sequences of their Arabidopsis homologues
(Kötting et al. 2010 ; Zeeman et al. 2010 ). Blastn
or tBlastn searches were also performed against
the LjEST database. Sequences of all the genes
identified were submitted to multiple alignments
to determine whether they indeed corresponded
to theL. japonicushomologue of theArabidopsis
gene in question. Where definitive, allL. japo-
nicusgenes encoding enzymes of starch metab-
olism were given the same name as their
Arabidopsishomologues to aid later compari-
sons. Whenever possible, these genes were
mapped onto the genetic linkage map of L.
japonicus using information provided by the
Miyakogusa genome database (version 1.0)
(Vriet et al. 2010 ). Progress in genome
sequencing of L. japonicus since 2010 has
allowed us to update the list of orthologues of the
Arabidopsisgenes in this species for this volume
(using version 2.5 and Lj3.0, a prerelease ver-
sion), and data from both these versions are
presented in Table10.1. We have also included
genes encoding enzymes of the committed steps
in sucrose synthesis and catabolism.
It is clear that almost all of the major enzymes
and isoform classes of starch and sucrose
metabolism present in Arabidopsis are also
present inL. japonicus, although in several cases
duplications have led to different numbers of
isoforms of a particular class in the two species.
For example, as in many species,L. japonicus
has two genes encoding starch synthase 2 and
granule-bound starch synthase, whereasArabid-
opsishas only one gene encoding each isoform
class. A notable exception to the generally high
level of conservation is in theβ-amylase gene
family. The BAM4 isoform from Arabidopsis
does not appear to be represented inL. japonicus.
This is of particular interest for two reasons.
First, in Arabidopsis, this isoform is in the
chloroplast, together with BAM1 and BAM3,
and thus is likely to be involved in some way
with starch degradation. Isoforms BAM 5 to
BAM 9 are not chloroplastic and are not involved
in starch degradation. Second, BAM4 in Ara-
bidopsis is catalytically inactive and yet is
essential for normal rates of starch degradation. It
has been proposed to play a regulatory role,
perhaps as part of a protein complex (Fulton
et al. 2008 ). Thus,L. japonicusapparently lacks
a BAM that is regulatory and colocated with
starch.10.4 Spatial and Temporal Patterns
of Expression of Genes
Encoding Enzymes of Starch
and Sucrose MetabolismWe have investigated the spatial and develop-
mental expression patterns ofL. japonicusgenes
encoding enzymes of starch metabolism using
the transcriptomic data within the Lotus Gene
Expression Atlas (http://mtgea.noble.org/v3/)
(Verdier et al. 2013 ). Expression patterns of the
genes encoding enzymes of sucrose catabolism
inL. japonicushave been published previously
(Horst et al. 2007 ; Welham et al. 2009 ) and were
used to validate the robustness of this analysis.
The pattern and level of expression obtained for
four sucrose synthase genes from the Lotus Gene
Expression Atlas were very similar to those
published (Horst et al. 2007 );LjSUS1was the
main gene expressed in leaves, stem, uninocu-
lated roots andflowers, whereasLjSUS3was the
most highly expressed gene in nodules. Expres-
sion ofLjSUS3was higher in nodules than in any
other organ.
Figure 10.2 shows the absolute transcript
levels of starch genes in a number of organs
sampled according to the information in the
Atlas. Genes encoding the plastidial isoforms of
phosphoglucoisomerase and phosphoglucomu-
tase and the major small subunit of ADP glucose
pyrophosphorylase (LjPGI1, LjPGM1 and
LjAPS1) were significantly expressed in all
organs analysed (Fig. 10.2). LjAPL1was the
main gene encoding a large subunit of ADP
glucose pyrophosphorylase that was expressed in
leaves, with lower expression in stems and
flowers, and very little to no expression in roots,
nodules and seeds. In contrast,LjAPL3was the
most highly expressed large subunit gene in all
organs except leaves, where its expression was
lower than that ofLjAPL1.LjAPL2was only
very weakly expressed in leaves, but it was the100 C. Vriet et al.