Genomics of Rhodococcus for Biofuels Figure 3. Analysis of genes and gene families implicated in the TAGs cycle. a) The number of genes in the TribeMCL gene-clusters implicated by metabolic reconstruction for each reaction of the TAGs cycle are displayed in a heat map with species clustered according to their TAGs cycle genetic profile. The number of genes corresponding to TribeMCL gene-clusters implicated for each biochemical reaction (EC number) is color coded from 0 to .15. b) The sum of unique genes for each bacterial species implicated for the TAGs cycle by metabolic reconstruction and TribeMCL analysis. doi:10.1371/journal.pgen.1002219.g003 (Figure 1a). Streptomyces are rich in methyl-branched lipids [40,41] that are shorter than the methyl-branched lipids observed in Mycobacterium indicating a difference in the biosynthetic workload between MAS-family and FAS II genes that could result from the absence of the type 1a synthase gene in Streptomyces. Large Expansions of Gene Families Implicated in the Rhodococcus TAGs Cycle of Biosynthesis and Catabolism The TAGs cycle includes twenty distinct enzymatic reactions starting from acetyl-CoA. The biochemical details of this cycle are presented with the corresponding EC number (Figure S5)(http:// tinyurl.com/TAGs-cycle). The large expansions in homologous genes implicated in the TAGs cycle we identified in our initial metabolic reconstruction led us to further analyze the gene- families. We grouped the implicated TAGs cycle genes and families of genes based on protein similarity using the TribeMCL algorithm [42] on a small set of related bacterial species. We found that the genus Rhodococcus was deeply enriched in TAGs cycle genes including gene-families of very different sizes and there were no metabolic deficiencies in the multi-step metabolic-cycle PLoS Genetics | www.plosgenetics.org 6 September 2011 | Volume 7 | Issue 9 | e1002219