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

Abstract

The genomes of two nitrogen-fixing Frankia strains, AgB32 and AgKG'84/4, were isolated from spore-containing (spore+) and spore-free (spore-) root nodules of Alnus glutinosa , but they did not sporulate upon reinfection. The two strains are described as representatives of two novel candidate species . Phylogenomic and ANI analyses indicate that each strain represents a novel species within cluster 1, with genome sizes of 6.3 and 6.7 Mb smaller than or similar to those of other cultivated Alnus -infective cluster 1 strains. Genes essential for nitrogen-fixation, clusters of orthologous genes, secondary metabolite clusters and transcriptional regulators analyzed by comparative genomic analyses were typical of those from Alnus -infective cluster 1 cultivated strains in both genomes. Compared to other cultivated Alnus -infective strains with large genomes, those of AgB32 and AgKG'84/4 had lost 380 or 409 genes, among which one hup cluster, one shc gene and the gvp cluster, which indicates genome erosion is taking place in these two strains.

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

“…Ag45/Mut15, AgPM24, AgB32, AgKG'84/4) [22] including AiPa1, but not AiPs1 in this study, while others such as shc are lost less frequently (e.g. only in AgB32, AgKG'84/4) [23]. The numbers of genes lost by individual strains differ significantly, e.g.…”

“…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 Genome of Frankia sp. Strain R82, an Isolate from Root Nodules of Myrica gale

“…The DNA concentration was measured with a Qubit 2.0 fluorometer (Life Technologies, Carlsbad, USA). The DNA was moderately fragmented to 1,000 nucleotides (nt), and the libraries were prepared for sequencing using standard protocols for Illumina tagmentation and a NextSeq 2000 machine (2 × 150 bp) at the Microbial Genomics Sequencing Center (Pittsburgh, PA, USA) ( 6 , 7 ). The total number of reads was 7,362,308, and the average length was 147.8 bp.…”