis and recombination activities of pachytene.