The Lotus japonicus Genome

17

A Tutorial onLotus japonicus

Transcriptomic Tools

Jerome Verdier, Kaustav Bandyopadhyay,

and Michael Udvardi

Abstract

Lotus japonicusis widely used as a model species for legume biology.

The rapid growth of transcriptomic data available for this species

represents an asset for the understanding of molecular mechanisms

underlying different processes of legume development. In this chapter, we

review the history ofL. japonicustranscriptomic studies before focusing

on two tools developed recently to store, visualize, and analyze

transcriptomic data: theL. japonicusgene expression atlas (LjGEA) and

the legume gene regulatory network Web server (LegumeGRN). A

description of the features available on these Web servers is provided with

a tutorial describing their uses. These tools are already connected to

available transcriptomic data from two other model legumes,Medicago

truncatulaandGlycine max, which enables comparative genomic studies.

17.1 Early Transcriptomic Studies

Transcriptomic studies in Lotus were initiated

during thefirst half of the last decade. The earliest

approach was identification of expressed sequence

tags (ESTs) (Endo et al. 2000 , 2002 ), which

enabled development of cDNA arrays in nylon

filters. These arrays were used to quantify labeled

cDNAs derived from RNA of organs of interest,

via hybridization. Being a model for nitrogen

fixation research, it is not surprising that thefirst

efforts were focused on nodule and root tissues. In

2002, Colebatch et al. ( 2002 ) identified changes in

the expression of 83 genes between root and

nodule organs in an array of about 2,300 cDNA

clones. By 2004, the number of arrayed probes

had increased to around 5,000 cDNA clones

derived from nodules (Colebatch et al. 2004 ) and

J. Verdier (&)
K. Bandyopadhyay
M. Udvardi
Plant Biology Division, The Samuel Roberts Noble
Foundation, 2510 Sam Noble Parkway, Ardmore,
OK 73401, USA
e-mail: [email protected]

K. Bandyopadhyay
e-mail: [email protected]

M. Udvardi
e-mail: [email protected]

J. Verdier
Shanghai Center for Plant Stress Biology (PSC),
Shanghai Institutes of Biological Sciences, Chinese
Academy of Sciences, 3888 Chenhua Road,
Shanghai 201602, People’s Republic of China

S. Tabata and J. Stougaard (eds.),The Lotus japonicus Genome, Compendium of Plant Genomes,
DOI 10.1007/978-3-662-44270-8_17,©Springer-Verlag Berlin Heidelberg 2014

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