Permanent Draft Genome Sequence of the French Bean Symbiont Rhizobium sp . Strain RSm-3 Isolated from the Eastern Himalayan Region of India

The genus Rhizobium contains many species able to form nitrogenfixing nodules on plants of the legume family. Here, we report the 6.9-Mbp draft genome sequence of Rhizobium sp. strain RSm-3, with a G C content of 61.4% and 6,511 candidate protein-coding genes. The genus Rhizobium, established in 1889, is a group of motile, aerobic, and Gramnegative bacteria in the alphaproteobacterial group with a moderate G C percentage (60%) (1, 2). Members of the genus Rhizobium form a symbiotic association with various legume plants of the Fabaceae family (3–5) and form nodules on the root surface. These nodules are the sites of nitrogen fixation. The symbiosis between Rhizobium and legumes is of great importance (6). Compared to the use of chemical fertilizers, symbiosis offers cheaper and more effective agronomic practices by providing an adequate supply of N for legume-based crops (7, 8). The French bean, or common bean (Phaseolus vulgaris L.), is one of the most important plant hosts of Rhizobium spp. , with the broadest genetic base (9, 10), and is one of the major cultivated crops containing large amounts of protein, minerals, and antioxidant compounds (11). Rhizobium sp. strain RSm-3 was isolated from the root nodules of P. vulgaris collected from the Sonada region of Darjeeling district (26.9400°N, 88.250°E; altitude, 5,157 ft) of West Bengal, India. The strain showed antagonistic activity against the fungal pathogen Fusarium solani and resistance against most of the antibiotics tested against it. These interesting features led us to do 16S rRNA gene sequencing, which identified the strain as Rhizobium sp. and shared 99% identity with Rhizobium etli EBRI 21 (accession no. AY221176.1). This strain was sequenced to provide a greater understanding of these physiological properties and its interaction with P. vulgaris. Sequencing of the draft genome of Rhizobium sp. strain RSm-3 was performed at the Hubbard Center for Genome Studies (University of New Hampshire, Durham, NH) using Illumina techniques (12). A standard Illumina shotgun library was constructed and sequenced using the Illumina HiSeq 2500 platform, which generated 1,585,078 reads (260-bp insert size) totaling 341 Mbp. The Illumina sequence data were trimmed by Trimmonatic version 0.32 (13) and assembled using SPAdes version 3.5 (14), and ALLPaths-LG version r52488 (15). The final draft assembly for Rhizobium sp. strain RSm-3 consisted of 60 contigs, with an N50 contig size of 313.1 kb and 54.3 coverage of the genome. The final assembled genome contained a total sequence length of 6,912,093 bp, with a G C content of 61.4%. The assembled RSm-3 genome was annotated via the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) and resulted in 6,511 candidate protein-coding genes, 46 Received 14 February 2017 Accepted 16 February 2017 Published 13 April 2017 Citation Rai R, Swanson E, Sarkar I, Lama D, Abebe-Aleke F, Simpson S, Morris K, Thomas WK, Kar P, Gtari M, Sen A, Tisa LS. 2017. Permanent draft genome sequence of the French bean symbiont Rhizobium sp. strain RSm-3 isolated from the Eastern Himalayan region of India. Genome Announc 5:e00175-17. https://doi.org/10.1128/genomeA.00175-17. Copyright © 2017 Rai et al. This is an openaccess article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Louis S. Tisa, louis.tisa@unh.edu. This is scientific contribution number 2711. PROKARYOTES