Genome Sequence of Rhizobium jaguaris CCGE525T, a Strain Isolated from Calliandra grandiflora Nodules from a Rain Forest in Mexico

We present the genome sequence of Rhizobium jaguaris CCGE525T, a nitrogen-fixing bacterium isolated from nodules of Calliandra grandiflora. CCGE525T belongs to Rhizobium tropici group A, represents the symbiovar calliandrae, and forms nitrogen-fixing nodules in Phaseolus vulgaris.


R hizobium jaguaris CCGE525 T was isolated from nodules of the medicinal legume
Calliandra grandiflora growing in a rain forest in Chiapas, Mexico, and was described as related to Rhizobium tropici group A (1). R. tropici group A was defined by 16S rRNA gene sequences and distinctive phenotypic characteristics (2). We report the genome sequence of strain CCGE525, the type strain of Rhizobium jaguaris.
A single colony from a freeze-dried culture sample of R. jaguaris CCGE525 T was incubated on peptone yeast (PY) medium (5 g/liter peptone, 3 g/liter yeast extract, and 0.6 g/liter CaCl 2 ) for 3 days at 30°C. DNA was extracted from 3 ml of culture using a kit for cells and tissues (Roche Applied Science, Germany). A SMRTbell library of 15-to 20-kb insert size was constructed using standard protocols. The library was sequenced on a PacBio RS II sequencer (3) using P6-C4 chemistry, which yielded 3.4 Gb of data. Reads were filtered and assembled de novo using Canu v.1.5 (4). Annotation was performed using the NCBI Prokaryotic Genome Annotation Pipeline (https://www.ncbi .nlm.nih.gov/genome/annotation_prok/) (5). Amino acid sequences served as input to PhyloPhlAn (6) to predict evolutionary relationships. The progressive Mauve tool was used for genome alignments (7). DNA-DNA hybridization (DDH) values were computed using the Genome-to-Genome Distance Calculator v.2.1 (8). Average nucleotide identity (ANI) values were calculated as previously proposed (9) using the ANI calculator from the Konstantinidis Lab (http://enve-omics.ce.gatech.edu/ani/) (10). Default parameters were used for all programs.
The R. tropici group A affiliation of R. jaguaris CCGE525 T was supported by its position in a genome tree (Fig. 1A). This phylogenomic approach increased resolution and confirmed the placement of R. jaguaris CCGE525 T as an isolated branch in the vicinity of Rhizobium leucaenae USDA 9039 T .
R. jaguaris CCGE525 T is classified within the symbiovar calliandrae and has the capacity to form nitrogen-fixing nodules with common bean (1). A multiple sequence alignment revealed that the symbiotic plasmid of R. jaguaris CCGE525 T was less conserved and presented rearrangements compared to the similar symbiotic plasmids of Rhizobium tropici CIAT 899 T and R. leucaenae USDA 9039 T (Fig. 1B).
Sequence comparisons between the symbiotic plasmid of R. jaguaris CCGE525 T and the counterparts of R. tropici CIAT 899 T and R. leucaenae USDA 9039 T revealed ANI values of 85.40% and 85.48%, respectively. DDH estimates were 29.00% and 29.20% between the corresponding symbiotic plasmids. Thus, the symbiovar calliandrae is further validated.
Data availability. The genome sequence was deposited in GenBank under accession numbers CP032694 to CP032697. Raw sequences were submitted to the SRA database under accession number SRP174341.