Draft genomes of non-nitrogen-fixing Frankia strains

Abstract

In this study, we describe the genomes of two novel candidate species of non-nitrogen fixing Frankia that were isolated from the root nodules of Coriaria nepalensis and Alnus glutinosa , genospecies CN and Ag, respectively . Comparative genomic analyses revealed that both genospecies lack genes essential for nitrogen-fixation and possess genes involved in the degradation of plant cell walls. Additionally, we found distinct biosynthetic gene clusters in each genospecies. The availability of these genomes will contribute to the study of the taxonomy and evolution of actinorhizal symbioses.

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

“…Genome sizes of both strains were about 6.4 Mb and 6.7 Mb, respectively, and thus smaller than genomes of most cluster 1 and some cluster 3 frankiae (7.5 Mb to 7.9 Mb), though genomes of Frankia casuarinae (4.9 to 5.6 Mb) and F. nodulisporulans (4.9 Mb), as well as F. coriariae as cluster 2 representative (5.8 Mb) were even smaller (see 5 for review). Some cluster 3 frankiae were much larger in size (9.0 to 10.4 Mb) 29 - 31 , similar to many cluster 4 frankiae (8.8 to 10.7 Mb) 11 . Frankiae with larger genomes that often result from duplications of genes involved in substrate transfers into central metabolic pathways (e.g.…”

“…As summarized by Normand and Fernandez 10 , cluster 1 is currently the most extensively described cluster with four species and two candidate species described, while one species and three candidate species are identified in cluster 2. Four species belong to cluster 3, and three species to cluster 4, with genomes of two additional potential species published recently 11 . For cluster 1, comparative sequence analyses of amplicons of an actinobacteria-specific insertion in the 23S rRNA genes of frankiae identified several strains clustering together but distinct from type strains of cluster 1 12 .…”

Draft Genomes of Frankia strains AiPa1 and AiPs1 Retrieved from Soil with Monocultures of Picea abies or Pinus sylvestris using Alnus incana as Capture Plant

“…Genome sizes of Frankia strains have been found to be quite variable, with size ranging from 4.9 Mb to 10.7 Mb. Initial studies determined relatively consistent sizes of 7.5 Mb to 7.7 Mb for genomes of Alnus-infective cluster 1 and some cluster 3 frankiae, however, other genomes of cluster 3 frankiae were much larger (9.0 to 10.4 Mb) [45][46][47], similar to many cluster 4 frankiae (8.8 to 10.7 Mb) [21,48,49]. In contrast, genomes of cluster 1 species Frankia casuarinae (4.9 to 5.6 Mb) and Candidate species F. nodulisporulans (4.9 Mb) were smaller, similar to F. coriariae as cluster 2 representative (5.8 Mb) (see [50] for review).…”

“…Five candidate species have also been described using whole genome analyses of uncultured Frankia populations in root nodules [6,[18][19][20]. The number of available whole genome sequences for Frankia strains has increased significantly during the last years, with many strains potentially representing new species [21][22][23]. These data indicate that the genus Frankia is probably much more diverse than the twelve species and five candidate species described so far [13,[24][25][26][27].…”

Draft Genomes of Symbiotic Frankia Strains AgB32 and AgKG'84/4 from Root Nodules of Alnus Glutinosa growing under Contrasted Environmental Conditions

“…Comparative analyses of whole genome sequences between Frankia populations have resulted in the description of twelve species and five candidate species for uncultured populations so far 6 . These numbers were based on the availability of 37 genomes 39 , a number that is increasing regularly 15 , 40 . Comparative sequences analyses of whole genomes and metrics such as ANI 26 or dDDH 41 are now used as foundation for the description of microbial genera, species and subspecies.…”