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A spreading technique was used to perform a structural analysis of prophase I nuclei in pollen mother cells (PMCs) of wild-type Arabidopsis thaliana. In leptotene, all chromosomes developed fully axial elements before a presynaptic alignment was observed. Pairing and synapsis start in regions close to the telomeres at early zygotene. Interstitial synaptonemal complex (SC) stretches were found to occur at several sites per bivalent at mid zygotene. Within individual bivalents, extensive regions of SC formation often existed at the same time as other extensive regions that were unsynapsed. Also in the same nucleus, one bivalent might have several SC segments, while other bivalents have only a few. The classical bouquet was not so evident as in other plant species. Length measurements of the five pachytene bivalents have allowed the elaboration of a pachytene karyotype. Pachytene chromatin compaction in Arabidopsis was significantly less than that observed in the other species analysed and this is paralleled with a higher recombination rate (centimorgans per megabase).