Bioinformatic identification of Ty1/Copia-like transposable elements in Deschampsia antarctica E. Desv.

  • I. O. Andreev
  • I. I. Konvalyuk
  • V. A. Kunakh
DOI: https://doi.org/10.7124/FEEO.v24.1122

Abstract

Aim. Identification of Ty1/Copia-like transposable elements in Deschampsia antarctica E Desv. in silico.
Methods. Bioinformatic analysis of sequence read archives of D. antarctica genome and transcriptome contained in the GenBank database was conducted. The search was carried out using the rice Ty1/Copia TE Tos 17 as a reference sequence. Results. The search revealed the sequences of Ty1/Copia retrotransposons in the D. antarctica genome to show a high level of identity (up to 75% in the homologous regions) to Tos 17. The uneven distribution of the found reads along the reference sequence indicates the existence of a group of the sequences in the genome to contain elements typical of the family and have varying degrees of identity to Tos 17, with more conservative ones being represented in correspondingly greater numbers among the found reads. The presence of the reads identical to Tos 17 in transcriptome indicates that the TE sequences identified in genome have a certain background level of transcriptional activity.
Conclusions. Transcriptionally active Ty1/Copia-like transposable elements were identified in silico in D. antarctica genome using methods of bioinformatics. The sequences found can be used to construct primers for PCR and to analyze the activity of the TE of this family in D. antarctica in further studies.

Keywords: bioinformatic analysis, Deschampsia antarctica E Desv., transposable elements, Ty1/Copia.

References

McClintock B. The signifiance of responses of the genome to challenge. Science. 1984. Vol. 226. P. 792–801.

Devos K.M., Brown J.K., Bennetzen J.L. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 2002. Vol. 12. P. 1075–1079.

Bennetzen J.L. Transposable element contributions to plant gene and genome evolution. Plant Mol. Biol. 2000. Vol. 42. P. 251–269.

Todorovska E. Retrotransposons and their role in plant – genome evolution. Biotechnology & Biotechnological Equipment. Vol. 21 (3). P. 294–305. doi: 10.1080/13102818.2007.10817464.

Gerashchenkov G.A., Rozhnova N.A. Mobile genetic elements in plant sex evolution. Russ. J. Genet. 2010. Vol. 46 (11). P. 1271–1281. doi: 10.1134/S1022795410110013g.

Kunakh V.A. Mobile genetic elements and plant genome plasticity. Kyiv: Logos, 2013. 288 p. ISBN 978-966-171-721-2. [in Ukrainian]

Oliver K.R., McComb J.A., Greene W.K. Transposable elements: powerful contributors to angiosperm evolution and diversity. Genome Biol. Evol. 2013. Vol. 5(10). P. 1886–1901. doi: 10.1093/gbe/evt141.

Wicker T., Sabot F., Hua-Van A. et al. A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet. 2007. Vol. 8. P. 973–982. doi: 10.1038/nrg2165.

Pearce S.R., Pich U., Harrison G. et al. The Ty1-copia group retrotransposons of Allium cepa are distributed throughout the chromosomes but are enriched in the terminal heterochromatin. Chromosome Res. 1996. Vol. 4. P. 357–364.

Kumar A., Bennetzen J.L. Plant retrotransposons. Annu. Rev. Genet. 1999. Vol. 33. P. 479–532.

Bennetzen J.L., Ma J., Devos K.M. Mechanisms of recent genome size variation in flowering plants. Ann. Bot. 2005. Vol. 95. P. 127–132. doi: 10.1093/aob/mci008.

Sabot F. Tos17 rice element: incomplete but effective. Mobile DNA. 2014. Vol. 5 (1). P. 10. doi: 10.1186/1759-8753-5-10.

Orłowska R., Machczyńska J., Oleszczuk S. et al. DNA methylation changes and TE activity induced in tissue cultures of barley (Hordeum vulgare L.). J. Biol. Res. 2016. Vol. 23 (1). P. 19. doi: 10.1186/s40709-016-0056-5.

Picault N., Chaparro C., Piegu B., Stenger W., Formey D., Llauro C., Descombin J., Sabot F., Lasserre E., Meynard D., Guiderdoni E., Panaud O. Identification of an active LTR retrotransposon in rice. Plant J. 2009. Vol. 58. P. 754–765. doi: 10.1111/j.1365-313X.2009.03813.x.

Makarevitch I., Waters AJ, West PT, Stitzer M, Hirsch CN, et al. Transposable elements contribute to activation of maize genes in response to abiotic stress. PLoS Genet. 2015. Vol. 11 (1). e1004915. doi: 10.1371/journal.pgen.1004915.

Dubin M.J., Scheid O. M., Becker C. Transposons: a blessing curse. Current Opinion in Plant Biology. 2018. Vol. 42. P. 23–29. doi: 10.1016/j.pbi.2018.01.003.

Ozheredova I.P., Parnikoza I.Yu., Poronnik O.O., Kozeretska I.A., Demidov S.V., Kunakh V.A. Mechanisms of Antarctic vascular plant adaptation to abiotic environmental factors. Cytol. Genet. 2015.Vol. 49 (2). P. 139–145.

Lee J., Kang Y., Shin S.C., Park H., Lee H. Combined analysis of the chloroplast genome and transcriptome of the Antarctic vascular plant Deschampsia antarctica Desv. Plos One. 2014. Vol. 9 (6). e101100. doi: 10.1371/journal.pone.0092501.

Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K.., Madden T.L. BLAST+: architecture and applications. BMC Bioinformatics. 2009.Vol. 10. P. 421. doi: 10.1186/1471-2105-10-421.

Rice genome: Os-Nipponbare-Reference-IRGSP-1.0 pseudomolecules. URL: http://rice.plantbiology.msu.edu/annotation_pseudo_current.shtml (Last accessed: 2019).

Okonechnikov K, Golosova O, Fursov M; UGENE team. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics. 2012. Vol. 28 (8). P. 1166–1167. doi: 10.1093/bioinformatics/bts091.