bethesdensis (AY788950), A. cryptum (D30773), Swaminathania salitolerans (AB445099), Saccharibacter floricola (NR_024819), and Neoasaia chiangmaiensis (AB208549), were obtained from the NCBI website at http://www.ncbi.nlm.nih.gov/. To construct the phylogenetic tree of AAB, these 37 sequences were collected and nucleotide sequence alignment was carried out using clustalw (Larkin et al., 2007). We Cell Cycle inhibitor used the mega version 4.0 package

to generate phylogenetic trees to study the phylogenetic relationship based on 16S rRNA gene with the neighbor-joining (NJ) approach and 1000 bootstrap replicates (Tamura et al., 2007). Three hundred and ninety-one unique complete microbial genome sequences (one genome per genus) were obtained from the NCBI FTP website at ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/. Only amino acid-coding sequences on the chromosomes were used

for comparative analysis. For a homology search, a dataset of all proteins was constructed. The dataset of all proteins was constructed from all amino acid sequences from 391 complete microbial genomes. Four hundred and forty-three proteins on the KEGG metabolic map of G. oxydans were used as a query for the blastp homology search against the dataset of all proteins (Altschul et al., 1997; Kanehisa, 1997; Ogata et al., 1999; Kanehisa & Goto, 2000; LY2835219 Kanehisa et al., 2002, 2004, 2006, 2008, 2010). Of the 443 proteins, 293 were selected for further analysis because these ORFs exist in all three genera, Gluconobacter, Gluconacetobacter, and Acetobacter. Each homolog was identified by a homology search of amino acid sequence using the blastp filtering

expectation value of e-value ≤10−10 and sequence overlap ≥70% (Altschul et al., 1997). The top 50 hits were collected and multifasta files were created for phylogenetic analysis using house-written ruby scripts. The previously published complete genome sequences MRIP of Acetobactericeae, G. oxydans, G. diazotrophicus, A. pasteurianus, G. bethesdensis, and A. cryptum were obtained from the NCBI FTP website at ftp://ftp.ncbi.nih.gov/genomes/Bacteria/ (Prust et al., 2005; Greenberg et al., 2007; Azuma et al., 2009; Bertalan et al., 2009). Only protein-coding genes on the chromosomes were used for the identification of orthologous groups. Each orthologous gene was identified by homology searches for amino acid sequence using the blastp filtering expectation value of e-value ≤10−10 and sequence overlap ≥70% (Altschul et al., 1997). All ORFs were searched against each species, and the reciprocal best hits were regarded as being orthologous genes. If genes were orthologous among all species present, the group was defined as a unique orthologous dataset.