Draft Genome Sequence of Bradyrhizobium japonicum Is-1, Which Is Incompatible with Rj₂ Genotype Soybeans

Abstract

We report the draft genome sequence of Bradyrhizobium japonicum Is-1, which is incompatible with Rj₂ genotype soybeans. The estimated genome size of this strain is 8.9 Mb. Genome sequence information of this strain will help to identify a causal gene for this incompatibility.

GENOME ANNOUNCEMENT

Bradyrhizobium japonicum is known to form nodules on the roots of soybean (Glycine max). However, nodulation of B. japonicum strains Is-1 and USDA 122 is restricted by some soybean cultivars (e.g., Hardee) (1–3). This nodulation incompatibility is due to the Rj₂ gene in soybean. Yang et al. revealed that this gene encodes members of the Toll-interleukin receptor/nucleotide-binding site/leucine-rich repeat (TIR-NBS-LRR) class of plant resistance proteins (4). In contrast, a causal gene in the incompatible Bradyrhizobium strains has not been revealed (2, 3).

Genomic DNA of B. japonicum Is-1 was extracted by using the Wizard Genomic DNA purification kit (Promega, Madison, WI, USA), and fragmented to 400 bp using the Covaris S2-A system (Covaris, Woburn, MA, USA). A library for sequencing was prepared by a NEBNext DNA library prep master mix set for Illumina (New England Biolabs, Ipswich, MA, USA), and paired-end sequenced (2 × 302 bp) on a MiSeq sequencer using a MiSeq version 3 reagent kit (Illumina KK, Tokyo, Japan). Raw reads were trimmed and de novo assembled using CLC Genomics Workbench version 7.5.1 (Qiagen, Valencia, CA, USA). Parameters for the trimming were as follows: ambiguous limit, 2; quality limit, 0.001; number of 5′ terminal nucleotides, 10; number of 3′ terminal nucleotides, 40. Parameters for the de novo assembly were as follows: mapping mode, map reads back to contigs (slow); update contigs, yes; bubble size, 600; minimum contig length, 1,000; automatic word size, 51; perform scaffolding, yes; auto-detect paired distances, yes; mismatch cost, 2; insertion cost, 3; deletion cost, 3; length fraction, 0.8; similarity fraction, 0.95.

The draft genome of B. japonicum Is-1 was assembled into 109 contigs, with an accumulated length of 8,983,878 bp (N₅₀ = 358,317 bp) and an average GC content of 64.0%. The genome was annotated by the Prokaryotic Genome Annotation Pipeline (PGAP version 2.10), and a total of 8,066 coding sequences (CDSs), 3 rRNAs, and 50 tRNAs were predicted.

Tsukui et al. reported that disruptants of type III secretion (T3SS) structural genes in the incompatible Bradyrhizobium strains overcame the nodulation restriction of Rj₂ genotype soybeans (2). This result indicates that a causal gene in the incompatible Bradyrhizobium strains may encode a T3SS effector protein. The genome sequence of B. japonicum Is-1 will facilitate the identification of this causal gene.

Nucleotide sequence accession number.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number LGUJ00000000.