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Background  Apomixis is an intriguing trait in plants that results in maternal clones through seed reproduction. Apomixis is an elusive, but potentially revolutionary, trait for plant breeding and hybrid seed production. Recent studies arguing that apomicts are not evolutionary dead ends have generated further interest in the evolution of asexual flowering plants.    Results  In the present study, we investigate karyotypic variation in a single chromosome responsible for transmitting apomixis, the Apospory-Specific Genomic Region carrier chromosome, in relation to species phylogeny in the genera  Pennisetum  and  Cenchrus . A 1 kb region from the 3' end of the  ndh F gene and a 900 bp region from  trn L-F were sequenced from 12 apomictic and eight sexual species in the genus  Pennisetum  and allied genus  Cenchrus . An 800 bp region from the Apospory-Specific Genomic Region also was sequenced from the 12 apomicts. Molecular cytological analysis was conducted in sixteen  Pennisetum  and two  Cenchrus  species. Our results indicate that the Apospory-Specific Genomic Region is shared by all apomictic species while it is absent from all sexual species or cytotypes. Contrary to our previous observations in  Pennisetum squamulatum  and  Cenchrus ciliaris , retrotransposon sequences of the Opie-2-like family were not closely associated with the Apospory-Specific Genomic Region in all apomictic species, suggesting that they may have been accumulated after the Apospory-Specific Genomic Region originated.    Conclusions  Given that phylogenetic analysis merged  Cenchrus  and newly investigated  Pennisetum  species into a single clade containing a terminal cluster of  Cenchrus  apomicts, the presumed monophyletic origin of  Cenchrus  is supported. The Apospory-Specific Genomic Region likely preceded speciation in  Cenchrus  and its lateral transfer through hybridization and subsequent chromosome repatterning may have contributed to further speciation in the two genera.

Evolution of the apomixis transmitting chromosome in Pennisetum