We report here a comparative analysis of the genome sequence of Methanosarcina 
barkeri with those of Methanosarcina acetivorans and Methanosarcina mazei. The 
genome of M. barkeri is distinguished by having an organization that is well 
conserved with respect to the other Methanosarcina spp. in the region proximal 
to the origin of replication, with interspecies gene similarities as high as 
95%. However, it is disordered and marked by increased transposase frequency and 
decreased gene synteny and gene density in the distal semigenome. Of the 3,680 
open reading frames (ORFs) in M. barkeri, 746 had homologs with better than 80% 
identity to both M. acetivorans and M. mazei, while 128 nonhypothetical ORFs 
were unique (nonorthologous) among these species, including a complete formate 
dehydrogenase operon, genes required for N-acetylmuramic acid synthesis, a 
14-gene gas vesicle cluster, and a bacterial-like P450-specific ferredoxin 
reductase cluster not previously observed or characterized for this genus. A 
cryptic 36-kbp plasmid sequence that contains an orc1 gene flanked by a 
presumptive origin of replication consisting of 38 tandem repeats of a 
143-nucleotide motif was detected in M. barkeri. Three-way comparison of these 
genomes reveals differing mechanisms for the accrual of changes. Elongation of 
the relatively large M. acetivorans genome is the result of uniformly 
distributed multiple gene scale insertions and duplications, while the M. 
barkeri genome is characterized by localized inversions associated with the loss 
of gene content. In contrast, the short M. mazei genome most closely 
approximates the putative ancestral organizational state of these species.