Non-coding genes and miscellaneous features were predicted using tRNAscan-SE , Infernal , RNAMMer , Rfam , TMHMM , and SignalP . Genome properties The genome includes one plasmid, for a total size of 3,222,008 bp, with one circular chromosome of 3,135,752 bp (68.44% G+C content) and one plasmid of 86,256 bp (63.20% G+C content) selleck chemicals Bosutinib [Figure 3 and Figure 4]. For the main chromosome, 2,856 genes were predicted, 2,791 of which are protein-coding genes. 1,632 (57%) of the protein-coding genes were assigned to a putative function with the remaining annotated as hypothetical proteins. 1,914 protein coding genes belong to 396 paralogous families in this genome corresponding to a gene content redundancy of 66.8%. The properties and the statistics of the genome are summarized in Table 3, Tables 4 and and55.
Figure 3 Graphical map of the chromosome (not drawn to scale with plasmid). From the outside in: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), GC content, GC skew. Figure 4 Graphical map of the plasmid pCha1 (not drawn to scale with chromosome). From the outside in: Genes on forward strand (color by COG categories), genes on reverse strand (color by COG categories), GC content, GC skew. Table 3 Summary of genome: one chromosome and one plasmid Table 4 Genome Statistics Table 5 Number of genes associated with the general COG functional categories Acknowledgements Christian R��ckert acknowledges funding through a grant by the Federal Ministry for Eduction and Research (0316017) within the BioIndustry2021 initiative.
Herbaspirillum massiliense strain JC206T (= CSUR P159 = DSMZ 25712) is the type strain of H. massiliense sp. nov. This bacterium was isolated from the stool of a healthy Senegalese patient. It is a Gram-negative, aerobic, flagellated, indole-negative bacillus. The current approach to classification of prokaryotes, generally referred to as polyphasic taxonomy, relies on a combination of phenotypic and genotypic characteristics . However, as more than 3,000 bacterial genomes have been sequenced , we recently proposed that genomic information should be integrated in the description of new bacterial species [3,4]. The genus Herbaspirillum (Baldani et al. 1986) was created in 1986 [5,6]. To date, this genus, comprised of nitrogen-fixing, Gram-negative bacilli, contains 13 species and two subspecies, including H.
aquaticum (Dobritsa et al. 2010) , H. aurantiacum (Carro et al. 2011) , H. autotrophicum (Aragno and Schlegel 1978) Ding and Yokota 2004 , H. canariense (Carro et al. AV-951 2011) , H. chlorophenolicum (Im et al. 2004) , H. frisingense (Kirchhof et al. 2001) , H. hiltneri (Rothballer et al. 2006) , H. huttiense subsp. huttiense (Leifson 1962) Ding and Yokota 2004 , H. huttiense subsp. putei (Ding and Yokota 2004) Dobritsa et al. 2010 , H.