isolated infield plant passage experiments that
showed the horizontal transfer of a large gene
cluster from ICMP3153 to indigenous non-sym-
biotic mesorhizobia (Sullivan et al. 1995 , 1996 ).
The strain MAFF303099 was originally obtained
in Japan from wildL. japonicus. Shortly after the
determinationofthecomplete genomesequenceof
this strain, Turner and colleagues argued that
MAFF303099 should be classified asMesorhizo-
bium huakuiirather thanM. loti, because the
nucleotide sequences of MAFF303099 for 16S
rRNA,recA, and some other genes are more sim-
ilar to those ofM. huakuiitype strain CCBAU2609
(synonymous to IFO15243 and IAM14158) than
those ofM. lotitype strain NZP2213 (Turner et al.
2002 ). According to this claim, some authors use
M. huakuiibiovarlotiMAFF303099 orMeso-
rhizobiumsp. MAFF303099.
Complicating this analysis, heterogeneity was
reported for the M. lotitype strain NZP2213
stocked in a number of culture collections (Wil-
lems et al. 2001 ). Some of culture stock strains
synonymous to NZP2213 (ATCC33669,
LMG6124, LMG17826, and IAM13588) were
not homogenous and possessed 16S rRNA
sequences more similar to those of theM. huakuii
type strain than the originally registered nucleo-
tide sequence of 16S rRNA gene for NZP2213
(GenBank accession number D14514). It is also
documented that some of the stocks contained
strains with morphological and protein profile
diversities. It is unknown how these manifold
type strains have emerged or kept coexistence.
However, it might be noted that 16S rRNA
sequences ofM. lotistrains MAFF303099, R7A,
and NZP2037 are more similar to those ofM.
huakuii type strain than the sequence of
NZP2213 (D14514), and hence, that“M. loti”
strains fall into at least two distinct clusters that
could be considered separate species.
Despite the disputes on taxonomic nomen-
clature, the accumulating data suggest that most
rhizobial strains nodulatingLotusspecies contain
similar sets of symbiosis genes present as part of
the accessory genome, a symbiosis island, on
chromosomes belonging to a certain range of
Phyllobacteriumspecies (Sullivan et al. 1996 ).
ThenodAgene of MAFF303099 (and R7A and
NZP2037) is more closely related to that from
NZP2213 than to theM. huakuii nodAsequen-
ces, as reported by Turner et al. ( 2002 ). It is also
clearly distinguishable from other rhizobia such
as Rhizobium etli CE3 and Rhizobium sp.
NGR234 (or Sinorhizobium sp. NGR234 or
Ensifer fredii NGR234) (Banba et al. 2001 ;
Hussain et al. 1999 ; Schumpp et al. 2009 ).5.3 Genome Structure ofM. loti
StrainsThe complete genome sequence of M. loti
MAFF303099 was reported in 2000 as thefirst
rhizobial genome sequenced (Kaneko et al.
2000 ). The MAFF303099 genome consists of
three circular replicons, a chromosome
(7,036,071 bp) and two plasmids designated as
pMLa (351,911 bp) and pMLb (208,315 bp). The
genome comprises 7,281 potential protein-cod-
ing genes, two identical and consecutive sets of
rRNA genes, 50 tRNA genes representing 47
tRNA species together with an RNase P RNA
gene. Of the protein-coding genes, 6,752 genes
are on the chromosome. About 80 % of the
chromosomal genes show homology to genes of
known function, while the ratios are about 50 and
35 % for those located on pMLa and pMLb.
Adjacent to the single phenylalanine tRNA (phe-
tRNA) gene, a 610,975-bp DNA segment is
inserted on the chromosome with a 17-bp
duplication of the 3′-terminal part of the tRNA
gene demarcating the other end of the inserted
element and with a phage P4-type integrase gene
(mll6432) as thefirst gene at the phe-tRNA end
of the element. This inserted element corre-
sponds to the symbiosis island as defined in
M. lotiR7A and contains a number of genes for
nitrogenfixation and symbiosis (Sullivan et al.
2002 ). The MAFF303099 symbiosis island and
the two plasmids have GC contents (59.8, 59.3,
and 59.9 %) lower than those of the core (non-
symbiosis island part) chromosome (63.0 %).
The GC content difference reflects the difference
in the third position of codons of protein-coding
genes: 70.2, 69.6, 71.2, and 80.5 % for symbiosis
island, pMLa, pMLb, and the core chromosome,5 Genome Sequence and Gene Functions... 43