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Evolution of Root Nodule Symbioses
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Evolution of Root Nodule Symbioses

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (20 December 2022) | Viewed by 8536

Special Issue Editor

Prof. Dr. Katharina Pawlowski

E-Mail Website
Guest Editor
Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
Interests: plant; evolution; root nodule symbioses; arbuscular mycorrhiza
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The evolution of nitrogen-fixing root nodule symbioses comprises the evolution of the host, the microsymbiont, as well as their co-evolution.

In the last two years, the increased application of phylogenomics approaches enabled by the growing number of sequenced genomes of host plants has led to breakthroughs. Large-scale analyses of epigenetic changes and of non-coding RNAs have been added to the arsenal of researchers. Nevertheless, there are still a lot of open questions which should be answered based on the available tools: What is the basis for symbiotic efficiency—the adaptation of a particular microsymbiont to a particular host is an ongoing evolutionary process, but what are the molecular players? What is the molecular basis for the induction of legume nodules without infection threads formed in root hairs? Which host features are responsible for the accommodation of rhizobia in symbiosomes instead of fixation threads? What are the signal factors of Frankia strains? What are the reasons for the loss of the symbiosis in the majority of plant lineages derived from the common ancestor of Fabales, Fagales, Cucuribtales, and Rosales? The forthcoming Special Issue aims to present a platform for the discussion of these new developments in root nodule symbioses.

Prof. Dr. Katharina Pawlowski
Guest Editor

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Keywords

  • evolution
  • symbiosis
  • biological nitrogen fixation
  • root nodules
  • intracellular
  • rhizobia
  • frankia
  • legumes
  • actinorhizal plants
  • lipochito-oligosaccharides
  • NIN
  • type III secretion systems

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Related Special Issue

Published Papers (2 papers)

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Research

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19 pages, 1226 KiB  
Article
Genomic Insights of Alnus-Infective Frankia Strains Reveal Unique Genetic Features and New Evidence on Their Host-Restricted Lifestyle
by Sandra Kim Tiam, Hasna Boubakri, Lorine Bethencourt, Danis Abrouk, Pascale Fournier and Aude Herrera-Belaroussi
Genes 2023, 14(2), 530; https://doi.org/10.3390/genes14020530 - 20 Feb 2023
Cited by 4 | Viewed by 2334
Abstract
The present study aimed to use comparative genomics to explore the relationships between Frankia and actinorhizal plants using a data set made of 33 Frankia genomes. The determinants of host specificity were first explored for “Alnus-infective strains” (i.e., Frankia strains belonging [...] Read more.
The present study aimed to use comparative genomics to explore the relationships between Frankia and actinorhizal plants using a data set made of 33 Frankia genomes. The determinants of host specificity were first explored for “Alnus-infective strains” (i.e., Frankia strains belonging to Cluster Ia). Several genes were specifically found in these strains, including an agmatine deiminase which could possibly be involved in various functions as access to nitrogen sources, nodule organogenesis or plant defense. Within “Alnus-infective strains”, Sp+ Frankia genomes were compared to Sp− genomes in order to elucidate the narrower host specificity of Sp+ strains (i.e., Sp+ strains being capable of in planta sporulation, unlike Sp− strains). A total of 88 protein families were lost in the Sp+ genomes. The lost genes were related to saprophytic life (transcriptional factors, transmembrane and secreted proteins), reinforcing the proposed status of Sp+ as obligatory symbiont. The Sp+ genomes were also characterized by a loss of genetic and functional paralogs, highlighting a reduction in functional redundancy (e.g., hup genes) or a possible loss of function related to a saprophytic lifestyle (e.g., genes involved in gas vesicle formation or recycling of nutrients). Full article
(This article belongs to the Special Issue Evolution of Root Nodule Symbioses)
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Review

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23 pages, 1729 KiB  
Review
Adaptive Evolution of Rhizobial Symbiosis beyond Horizontal Gene Transfer: From Genome Innovation to Regulation Reconstruction
by Sheng Liu, Jian Jiao and Chang-Fu Tian
Genes 2023, 14(2), 274; https://doi.org/10.3390/genes14020274 - 20 Jan 2023
Cited by 11 | Viewed by 5709
Abstract
There are ubiquitous variations in symbiotic performance of different rhizobial strains associated with the same legume host in agricultural practices. This is due to polymorphisms of symbiosis genes and/or largely unexplored variations in integration efficiency of symbiotic function. Here, we reviewed cumulative evidence [...] Read more.
There are ubiquitous variations in symbiotic performance of different rhizobial strains associated with the same legume host in agricultural practices. This is due to polymorphisms of symbiosis genes and/or largely unexplored variations in integration efficiency of symbiotic function. Here, we reviewed cumulative evidence on integration mechanisms of symbiosis genes. Experimental evolution, in concert with reverse genetic studies based on pangenomics, suggests that gain of the same circuit of key symbiosis genes through horizontal gene transfer is necessary but sometimes insufficient for bacteria to establish an effective symbiosis with legumes. An intact genomic background of the recipient may not support the proper expression or functioning of newly acquired key symbiosis genes. Further adaptive evolution, through genome innovation and reconstruction of regulation networks, may confer the recipient of nascent nodulation and nitrogen fixation ability. Other accessory genes, either co-transferred with key symbiosis genes or stochastically transferred, may provide the recipient with additional adaptability in ever-fluctuating host and soil niches. Successful integrations of these accessory genes with the rewired core network, regarding both symbiotic and edaphic fitness, can optimize symbiotic efficiency in various natural and agricultural ecosystems. This progress also sheds light on the development of elite rhizobial inoculants using synthetic biology procedures. Full article
(This article belongs to the Special Issue Evolution of Root Nodule Symbioses)
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