Abstract
We report here the draft genome sequences of Bradyrhizobium elkanii strains BLY3-8 and BLY6-1, which are incompatible with Rj3 genotype soybean cultivars. The genome sequences of these strains will be useful to identify a causal gene for this incompatibility.
GENOME ANNOUNCEMENT
Bradyrhizobium elkanii is known to have the ability to form nodules on soybean (Glycine max) root (1). However, nodulation of B. elkanii strains BLY3-8 and BLY6-1 is restricted by soybean cultivars CNS (2) and D51 (our unpublished data). This restriction is due to the Rj3 gene in soybeans (3, 4). In order to aid in identification of the gene causing this incompatibility in strains BLY3-8 and BLY6-1, we conducted genome sequencing of these strains.
Genomic DNA of B. elkanii strains BLY3-8 and BLY6-1 was extracted using the ISOPLANT kit (Nippon Gene, Tokyo, Japan) and fragmented to 400 bp using a Covaris S2-A (Covaris, Woburn, MA). The libraries for sequencing were prepared by a NEBNext DNA library prep master mix set for Illumina (New England BioLabs, Ipswich, MA) and paired-end sequenced (2 × 300 bp) on a MiSeq sequencer using a MiSeq reagent kit version 3 (Illumina KK, Tokyo, Japan). Raw reads were trimmed and de novo assembled using CLC Genomics Workbench 7.5 (Qiagen, Valencia, CA). Parameters for the trimming were as follows: ambiguous limit, 0; quality limit, 0.01; number of 5′ terminal nucleotides, 10; number of 3′ terminal nucleotides, 14; minimum length, 150 bp. The default settings were used for the de novo assembly parameters (i.e., mapping mode, map reads back to contigs [slow]; mismatch cost, 2; insertion cost, 3; deletion cost, 3; length fraction, 0.8; similarity fraction, 0.9).
The draft genomes of B. elkanii strains BLY3-8 and BLY6-1 were assembled into 90 and 79 contigs, respectively. The accumulated lengths of these genomes were 9,198,916 bp (N50, 302,740 bp) and 9,202,892 bp (N50, 363,283 bp), respectively. The G+C content of both genomes was 63.8%. The total numbers of coding sequences (CDSs) predicted by the Prokaryotic Genome Annotation Pipeline (PGAP 3.1) were 8,036 and 8,049, respectively.
Accession number(s).
The whole-genome shotgun projects for B. elkanii strains BLY3-8 and BLY6-1 have been deposited at DDBJ/EMBL/GenBank under the accession numbers LWUI00000000 and LXEM00000000, respectively. The versions described in this paper are versions LWUI01000000 and LXEM01000000, respectively.
ACKNOWLEDGMENTS
This study was supported by Cooperative Research Grant of the Genome Research for BioResource, NODAI Genome Research Center, Tokyo University of Agriculture, Japan.
Footnotes
Citation Zaw Htwe A, Kanesaki Y, Yoshikawa H, Tsurumaru H, Yamakawa T. 2016. Draft genome sequences of Bradyrhizobium elkanii strains BLY3-8 and BLY6-1, which are incompatible with Rj3 genotype soybean cultivars. Genome Announc 4(5):e01169-16. doi:10.1128/genomeA.01169-16.
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