Phylogeny and evolutionary genetics ofFrankiastrains based on 16S rRNA andnifD–K gene sequences

Abstract

16S rRNA and nifD-nifK sequences were used to study the molecular phylogeny and evolutionary genetics of Frankia strains isolated from Hippöphae salicifolia D. Don growing at different altitudes (ecologically classified as riverside and hillside isolates) of the Eastern Himalayan region of North Sikkim, India. Genetic information for the small subunit rRNA (16S rRNA) revealed that the riverside Frankia isolates markedly differed from the hillside isolates suggesting that the riverside isolates are genetically compact. Further, for enhanced resolutions, the partial sequence of nifD (3' end), nifK (5' end) and nifD-K IGS region have been investigated. The sequences obtained, failed to separate riverside isolates and hillside isolates, thus suggesting a possible role of genetic transfer events either from hillside to riverside or vice versa. The evolutionary genetic analyses using evogenomic extrapolations of gene sequence data obtained from 16S rRNA and nifD-K provided differing equations with the pace of evolution being more appropriately, intermediate. Values of recombination frequency (R), nucleotide diversity per site (Pi), and DNA divergence estimates supported the existence of an intermixed zone where spatial isolations occurred in sync with the temporal estimates. J. Basic Microbiol. 2015, 54, 1-9.

Isolation and molecular characterization of Frankia strains resistant to some heavy metals

“…Therefore, depending on host/ Frankia infectivity, our Frankia strains are belonging to cluster 1 of Casuarina ‐group or Clade II . Establishment of phylogenetic relationships using 16S rRNA is proved to be excellent tool in the classification of genetically closely Frankia strains .…”

“…The genetic variation among strains of the same species based on 16S rRNA sequences may be occur as result of horizontal gene transfer and the variability of 16S rRNA gene copies . Mishra et al used 16S rRNA for studying the genetic relationships among Frankia strains isolated from the Eastern Himalayan region of North Sikkim, India (ecologically classified as riverside and hillside‐isolates). The analysis of 16S rRNA also showed that the riverside Frankia isolates are significantly differed from those of the hillside.…”

Spatial heterogeneity in genetic diversity and composition of bacterial symbionts in a single host species population

“…We focused on intrageneric variation of Frankia based on the nifD-K IGS region. The genetic marker is considered to be one of the useful genetic markers for resolution at the species level of Frankia because the genetic region includes higher variable than ribosomal RNA (Anderson et al 2009;Mishra et al 2015). PCR amplification was performed as follows: 1 cycle at 95 °C for 2 min, followed by 35 cycles of 95 °C for 1 min and 64 °C for 5min, and a final step of 1 cycle at 72 °C for 5 min.…”

“…Nevertheless, there is only a small body of literature on the genetic diversity of Frankia in natural ecosystems (Anderson et al 2009;Ben Tekaya et al 2018;Benson and Hanna 1983;Clawson et al 1998;Clawson et al 1999;Huguet et al 2001;Kennedy et al 2010;Mishra et al 2015;Pozzi et al 2018a;Pozzi et al 2015;Pozzi et al 2018b;Ridgway et al 2004;Roy et al 2017;Simonet et al 1994;Simonet et al 1989;Vanden Heuvel et al 2004;Wilcox and Cowan 2016).…”

“…Kennedy et al (2010) and Wilcox and Cowan (2016) surveyed in regions where the maximum distances were 336.8 km and 165.0 km respectively. Some previous studies have investigated genetic diversity of Frankia on small spatial scales and/or from a single host species (Benson and Hanna, 1983;Clawson et al 1999;Khan et al 2007;Mishra et al 2015;Pokharel et al 2011;Pozzi et al, 2015;Simonet et al 1994;Simonet et al 1989). However, the above studies assessed genetic diversity of Frankia with small sample size per study sites.…”