Supplemental website for Medicago symbiosis transcriptome


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Deep Sequencing of the Medicago truncatula Root Transcriptome Reveals a Massive and Early Interaction between Nodulation Factor and Ethylene Signals

Estíbaliz Larrainzar¹, Brendan K. Riely¹, Sang Cheol Kim³, Noelia Carrasquilla-Garcia¹, Hee-Ju Yu⁴, Hyun-Ju Hwang⁵, Mijin Oh⁵, Goon Bo Kim⁶, Anandkumar K. Surendrarao², Deborah Chasman⁷, Alireza F. Siahpirani⁸, Ramachandra V. Penmetsa¹, Gang-Seob Lee⁵, Namshin Kim³, Sushmita Roy^7,9, Jeong-Hwan Mun⁶ and Douglas R. Cook¹

Description of the work

The legume-rhizobium symbiosis is initiated through the activation of the Nodulation (Nod) factor-signaling cascade, leading to a rapid reprogramming of host cell developmental pathways. This website contains the data generated in (Larrainzar et al. 2015), where we combined transcriptome sequencing (RNA-seq) with molecular genetics and network analysis to quantify and categorize the transcriptional changes occurring in roots of the model legume Medicago truncatula from minutes to days after inoculation with Sinorhizobium medicae. We employed mutants with absent or decreased Nod factor sensitivities (i.e. Nodulation factor perception (nfp) and Lysine motif domain-containing receptor-like kinase 3 (lyk3), respectively) and an ethylene (ET)-insensitive, Nod factor-hypersensitive mutant (sickle, skl). This data set encompasses nine time points, allowing observation of the symbiotic regulation of diverse biological processes with high temporal resolution. With the goals of identifying interactions within and among these clusters, of predicting the target genes of annotated regulatory proteins (e.g. transcription factors and signaling proteins), and of identifying new genes involved in symbiosis, we applied the MERLIN (for modular regulatory inference with per-gene information) regulatory network inference algorithm (Roy et al. 2013).

How to check the expression profile and potential regulators/targets of your gene(s) of interest

Our RNA-seq data is based on the IMGA 3.5 v4 version of the M. truncatula genome. Several types of sequence IDs can be found in this version: one in the form " Medtr1g024370", as "contig_73581_1" or as "AC233572_1". Please make sure you enter the IDs of your genes of interest from this version of the genome. Now a new version of the M. truncatula genome has been released: IMGA 4.0 v1 (Visit http://medicago.jcvi.org/medicago/ to download it). If you need to convert your 4.0 IDs to these in version 3.5, you can use this table here. For overall questions and collaboration opportunities, please contact us: Doug R. Cook and Estibaliz Larrainzar.

1. Department of Plant Pathology, University of California, Davis, California 95616

2. Plant Biology Graduate Group, University of California, Davis, California 95616

3. Korean Research Institute of Bioscience and Biotechnology, Daejeon 305–806, Republic of Korea

4. Catholic University of Korea, Bucheon 420–743, Republic of Korea

5. Rural Development Administration, Jeonju 560–500, Republic of Korea

6. Myongji University, Yongin 449–728, Republic of Korea

7. Wisconsin Institute for Discovery, Madison, Wisconsin 53715

8. Department of Computer Sciences, University of Wisconsin, Madison, Wisconsin 53715

9. Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53715