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

  • I. O. Andreev
  • I. I. Konvalyuk
  • V. A. Kunakh


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.


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