In-Silico Identification of LTR type Retrotransposons and Their Transcriptional Activities in Solanum Tuberosum
Chandra Bhan Yadav1, Himansu Narayan Singh2
1Dr. Chandra Bhan Yadav (PHD) Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India.
2Mr. Himansu Narayan Singh Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India.
Manuscript received on February 05, 2013. | Revised Manuscript received on February 27, 2013. | Manuscript published on March 05, 2013. | PP: 160-164 | Volume-3 Issue-1, March 2013. | Retrieval Number: A1332033113/2013©BEIESP
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© The Authors. Published By: Blue Eyes Intelligence Engineering and Sciences Publication (BEIESP). This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)
Abstract: Eukaryotes genomes contains large amount of mobile genetic elements. More than two million EST (expressed sequence tags) sequences have been sequenced from potato crop plant and this amount of ESTs allowed us to analyze the transcriptional activity of the potato transposable elements. We predicted the full length LTR from potato genomic database using LTR finder software. Maximum number of full length Gypsy type LTRs were present on chromosome 03 (197) and Copia type retrotransposons on chromosome number 01 (172). We have also investigated the transcriptional activities of LTR type retrotransposons in different potato organs based on the systematic search of more than two million expressed sequence tags. At least 0.86% potato ESTs show sequence similarity with LTR type retrotransposons. According to these data, the patterns of expression of each LTRs (Gypsy & Copia) is variable among various tissue specific EST libraries. In general, transcriptional activity of the Gypsy-like retrotransposons is higher compared to Copia type. Transcriptional activity of several transposable elements is especially high in Flower, Callus and root tissues. The use of powerful high-throughput sequencing technologies allowed us to elucidate the transcriptional activation in various cells of potato. In this study, we observed that Gypsy and Copia like retrotransposons have a considerable transcriptional activity in some tissues which indicate that the transposition is more frequent in various tissues specific EST libraries.
Keywords: Retrotransposons, LTR, Solanum tuberosum, Gypsy, Copia.