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Genomic approaches toward understanding the actinorhizal symbiosis: an update on the status of the Frankia genomes

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Abstract

The actinorhizal symbiosis is a mutualistic relationship between an actinobacterium from the genus Frankia and a wide variety of dicotyledonous plants representing 8 different families of angiosperms. Molecular phylogenetic approaches have identified four major Frankia lineages that have distinctive plant host ranges. Since the first published three Frankia genomes, an effort was undertaken to provide full genomic databases covering all four well established Frankia lineages and to provide depth of the number of strains covered. Here, we report on the updated status of these sequencing efforts. At present, there are 25 complete or draft Frankia genomes that have been sequenced and annotated, and several others are now in the pipeline being sequenced. An overview of the Frankia genomes will be presented focusing on their general genomic properties including size of the pan- and core-gene pool, size relationship and genome plasticity. Furthermore, a description of biosynthetic potential and a discussion about genes (nitrogenase, hopanoid biosynthesis, truncated hemoglobin, hydrogenase uptake gene clusters) involved in the symbiosis will be discussed. The absence of common nod genes within these Frankia genomes provides clues about the host-microbe recognition process for the actinorhizal symbiosis

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Acknowledgment

Partial funding was provided by the New Hampshire Agricultural Experiment Station. This is Scientific Contribution Number 2649. This work was supported by the USDA National Institute of Food and Agriculture Hatch 022821 (LST), Agriculture and Food Research Initiative Grant 2015-67014-22849 from the USDA National Institute of Food and Agriculture (LST), and the College of Life Science and Agriculture at the University of New Hampshire-Durham. MG and AK were supported by MERS research project no LR03ES03. AS acknowledges the grant received from Department of Biotechnology, Govt. of West Bengal (Project No. 206/BT-Estt./RD-22/2014) and DBT, India for allowing the work to be done at NBU bioinformatics Facility. IS was supported by a BSR, UGC Fellowship.

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  1. Department of Molecular, Cellular & Biomedical Sciences, University of New Hampshire, 46 College Road, Durham, NH, 03824-2617, USA

    Louis S. Tisa & Rediet Oshone

  2. NBU Bioinformatics Facility, Department of Botany, University of North Bengal, Siliguri, 734013, India

    Indrani Sarkar & Arnab Sen

  3. Laboratoire Microorganismes et Biomolécules Actives, Université de Tunis Elmanar (FST) & Université de Carthage (INSAT), Tunis, Tunisia

    Amir Ktari & Maher Gtari

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  1. Louis S. Tisa
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  5. Arnab Sen
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Correspondence to Louis S. Tisa.

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Presented at the 18th International Meeting on Frankia and Actinorhizal Plants (ACTINO2015), August 24–27, 2015, Montpellier, France

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Tisa, L.S., Oshone, R., Sarkar, I. et al. Genomic approaches toward understanding the actinorhizal symbiosis: an update on the status of the Frankia genomes. Symbiosis 70, 5–16 (2016). https://doi.org/10.1007/s13199-016-0390-2

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