17.3 Update of Published
“Affymetrix”Transcriptomes
Recent years of research onL. japonicushave
been marked by a rapid growth of publicly
available transcriptomic data. Databases of gene
expression, such as Array Express (Parkinson
et al. 2005 ), provide raw data from sets of tran-
scriptomic experiments covering all organs at
various stages of plant development (E-MEXP-
1726; Verdier et al. 2013 ), salt acclimatization
experiments on Gifu (E-MEXP-1204; Sanchez
et al. 2008 ) and on other Lotus species (E-MEXP-
2344; Sanchez et al. 2011 ), analysis of a plastidic
glutamine synthetase mutant in drought experi-
ments (E-MEXP-2690; Díaz et al. 2010 ), analysis
of arbuscular mycorrhizal symbiosis (Guether
et al. 2009 ), a detailed dissection of nodulation
mechanisms using treatments on wild-type and
mutant plants (E-TABM-715; Høgslund et al.
2009 ), analysis of cellular stress following water
deprivation (E-MEXP-3710; Betti et al. 2012 )
and regulation of photorespiration in wild-type
andLjgln2- 2 mutant lines (E-MEXP-3603; Pérez-
Delgado et al. 2013 ). Details about most of the
above-mentioned experiments are provided in
Table17.1.
A subset of 24 experiments covering all major
plant organs, i.e., stem, petiole, leaf, flower,
nodule (four developmental stages), root (eight
conditions with or without rizhobia inoculation at
various stages), pod (three developmental
stages), and seed (five developmental stages),
were selected to identify 2,949 genes/probe sets
specific or preferentially expressed in each
organs (Verdier et al. 2013 ). Genes that are
expressed specifically or preferentially in a par-
ticular organ can provide insight into specialized
processes in these organs. Previousfindings in
Arabidopsis showed a high correlation between
organ identity and gene expression, where tran-
script modulation represents a transcriptional
signature specific to each individual organ
(Aceituno et al. 2008 ). Organ-specific genes
represent good candidates for functional genomic
study of developmental process. Interestingly,
approximately 39 % of organ-specific genes were
nodule-specific, 21 %flower-specific, and 16 %
seed-specific, with fewer genes specific to other
organs. This may reflect a higher degree of
functional specialization in these organs. It has
also been reported that a large proportion of TFs
and transporters are differentially regulated
across all tissues and that their maxima of
expression is generally associated with a specific
organ, reflecting their specialization in certain
organs (Verdier et al. 2013 ). The gene sets
showing organ-specific expression are valuable
information for biotechnological use.
Promoters of organ-specific genes can be used
to direct expression of transgenes in specific
organs and/or at certain developmental stages,
which may be crucial for the regulation of genes of
interest for research or biotechnological applica-
tions. Using the same subset of experiments
described above, Verdier et al. ( 2013 ) identified
71 stably expressed genes across the different
organs, which represent potential reference genes
for normalization of expression data from qRT-
PCR or probe-hybridization approaches.17.4 Lotus japonicusGene
Expression Atlas (LjGEA)
Web ServerTo make the most of transcriptomic data, it is
important that the research community has free
access to all the published data and to a platform
upon which they can compare between experi-
ments and explore, analyze, and visualize the data.
To meet these needs, the LjGEA Web server was
developed. It is a centralized platform for analyz-
ing Lotus transcriptomic data. This open-access
server is hosted by the Samuel Roberts Noble
Foundation (http://ljgea.noble.org/). Expanding
beyond the number of experiments described
above, the Web server currently hosts gene
expression data from 237 GeneChips from 83
different experiments, covering a broad range of
developmental and environmental conditions. The
LjGEA utilizes the architecture and tools of the
Medicago truncatula Gene Expression Atlas
(MtGEA) server (He et al. 2009 ). To normalize17 A Tutorial onLotus japonicusTranscriptomic Tools 185