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A Tutorial on Lotus japonicus Transcriptomic Tools

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The Lotus japonicus Genome

Part of the book series: Compendium of Plant Genomes ((CPG))

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Abstract

Lotus japonicus is 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 of L. japonicus transcriptomic studies before focusing on two tools developed recently to store, visualize, and analyze transcriptomic data: the L. japonicus gene 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 truncatula and Glycine max, which enables comparative genomic studies.

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Authors and Affiliations

  1. Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA

    Jerome Verdier, Kaustav Bandyopadhyay & Michael Udvardi

  2. 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

    Jerome Verdier

Authors
  1. Jerome Verdier
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  2. Kaustav Bandyopadhyay
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  3. Michael Udvardi
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Corresponding author

Correspondence to Jerome Verdier .

Editor information

Editors and Affiliations

  1. Kazusa DNA Research Institute, Kisarazu, Chiba, Japan

    Satoshi Tabata

  2. Department of Molecular Biology and Genetics, University of Aarhus, Aarhus, Denmark

    Jens Stougaard

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Verdier, J., Bandyopadhyay, K., Udvardi, M. (2014). A Tutorial on Lotus japonicus Transcriptomic Tools. In: Tabata, S., Stougaard, J. (eds) The Lotus japonicus Genome. Compendium of Plant Genomes. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-44270-8_17

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