extended sequence of contig CM0292 may reveal
further candidate genes in this region.
As the perceived absence of gene clusters for
some classes of plant-specialized metabolites has
been a question of interest, the existence of a gene
cluster for a branch of the phenylpropanoid path-
way directly involved in plant–microbe interac-
tions is particularly noteworthy. That such a gene
cluster for isoflavonoid biosynthesis exists inL.
japonicus,withIFS1and HI4′OMTreportedly
localized to TAC clone LjT24P23 (Shimada et al.
2007 ), was not yet recognized in the gene cluster
literature. The encoded enzymes catalyze thefirst
two steps in the isoflavonoid-specific branch of
flavonoid metabolism. Since the original Shimada
et al. ( 2007 ) publication making this observation,
more sequence data and chromosomal locations
for specific biosynthetic genes have become
available. It is now clear that IFS1 (chr4.
CM0432.2900) and HI4′OMT (chr4.CM0432.
2880) are adjacent genes spaced 18.5 kb apart.
Moreover, IFS2 (chr4.CM0432.3190) and the
pseudogeneIFS3(chr4.CM0432.3150) are now
included on this same contig, and the distance
betweenIFS1andIFS2is approximately 290 kb.
This region also contains several pseudogenes
related to HI4′OMT. Similarly, pseudogenes
resemblingCYP736A2were also observed in the
cyanogenic glucoside gene cluster, suggesting a
dynamic evolution of these regions involving gene
duplications, possible functional divergence, and
gene loss. The next step of the isoflavonoid path-
way is mediated by the enzyme 2-hydroxyiosf-
lavanone dehydratase (HID) which has been
positioned on chromosome 5 (chr5.CM0200.
1460) and is therefore not part of the gene cluster.
The CYP81E6 gene encoding isoflavone 2′-
hydroxylase (I2′H, chr4.CM0026.1220) is, how-
ever, genetically linked to the partial cluster at a
distance of approximately 6 cM and consequentlyFig. 14.3 Graphical representation of three regions in the
genome ofL. japonicuswhich contain biosynthetic gene
clusters for cyanogenic glucosides, isoflavonoids, and
terpenoids.Arrowsrepresent gene sequences as annotated
in the Kazusa DNA Research Institute genome assembly
build 2.5. Functional genes with a confirmed role in the
biosynthetic pathway are indicated above each contig bar.
Functional genes with no confirmed role, or partial-/
pseudogenes, are indicated below each contig bar. Gene
annotations marked as partial- and/or pseudogenes are
indicated with hatched linesandboxes. Biosynthetic
genes of interest are named and indicated withboxes. The
distance to genetic loci that fall outside the available
sequence of each contig is indicated in cM. All contigs are
drawn to the same scale158 A.M. Takos and F. Rook