Abstract
Rhizobium leguminosarum bv. viciae RCAM1026 is a strain first isolated in 1964 from nodules of “Ramensky 77” cultivar of garden pea (Pisum sativum L.) now routinely used as a model strain in inoculation experiments on pea. Assembly with SPAdes yielded 133 contigs longer then 200 bp (N50 = 202,321, GC% = 60.84). Resulting annotated genome is 7,248,686 bp encoding 6792 genes.
Keywords: Bacterial genomics, Symbiosis, Nitrogen-fixation, Nodule bacteria
| Specifications | |
|---|---|
| Organism/cell line/tissue | Rhizobium leguminosarum bv. viciae RCAM1026 |
| Sex | N.A. |
| Sequencer or array type | Illumina HiSeq 2000 |
| Data format | Processed |
| Experimental factors | Nodule bacteria |
| Experimental features | Whole genome sequence assembly and annotation |
| Consent | Level of consent allowed for reuse if applicable |
| Sample source location | Kostanay Region of Kazakhstan |
1. Direct link to deposited data
2. Introduction
Genus Rhizobium consists of aerobic, gram-negative bacteria capable of forming nitrogen-fixing symbiosis with plants of the Fabaceae family. Rhizobium leguminosarum species is subdivided into biovars that include strains isolated from the nodules of corresponding host plants (bv. viciae — from Vicia spp., Pisum sativum L., Lens spp., Lathyrus spp.; bv. trifolii — from Trifolium spp.; bv. phaseoli — from Phaseolus vulgaris L.) [1]. The Rhizobium leguminosarum bv. viciae strain RCAM1026 (deposited in Russian Collection of Agricultural Microorganisms (RCAM), ARRIAM, Saint-Petersburg, Russia) was originally isolated from nodules of “Ramensky 77” cultivar of pea in Kostanay Region of Kazakhstan. RCAM1026 can effectively nodulate garden pea and therefore is routinely used as a model active strain in inoculation experiments on pea of different genetic backgrounds [2], [3].
3. Strain isolation
The strain was originally isolated from ”Ramensky 77” cultivar of garden pea in the Kostanay Region of Kazakhstan [2] and later deposited in the Russian Collection of Agricultural Microorganisms(RCAM, http://:arriam.ru/kollekciya-kul-tur1/) belonging to the All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia.
4. DNA isolation and sequencing
Prior to sequencing a strain culture was cultivated for 3 days at 28 °C in a liquid medium (tryptone — 5 g/l, yeast extract — 3 g/l, CaCl2— 0.5 g/l, pH 7.0). 50 ml of the culture were pelleted by centrifugation and suspended in 50 μl of deionized water. DNA isolation was carried out with the GBD kit from Biosilica, Novosibirsk, Russia. Libraries were created and barcoded with the New England Biolabs NEBNext®Ultra™DNA Library Prep Kit for Illumina®, then additionally barcoded with NEBNext®Multiplex Oligos for Illumina®(Dual Index Primers Set 1). Genome was sequenced on an Illumina HiSeq 2000 platform with TruSeq PE Cluster Kit v3 and TruSeq SBS Kit v3 by Genotek Ltd, Moscow, Russia.
5. Genome assembly and annotation
De novo assembly was performed with SPAdes genome assembler (v3.9.0) set to default parameters [4]. Contigs shorter than 200 bp were deleted yielding a full genome sequence of 7,239,605 bp consisting of 133 contigs with G/C content of 60.84%. ORF prediction and automatic annotation was carried out with NCBI PGAAP pipeline. Complete genome contained 6792 genes, 48 tRNAs, 3 rRNAs and 4 ncRNA.
6. Phylogenetic analysis
The analysis was performed using the in silico DNA-DNA hybridization method [5]. The closest related strain appears to be Rhizobium leguminosarum bv. viciae strain GB30 with similarity of 95% (NCBI reference sequence NZ_ATTP00000000.1).
7. Nucleotide sequence accession numbers
This draft genome for Rhizobium leguminosarum bv. viciae RCAM1026 project has been deposited at GenBank under the accession MPZP00000000. The 133 contigs were deposited under accession numbers MPZP000000001-MPZP00000133.
8. Conflict of interest
The authors declare that there is no conflict of interests with respect to the work published in this paper.
Acknowledgments
This work was supported by Russian Science Foundation grant no. 14-24-00135.
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