High-Quality draft genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain CJ3Sym

Abstract

Mesorhizobium loti strain CJ3Sym was isolated in 1998 following transfer of the integrative and conjugative element ICEMlSym^R7A, also known as the R7A symbiosis island, in a laboratory mating from the donor M. loti strain R7A to a nonsymbiotic recipient Mesorhizobium strain CJ3. Strain CJ3 was originally isolated from a field site in the Rocklands range in New Zealand in 1994. CJ3Sym is an aerobic, Gram-negative, non-spore-forming rod. This report reveals the genome of M. loti strain CJ3Sym currently comprises 70 scaffolds totaling 7,563,725 bp. The high-quality draft genome is arranged in 70 scaffolds of 71 contigs, contains 7,331 protein-coding genes and 70 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.

Introduction

Mesorhizobium loti strain CJ3Sym was first described in work that showed that the symbiotic genes of M. loti strain R7A (a field reisolate of culture collection strain ICMP3153) were located on a large transmissible symbiosis island that could be transferred to nonsymbiotic mesorhizobia both in the laboratory and the environment [1, 2]. The symbiosis island was later classified as an integrative and conjugative element and renamed ICEMlSym^R7A [3]. CJ3Sym was derived from a nonsymbiotic Mesorhizobium strain CJ3 by transfer of the symbiosis island from R7A in a laboratory mating experiment. The CJ3Sym progenitor strain CJ3 was a nonsymbiotic Mesorhizobium strain that was isolated from the rhizosphere of a Lotus corniculatus L. bird's-foot trefoil cv. Grasslands Goldie (here after referred to as Lotus corniculatus cv. Grasslands Goldie) plant taken from a field site in the Rocklands range, Central Otago, New Zealand in 1994, near where ICEMlSym^R7A was discovered [4]. The study was initiated to locate nonsymbiotic rhizobia that were postulated to be the likely progenitors of the diverse symbiotic strains that had received the symbiosis island through horizontal gene transfer at the field site.

Seven strains (CJ1 to CJ7) which had a similar colony morphology to M. loti , but which could not nodulate Lotus corniculatus cv. Grasslands Goldie and lacked nod and nif genes were isolated. The strains were shown to be closely related to the diverse symbiotic strains from the site by RFLP analysis, whole genome DNA-DNA hybridization analysis, full 16S rRNA gene sequencing and multilocus enzyme electrophoresis. The seven strains fell into four genomic species of nonsymbiotic mesorhizobia with strains CJ3, CJ1, CJ4 and CJ6 belonging to the same genomic species as the diverse symbiotic isolates.

When strains CJ1 to CJ7 were characterized it was noticed that they grew poorly, and only formed microcolonies after prolonged incubation on defined G/RDM agar media, in comparison to growth on rich YMA media. Auxanographic analysis revealed that all 7 strains were auxotrophic for thiamin and biotin and all but CJ5 were auxotrophic for nicotinate. In contrast to CJ3, strain CJ3Sym is prototrophic for all three vitamins and consistent with this the genes required for their biosynthesis are located on ICEMlSym^R7A [5]. The CJ3Sym sequence confirms that these are the only operons for the biosynthesis of the three vitamins in the genome.

Organism information

Classification and features

Mesorhizobium loti strain CJ3Sym is in the order Rhizobiales of the class Alphaproteobacteria . Cells are described as non-sporulating, Gram-negative, non-encapsulated, rods (Fig. 1 Left). The rod-shaped form varies in size with dimensions of 0.25-0.5 μm in width and 1.25-1.5 μm in length (Fig. 1 Left and Right). It forms 2 mm diameter colonies within 6 days and has a mean generation time of approximately 8 h when grown in TY broth at 28 °C [2]. Colonies on G/RDM agar [6] and half strength Lupin Agar (½LA) [7] are opaque, slightly domed, mucoid with smooth margins (Fig. 1 Right).

Fig. 1

Images of Mesorhizobium loti strain CJ3Sym from a Gram stain (Left), using scanning electron microscopy (Center) and the appearance of colony morphology on ½LA (Right)

Strains of this organism are able to tolerate a pH range between 4 and 10. Carbon source utilization and fatty acid profiles of M. loti have been described previously [8–10]. Minimum Information about the Genome Sequence (MIGS) is provided in Table 1 and Additional file 1: Table S1.

Table 1 Classification and general features of Mesorhizobium loti strain CJ3Sym in accordance with the MIGS recommendations [30] published by the Genome Standards Consortium [31]

Figure 2 shows the phylogenetic neighborhood of M. loti strain CJ3Sym in a 16S rRNA gene sequence based tree. This strain has 99.8 % (1,364/1,366 bp) 16S rRNA gene sequence identity to M. loti R88B (GOLD ID: Gi08827) and 99.6 % sequence identity (1,361/1,366 bp) to M. australicum WSM2073 (GOLD ID: Gc02468). M. loti strain R88B is a diverse symbiotic strain isolated from the same field site as CJ3Sym, confirming the close relationship between symbiotic and nonsymbiotic mesorhizobia isolated from the site. It is interesting to note that both of these strains cluster with Mesorhizobium shangrilense , several Mesorhizobium ciceri strains and the type M. loti strain LMG 6125 (NZP2213) whereas M. loti strains R7A, NZP2037 and MAFF303099 form a separate cluster that shares only 98 % 16S rRNA gene sequence identity with CJ3Sym and R88B.

Fig. 2

Phylogenetic tree showing the relationships of Mesorhizobium loti CJ3Sym with other root nodule bacteria based on aligned sequences of the 16S rRNA gene (1,290 bp internal region). All sites were informative and there were no gap-containing sites. Phylogenetic analyses were performed using MEGA [40], version 5. The tree was built using the Maximum-Likelihood method with the General Time Reversible model [41]. Bootstrap analysis [42] with 500 replicates was performed to assess the support of the clusters. Type strains are indicated with a superscript T. Brackets after the strain name contain a DNA database accession number and/or a GOLD ID (beginning with the prefix G) for a sequencing project registered in GOLD [43]. Published genomes are indicated with an asterisk

Symbiotaxonomy

Mesorhizobium sp. strain CJ3Sym was isolated from a laboratory mating experiment in which ICEMlSym^R7A was transferred from the donor strain R7A to the nonsymbiotic Mesorhizobium strain CJ3 [2]. The nonsymbiont strain CJ3 was isolated from the rhizosphere of a Lotus corniculatus cv. Grasslands Goldie plant located at a field site that was an undeveloped tussock (Festuca novae-zealandiae and Chionochloa rigida ) grassland located at an elevation of 885 m in Lammermoor, the Rocklands range, Otago, New Zealand in 1994 [4]. The soil was a dark brown silt loam with an acid pH (4.9) and a low (0.28 %) total nitrogen content [11]. CJ3 existed as a soil saprophyte that lacked symbiotic DNA. CJ3Sym forms effective nodules on L. corniculatus cv. Grasslands Goldie but has not yet been tested on any other Lotus species or ecotypes.

Genome sequencing information

Genome project history

This organism was selected for sequencing on the basis of its environmental and agricultural relevance to issues in global carbon cycling, alternative energy production, and biogeochemical importance, and is part of the Genomic Encyclopedia of Bacteria and Archaea, Root Nodulating Bacteria project at the U.S. Department of Energy, Joint Genome Institute. The genome project is deposited in the Genomes OnLine Database [12] and a high-quality permanent draft genome sequence in IMG [13]. Sequencing, finishing and annotation were performed by the JGI using state of the art sequencing technology [14]. A summary of the project information is shown in Table 2.

Table 2 Project information

Growth conditions and genomic DNA preparation

M. loti strain CJ3Sym was grown to mid logarithmic phase in TY rich medium [15] on a gyratory shaker at 28 °C. DNA was isolated from 60 mL of cells using a CTAB (Cetyl trimethyl ammonium bromide) bacterial genomic DNA isolation method [16]

Genome sequencing and assembly

The draft genome of M. loti CJ3Sym was generated at the DOE Joint Genome Institute using Illumina technology [17]. An Illumina standard shotgun library was constructed and sequenced using the Illumina HiSeq 2000 platform, which generated 26,326,824 reads totaling 3,949 Mbp.

All general aspects of library construction and sequencing performed at the JGI can be found at the JGI’s web site [18]. All raw Illumina sequence data was passed through DUK, a filtering program developed at JGI, which removes known Illumina sequencing and library preparation artifacts (Mingkun L, Copeland A, Han J, Unpublished). The following steps were then performed for assembly: (1) filtered Illumina reads were assembled using Velvet [19] (version 1.1.04), (2) 1–3 Kbp simulated paired end reads were created from Velvet contigs using wgsim [20], (3) Illumina reads were assembled with simulated read pairs using Allpaths–LG [21] (version r41043). Parameters for assembly steps were: 1) Velvet --v --s 51 --e 71 --i 4 --t 1 --f "-shortPaired -fastq $FASTQ" --o "-ins_length 250 -min_contig_lgth 500"), 2) wgsim (−e 0–1 100–2 100 -r 0 -R 0 -X 0), 3) Allpaths–LG (STD_1,project,assembly,fragment,1,200,35,,,inward,0,0.

SIMREADS,project,assembly,jumping,1,,,3000,300,inward,0,0). The final draft assembly contained 71 contigs in 70 scaffolds. The total size of the genome is 7.6 Mbp and the final assembly is based on 3,949 Mbp of Illumina data, which provides an average of 522x coverage of the genome.

Genome annotation

Genes were identified using Prodigal [22] as part of the DOE-JGI genome annotation pipeline [23], followed by a round of manual curation using the JGI GenePrimp pipeline [24]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information non-redundant database, UniProt, TIGRFam, Pfam, KEGG, COG, and InterPro databases. The tRNAScanSE tool [25] was used to find tRNA genes, whereas ribosomal RNA genes were found by searches against models of the ribosomal RNA genes built from SILVA [26]. Other non–coding RNAs such as the RNA components of the protein secretion complex and the RNase P were identified by searching the genome for the corresponding Rfam profiles using INFERNAL [27]. Additional gene prediction analysis and manual functional annotation was performed within the Integrated Microbial Genomes-Expert Review (IMG-ER) system [28].

Genome properties

The genome is 7,563,725 nucleotides with 62.15 % GC content (Table 3) and is comprised of a single scaffold. From a total of 7,401 genes, 7,331 were protein encoding and 70 RNA-only encoding genes. The majority of genes (76.76 %) were assigned a putative function whilst the remaining genes were annotated as hypothetical. The distribution of genes into COGs functional categories is presented in Table 4.

Table 3 Genome statistics

Table 4 Number genes associated with general COG functional categories

Conclusions

The M. loti strain CJ3Sym genome was completed to the stage where 70 scaffolds comprising 71 contigs and 7.56 Mb were obtained. A total of 7,401 genes were annotated. It is likely that the genome consists of a single chromosome and a single plasmid; however further assembly is required to confirm this. CJ3Sym is a strain that was derived from nonsymbiotic Mesorhizobium strain CJ3 by transfer of the symbiosis island ICEMlSym^R7A from M. loti strain R7A in a laboratory mating experiment [2]. After the discovery of diverse M. loti strains containing ICEMlSym^R7A at a New Zealand field site, a second adjacent field site was established and sampled to identify nonsymbiotic mesorhizobia that were the likely progenitors of the diverse symbiotic strains. Strain CJ3 was one of seven non-symbiotic Mesorhizobium strains isolated from the rhizosphere of Lotus corniculatus cv. Grasslands Goldie plants and one of the four that belonged to the same genomic species as the diverse symbiotic isolates that contained ICEMlSym^R7A [4]. The genome of CJ3Sym is likely to contain a plasmid, as scaffold 17.18 contains a trb gene cluster (Locus tags 05060–05072 coordinates 16432–26076) and traG (locus tag 05072 coordinates 26704–28695) highly similar to genes on the M. loti strain MAFF303099 pMlb plasmid [29]. The same scaffold also contains likely plasmid replication genes.