Abstract
BackgroundFrankia is a genus of soil actinobacteria forming nitrogen-fixing root-nodule symbiotic relationships with non-leguminous woody plant species, collectively called actinorhizals, from eight dicotyledonous families. Frankia strains are classified into four host-specificity groups (HSGs), each of which exhibits a distinct host range. Genome sizes of representative strains of Alnus, Casuarina, and Elaeagnus HSGs are highly diverged and are positively correlated with the size of their host ranges.ResultsThe content and size of 12 Frankia genomes were investigated by in silico comparative genome hybridization and pulsed-field gel electrophoresis, respectively. Data were collected from four query strains of each HSG and compared with those of reference strains possessing completely sequenced genomes. The degree of difference in genome content between query and reference strains varied depending on HSG. Elaeagnus query strains were missing the greatest number (22–32%) of genes compared with the corresponding reference genome; Casuarina query strains lacked the fewest (0–4%), with Alnus query strains intermediate (14–18%). In spite of the remarkable gene loss, genome sizes of Alnus and Elaeagnus query strains were larger than would be expected based on total length of the absent genes. In contrast, Casuarina query strains had smaller genomes than expected.ConclusionsThe positive correlation between genome size and host range held true across all investigated strains, supporting the hypothesis that size and genome content differences are responsible for observed diversity in host plants and host plant biogeography among Frankia strains. In addition, our results suggest that different dynamics of shuffling of genome content have contributed to these symbiotic and biogeographic adaptations. Elaeagnus strains, and to a lesser extent Alnus strains, have gained and lost many genes to adapt to a wide range of environments and host plants. Conversely, rather than acquiring new genes, Casuarina strains have discarded genes to reduce genome size, suggesting an evolutionary orientation towards existence as specialist symbionts.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-609) contains supplementary material, which is available to authorized users.
Highlights
Frankia is a genus of soil actinobacteria forming nitrogen-fixing root-nodule symbiotic relationships with non-leguminous woody plant species, collectively called actinorhizals, from eight dicotyledonous families
Strains belonging to the same host-specificity groups (HSGs) were phylogenetically very close, showing > 99% identity in 16S rDNA sequences (Figure 1) and > 95% identity in gyrB (DNA gyrase subunit B gene) and recA sequences
We refer to segments that showed coverage rates of < 20% as low-coverage-rate (LCR) segments, consisting of LCR genes and LCR intergenic regions (IGRs)
Summary
Frankia is a genus of soil actinobacteria forming nitrogen-fixing root-nodule symbiotic relationships with non-leguminous woody plant species, collectively called actinorhizals, from eight dicotyledonous families. Frankia is a genus of soil actinobacteria with unique abilities to fix atmospheric dinitrogen (N2) and establish endosymbiotic associations with actinorhizal plants comprising various non-leguminous trees from eight dicotyledonous families [1,2,3]. This symbiosis, in which Frankia reduces N2 to ammonium and supplies the resulting product to host plants, takes place in root nodules. Alnus strain ACN14a possesses an intermediate-sized genome (7.5 Mbp) of approximately 6,800 genes This size divergence is the largest reported for any such closely related soil bacteria. Comparative genome analysis has revealed that the difference in genome size is due to acquisition, loss, and duplication of genes occurring at different rates in different strains [4]
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