J Genomics 2022; 10:49-56. doi:10.7150/jgen.74788 This volume

Research Paper

Draft Genomes of Nitrogen-fixing Frankia Strains Ag45/Mut15 and AgPM24 Isolated from Root Nodules of Alnus Glutinosa

Philippe Normand1✉, Petar Pujic1, Danis Abrouk1, Spandana Vemulapally2, Trina Guerra2, Camila Carlos-Shanley2, Dittmar Hahn2

1. Université Claude-Bernard Lyon 1, Université de Lyon, UMR 5557 CNRS Ecologie Microbienne, Villeurbanne, France.
2. Texas State University, Department of Biology, 601 University Drive, San Marcos, TX 78666, USA.

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Citation:
Normand P, Pujic P, Abrouk D, Vemulapally S, Guerra T, Carlos-Shanley C, Hahn D. Draft Genomes of Nitrogen-fixing Frankia Strains Ag45/Mut15 and AgPM24 Isolated from Root Nodules of Alnus Glutinosa. J Genomics 2022; 10:49-56. doi:10.7150/jgen.74788. Available from https://www.jgenomics.com/v10p0049.htm

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Abstract

Graphic abstract

The genomes of two nitrogen-fixing Frankia strains, Ag45/Mut15 and AgPM24, isolated from root nodules of Alnus glutinosa are described as representatives of a novel candidate species. Phylogenomic and ANI analyses confirmed that both strains are related to cluster 1 frankiae, and that both strains belong to a novel species. At 6.4 - 6.7 Mb, their genomes were smaller than those of other cultivated Alnus-infective cluster 1 strains but larger than that of the non-cultivated Alnus-infective cluster 1 Sp+ strain AgTrS that was their closest neighbor as assessed by ANI. Comparative genomic analyses identified genes essential for nitrogen-fixation, gene composition as regards COGs, secondary metabolites clusters and transcriptional regulators typical of those from Alnus-infective cluster 1 cultivated strains in both genomes. There were 459 genes present in other cultivated Alnus-infective strains lost in the two genomes, spread over the whole of the genome, which indicates genome erosion is taking place in these two strains.

Keywords: Frankia, Actinorhizal symbiosis, genome, nitrogen-fixing frankiae, biosynthetic gene clusters