respectively. Such differences indicate that the
island and plasmids have been acquired by hor-
izontal gene transfer from other genetic systems.
The presence of these accessory genomes con-
tributes to the existence of a number of genes
present in multiple copies in the genome. For
example, there are two rpoN genes for the
alternative sigma factor sigma-54 involved in
transcriptional control: one on the core chromo-
some (mll3196orrpoN1) and the other on the
symbiosis island (mlr5872orrpoN2). Also,five
sets ofgroES–groELgenes are present: three sets
on the core chromosome (mll2233–mll2232,
mlr2393–mlr2394, and mll8202–mll8201), one
in the island (msl5812–mll5810), and the other
on pMLa (msr9431–mlr9342).
5.3.1 Ongoing Genome Sequence
Projects
The genome sequences of NZP2037 and R7A
available at JGI and preliminary analysis of a few
otherM. lotistrains indicate that their total gen-
ome sizes are about 7 Mb (JGI Web site and
unpublished data). Some strains possess plas-
mids, while others do not; however, the main
chromosomes of all the strains are larger than
5.5 Mb and contain symbiosis islands. The pos-
session of symbiosis islands is a characteristic
also found inBradyrhizobiumspecies (Itakura
et al. 2009 ).
5.3.2 A Preliminary Whole-Genome
Comparison ofM. lotiStrains
A preliminary genome comparison of
MAFF303099 with R7A, NZP2037, and
NZP2213 using Illumina GAIIx data of the latter
three strains (Sakamoto and Saeki, original
analysis) aligned on MAFF303099 chromosome
is shown in Fig. 5.1. (The NZP2213 strain
examined here had 16S rRNA sequence identical
to that of D14514.) Shaded regions denote genes
similar to MAFF303099 genes. Red color shade
indicates similarity within the symbiosis island,
while gray denotes similarity in the core chro-
mosome. The mapping suggests that the extent of
similarity in the core chromosome is in accor-
dance with that of 16S rRNA genes. More than
85 and 80 % of the genes on MAFF303099
chromosome have homologues in R7A and
NZP2037, respectively, while only about 55 %
have homologues in NZP2213. The similarity
between MAFF303099 and R7A is more evident
in the core chromosome region than in the
symbiosis island: Nearly 95 % of MAFF303099
genes have homologues in R7A, and many such
genes, probably about 85 %, are only polymor-
phic at the nucleotide level. Nearly 85 % of the
MAFF303099 chromosomal genes seem to be
shared by NZP2037 with more polymorphisms,
including at the amino acid sequence level.
Similarity to NZP2213 seems less significant.
For the genes on the MAFF303099 symbiosis
island, about 45 % are also present in R7A,
NZP2037, and NZP2213. Similarity of the
shared genes seems more evident in R7A and
NZP2213 than in NZP2037. These observations
support the hypothesis that the diversity of
M. loti strains results from the transfer of
evolving symbiosis islands to diverse core
chromosomes.5.3.3 Chromosomal Genes Involved
in Symbiotic InteractionMutagenic analyses of genes for exopolysac-
charide (EPS) synthesis in NZP2037 and R7A
have revealed that the symbiotic phenotype of
EPS mutants of M. loti is influenced by the
particular mutant, host plant ecotype, and envi-
ronmental conditions (Hotter and Scott 1991 ;
Kelly et al. 2013 ). The EPS genes are located in
the core chromosome in MAFF303099 and are
syntenic in the three strains (Kaneko et al. 2000 ;
Kelly et al. 2013 ). Mutants affected in predicted
early biosynthetic steps (e.g., exoB) formed
nitrogen-fixing nodules onL. japonicus Gifu,
whereas mutants affected in mid- or late bio-
synthetic steps (e.g.,exoU)induced uninfected
nodule primordia and, occasionally, a few44 K. Saeki and C.W. Ronson