Genomic Insights of Alnus -Infective Frankia Strains Reveal Unique Genetic Features and New Evidence on Their Host-Restricted Lifestyle

• Published in: Genes Vol. 14; no. 2; p. 530
• Main Authors: Kim Tiam, Sandra, Boubakri, Hasna, Bethencourt, Lorine, Abrouk, Danis, Fournier, Pascale, Herrera-Belaroussi, Aude
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 20.02.2023; MDPI
• Subjects: actinorhizal symbiosis; Agmatine; Agmatine deiminase; Bacteria; Frankia; gas vesicles; Genes; Genomes; Genomics; Host specificity; Human health and pathology; HUP; in planta sporulation; Legumes; Life Sciences; Nitrogen; Nitrogen sources; Organogenesis; Protein families; Sporulation; Symbiosis; Taxonomy; Transcription factors; Corsica; HUP; actinorhizal symbiosis; gas vesicles; genome reduction; in planta sporulation; agmatine deiminase; Frankia; Frankia actinorhizal symbiosis in planta sporulation agmatine deiminase HUP gas vesicles genome reduction
• ISSN: 2073-4425; 2073-4425
• DOI: 10.3390/genes14020530

The present study aimed to use comparative genomics to explore the relationships between and actinorhizal plants using a data set made of 33 genomes. The determinants of host specificity were first explored for " -infective strains" (i.e., 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 " -infective strains", Sp+ genomes were compared to Sp- genomes in order to elucidate the narrower host specificity of Sp+ strains (i.e., Sp+ strains being capable of 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., genes) or a possible loss of function related to a saprophytic lifestyle (e.g., genes involved in gas vesicle formation or recycling of nutrients).