Characterization and identification of naturally transgenic species Linaria vulgaris pathogenic mycromycetes

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In nature there are species containing homologs of T-DNA genes of agrobacteria (сT-DNA) in their genomes. Such plants are called naturally transgenic ones. Interaction with the microbiota is one of the possible functions of cT-DNA, discussed in the literature. Linaria plants are the most suitable for the investigation of the probable ecological role of T-DNA, since they widely spread. The first stage in the evaluation of plant-microbial interactions involving these plants is the description of isolates with contrasting virulence for toadflax. The search and DNA-barcoding of such isolates of Phoma-like fungi was the goal of this work. 14 strains isolated from the plants of the families Plantaginaceae and Scrophullariaceae were analyzed. The of multilocus analysis included amplification and sequencing of internal transcribed spacers, a large subunit of RNA, a tubulin gene. Based on molecular data, 9 strains were assigned to the species Boeremia exigua, which has a wide range of habitats and a wide specialization. Strains of this species were virulent against L. vulgaris, but differed in aggressiveness with respect to this plant. Thus, a collection of strains was characterized, which can later be used for a more detailed study of the immune response of the naturally-transgenic L. vulgaris plant in response to inoculation with the B. exigua phytopathogen. As a result of the work, we identified the narrow host range fungi Heterophoma novae-verbascicola, and broad host range pathogens Plectosphaerella cucumerina, Phoma herbarum and Trichothecium roseum. Among them, only P. cucumerina was a weak pathogen of L. vulgaris. These results confirm the early data on the depleted mycobiota of L. vulgaris.

Sofia V. Sokornova

All-Russia Institute of Plant Protection

Author for correspondence.
SPIN-code: 3223-0513

Russian Federation, Pushkin, Saint Petersburg

Senior Researcher

Elena L. Gasich

All-Russia Institute of Plant Protection

SPIN-code: 1101-5323

Russian Federation, Pushkin, Saint Petersburg

Senior Researcher

Victoria D. Bemova

Saint Petersburg State University


Russian Federation, Saint Petersburg

Master Student

Tatiana V. Matveeva

Saint Petersburg State University

SPIN-code: 3877-6598

Russian Federation, Saint Petersburg


  1. Kyndt T, Quispe D, Zhai H, et al. The genome of cultivated sweet potato contains Agrobacterium T-DNAs with expressed genes: An example of a naturally transgenic food crop. Proc Natl Acad Sci USA. 2015;112(18): 5844-5849. doi: 10.1073/pnas.1419685112.
  2. Chen K, Otten L. Natural Agrobacterium Transformants: Recent Results and Some Theoretical Considerations. Front Plant Sci. 2017;8:1600. doi: 10.3389/fpls.2017.01600.
  3. Матвееева Т.В., Богомаз О.Д., Голованова Л.А., и др. Гомологи гена rolC природно-трансгенных льнянок Linaria vulgaris и Linaria creticola экспрессируются in vitro // Вавиловский журнал генетики и селекции. 2018;22(2):273-278. [Mat veeva TV, Bogomaz OD, Golovanova LA et al. Homologs of the rolC gene of naturally transgenic toadflaxes Linaria vulgaris and Linaria creticola are expressed in vitro. Russian Journal of Genetics: Applied Research. 2018;22(2):273-278 (In Russ.)]. doi: 10.18699/VJ18.359.
  4. Bulgakov VP, Tchernoded GK, Mischenko NP, et al. Effect of salicylic acid, methyl jasmonate, ethephon and cantharidin on anthraquinone production by Rubia cordifolia callus cultures transformed with the rolB and rolC genes. J Biotechnol. 2002;97(3):213-221. doi: 10.1016/s0168-1656(02)00067-6.
  5. Гюнтер Е.А., Попейко О.В., Шкрыль Ю.Н., и др. Влияние агробактериальных генов rol на содержание, строение пектиновых веществ и активность гликаназ в культурах трансгенных клеток Rubia cordifolia // Прикладная биохимия и микробиология. – 2013. – Т. 49. – № 4. – С. 409–416. [Gunter EA, Popeyko OV, Shkryl YN, et al. Effect of the rol Genes from Agrobacterium rhizogenes on the Content and Structure of Pectic Substances and Glycanase Activity in Rubia cordifolia Transgenic Cell Cultures. Applied biochemistry and microbiology. 2013;49(4):409-416. (In Russ.)]. doi: 1134/S0003683813040066.
  6. Veremeichik GN, Shkryl YN, Bulgakov VP, et al. Molecular cloning and characterization of seven class III peroxidases induced by overexpression of the agrobacterial rolB gene in Rubia cordifolia transgenic callus cultures. Plant Cell Rep. 2012;31(6):1009-1019. doi: 10.1007/s00299-011-1219-3.
  7. Bulgakov VP, Shkryl YN, Veremeichik GN, et al. Recent advances in the understanding of Agrobacterium rhizogenes-derived genes and their effects on stress resistance and plant metabolism. Adv Biochem Eng Biotechnol. 2013;134:1-22. doi: 10.1007/10_2013_179.
  8. [интернет]. Определитель растений on-line [доступ от 01.10.2017]. Доступ по ссылке [ [Internet]. Identification guide for plants [cited 2017 October 1]. Available from: (In Russ.)]
  9. Сокорнова С.В., Гасич Е.Л., Матвеева Т.В., Афонин А.Н. Микромицеты растений рода Linaria, содержащих в геноме т-ДНК // Микология и фитопатология. – 2015. – Т. 49. – № 3. – С. 188–193. [Sokornova SV, Gasich EL, Matveeva TV, Afonin AN. Micromycetes of plants Linariacontaining DNA sequences of agrobacterial origin in their genomes. Mikol Fitopatol. 2015;49(3):188-193. (In Russ.)]
  10. Boerema GH, de Gruyter J, Noordeloos ME, Hamers MEC Phoma identification Manual: differentiation of Specific and Infra-specific Taxa in Culture. Wallingford: CABI Publishing; 2004.
  11. Aveskamp MM, de Guyter J, Crous PW. Biology and recent developments in the systematics of Phoma, a complex genus of major quarantine significance. Fungal Divers. 2008;31:1-18.
  12. Chen Q, Jiang JR, Zhang GZ, et al. Resolving the Phoma enigma. Stud Mycol. 2015;82:137-217. doi: 10.1016/j.simyco.2015.10.003.
  13. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol. 2016;33(7):1870-1874. doi: 10.1093/molbev/msw054.
  14. White TJ, Bruns T, Lee S, Taylor JW. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, editors. PCR Protocols: A Guide to Methods and Applications. New York: Academic Press; 1990. P. 315-322.
  15. Rehner SA, Samuels GJ. Taxonomy and phylogeny of Gliocladium analysed from nuclear large subunit ribosomal DNA sequences. Mycol Res. 1994;98(6):625-34. doi: 10.1016/s0953-7562(09)80409-7.
  16. Vilgalys R, Hester M. Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J Bacteriol. 1990;172(8):4238-4246. doi: 10.1128/jb.172.8.4238-4246.1990.
  17. O’Donnell K, Cigelnik E. Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous. Mol Phylogenet Evol. 1997;7(1):103-116. doi: 10.1006/mpev.1996.0376.
  18. Woudenberg JH, Aveskamp MM, de Gruyter J, et al. Multiple Didymella teleomorphs are linked to the Phoma clematidina morphotype. Persoonia. 2009;22:56-62. doi: 10.3767/003158509X427808.
  19. Van der Aa HA, Boerema GH, de Gruyter J Contributions towards amonograph of Phoma (Coelomycetes) VI-1. Section Phyilostictoides: Characteristics and nomenclature of its type species Phoma exigua. Persoonia. 2000;17(Pt 1): 435-456.
  20. Tsuchiya Y, McCourt P. Strigolactones: a new hormone with a past. Curr Opin Plant Biol. 2009;12(5):556-61. doi: 10.1016/j.pbi.2009.07.018.
  21. Matveeva TV, Sokornova SV, Lutova LA. Influence of Agrobacterium oncogenes on secondary metabolism of plants. Phytochem Rev. 2015;14(3):541-554. doi: 10.1007/s11101-015-9409-1.
  22. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution. 1993;10:512-526.
  23. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution. 1993;33:1870-1874.
  24. Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution. 1985;39: 783-791.
  25. Rai MK, Tiwari VV, Irinyi L, Kövics GJ. Advances in Taxonomy of Genus Phoma: Polyphyletic Nature and Role of Phenotypic Traits and Molecular Systematics. Indian J Microbiol. 2013;54(2):123-128. doi: 10.1007/s12088-013-0442-8.

Supplementary files

Supplementary Files Action
1. Fig. 1. Molecular Phylogenetic analysis by Maximum Likelihood method. The evolutionary history was inferred by using the Maximum Likelihood method based on the Tamura-Nei model [22]. The bootstrap consensus tree inferred from 500 replicates [24] is taken to represent the evolutionary history of the taxa analyzed [24]. Branches corresponding to partitions reproduced in less than 40% bootstrap replicates are collapsed. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches [24]. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Compo site Likelihood (MCL) approach, and then selecting the topology with superior log likelihood value. The analysis involved 21 nucleotide sequences. Codon positions included were 1st+2nd+3rd+Noncoding. All positions containing gaps and missing data were eliminated. There was a total of 295 positions in the final dataset. Evolutionary analyses were conducted in MEGA7 [23]. Disclaimer: Although utmost care has been taken to ensure the correctness of the caption, the caption text is provided “as is” without any warranty of any kind. Authors advise the user to carefully check the caption prior to its use for any purpose and report any errors or problems to the authors immediately ( In no event shall the authors and their employers be liable for any damages, including but not limited to special, consequential, or other damages. Authors specifically disclaim all other warranties expressed or implied, including but not limited to the determination of suitability of this caption text for a specific purpose, use, or application View (114KB) Indexing metadata


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Copyright (c) 2018 Sokornova S.V., Gasich E.L., Bemova V.D., Matveeva T.V.

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