Epigenetic Stress and Long-Read cDNA Sequencing of Sunflower (Helianthus annuus L.) Revealed the Origin of the Plant Retrotranscriptome

Transposable elements (TEs) contribute not only to genome diversity but also to transcriptome diversity in plants. To unravel the sources of LTR retrotransposon (RTE) transcripts in sunflower, we exploited a recently developed transposon activation method ('TEgenesis') along with long-read cDNA Nanopore sequencing. This approach allows for the identification of 56 RTE transcripts from different genomic loci including full-length and non-autonomous RTEs. Using the mobilome analysis, we provided a new set of expressed and transpositional active sunflower RTEs for future studies. Among them, a Ty3/Gypsy RTE called SUNTY3 exhibited ongoing transposition activity, as detected by eccDNA analysis. We showed that the sunflower genome contains a diverse set of non-autonomous RTEs encoding a single RTE protein, including the previously described TR-GAG (terminal repeat with the GAG domain) as well as new categories, TR-RT-RH, TR-RH, and TR-INT-RT. Our results demonstrate that 40% of the loci for RTE-related transcripts (nonLTR-RTEs) lack their LTR sequences and resemble conventional eucaryotic genes encoding RTE-related proteins with unknown functions. It was evident based on phylogenetic analysis that three nonLTR-RTEs encode GAG (HadGAG1-3) fused to a host protein. These HadGAG proteins have homologs found in other plant species, potentially indicating GAG domestication. Ultimately, we found that the sunflower retrotranscriptome originated from the transcription of active RTEs, non-autonomous RTEs, and gene-like RTE transcripts, including those encoding domesticated proteins.

The study of the antifungal activity of the Bacillus subtilis BZR 336g strain under the conditions of periodic cultivation with the addition of citric acid, corn extract and some microelements

We studied the antifungal activity of the Bacillus subtilis BZR 336g strain against the test culture of the fungus Fusarium oxysporum var. orthoceras App. et Wr. BZR 6, depending on the addition of citric acid crystalline hydrate, a microelements solution and corn extract to the liquid nutrient medium. It was found that citric acid at a concentration of 15 g/l improves the bioavailability of microelements and increases antifungal activity. Corn extract and microelements without the formation of a chelate form with citric acid do not affect the fungicidal properties of B. subtilis BZR 336g. However, the corn extract at a concentration of 3 g / l increases the titer of bacteria in the liquid culture from 2 ± 0.1 × 108 to 1 ± 0.08 × 108 CFU/ml. The combined use of the studied components allowed us to achieve a significant increase in the antifungal activity of B. subtilis BZR 336g by 3.1 times. At the same time, the effect of synergism in their complex interaction was noted, which is probably due to a qualitative and quantitative change in the composition of B. subtilis BZR 336g antifungal metabolites.