The predicted bacterial protein sequences were searched against the National Center for Biotechnology Information (NCBI) nonredundant (NR) and the Clusters selleck kinase inhibitor of Orthologous Groups (COG) databases using BLASTP. The tRNAScanSE tool [32] was used to find tRNA genes, whereas ribosomal RNAs were found by using RNAmmer [33] and BLASTn against the NR database. ORFans were identified if their BLASTP E-value were lower than 1e-03 for alignment length greater than 80 amino acids. If alignment lengths were smaller than 80 amino acids, we used an E-value of 1e-05. Such parameter thresholds have already been used in previous works to define ORFans. Genome properties The genome is 4,186,486 bp long (one chromosome but no plasmid) with a 59.73% GC content (Table 3 and Figure 5).

Of the 3,901 predicted genes, 3,847 were protein-coding genes, and 54 were RNAs. A total of 2,924 genes (74.95%) were assigned a putative function. ORFans accounted for 312 (8.0%) of the genes. The remaining genes were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4. The properties and the statistics of the genome are summarized in Tables 3 and and44. Table 3 Nucleotide content and gene count levels of the genome Figure 5 Graphical circular map of the chromosome. Genes are colored according to their COG categories as follows: information storage and processing (blue), cellular processing and signaling (green), metabolism (red) and poorly characterized (grey). Table 4 Number of genes associated with the 25 general COG functional categories Comparison with Herbaspirillum seropedicae To date, the genome from H.

seropedicae strain SmR1 is the only genome from Herbaspirillum species that has been sequenced [34]. By comparison with H. seropedicae, H. massiliense exhibited a smaller genome (4,186,486 bp vs 5,513,887 bp, respectively), a lower G+C content (59.73% vs 63.4%, respectively) and a smaller number of genes (3,901 vs 4,804). In contrast, H. massiliense had higher ratios of genes per Mb (0.93 vs 0.87) and genes with assigned functions (74.9% vs 64.7%). Conclusion On the basis of phenotypic, phylogenetic and genomic analyses, we formally propose the creation of Herbaspirillum massiliense sp. nov. that contains the strain JC206T. This bacterium has been found in Senegal. Description of Herbaspirillum massiliense sp.

nov. Herbaspirillum massiliense (mas.il.ien��se. L. gen. neutr. n. massiliense, of Massilia, the Latin name of Marseille where strain JC206T was cultivated). Colonies are 0.5 mm in diameter on blood-enriched Columbia agar and Brain Heart Infusion (BHI) agar. Cells are rod-shaped with a mean diameter of 0.44 ��m. Motile AV-951 with tufts of polar flagellae optimal growth occurs under aerobic conditions. Weak growth is observed under microaerophilic conditions and with 5% CO2.