BACKGROUND: While multiple replication origins have been observed in archaea, 
considerably less is known about their evolutionary processes. Here, we 
performed a comparative analysis of the predicted (proved in part) 
orc/cdc6-associated replication origins in 15 completely sequenced haloarchaeal 
genomes to investigate the diversity and evolution of replication origins in 
halophilic Archaea.
RESULTS: Multiple orc/cdc6-associated replication origins were predicted in all 
of the analyzed haloarchaeal genomes following the identification of putative 
ORBs (origin recognition boxes) that are associated with orc/cdc6 genes. Five of 
these predicted replication origins in Haloarcula hispanica were experimentally 
confirmed via autonomous replication activities. Strikingly, several predicted 
replication origins in H. hispanica and Haloarcula marismortui are located in 
the distinct regions of their highly homologous chromosomes, suggesting that 
these replication origins might have been introduced as parts of new genomic 
content. A comparison of the origin-associated Orc/Cdc6 homologs and the 
corresponding predicted ORB elements revealed that the replication origins in a 
given haloarchaeon are quite diverse, while different haloarchaea can share a 
few conserved origins. Phylogenetic and genomic context analyses suggested that 
there is an original replication origin (oriC1) that was inherited from the 
ancestor of archaea, and several other origins were likely evolved and/or 
translocated within the haloarchaeal species.
CONCLUSION: This study provides detailed information about the diversity of 
multiple orc/cdc6-associated replication origins in haloarchaeal genomes, and 
provides novel insight into the evolution of multiple replication origins in 
Archaea.