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, Volume 33, Issue 6, pp 1559–1570 | Cite as

Isolation and characterisation of Ty1-copia retrotransposons from Pongamia pinnata

  • Rahul G. Shelke
  • Latha RanganEmail author
Original Article
Part of the following topical collections:
  1. Functional Genomics

Key message

This manuscript mainly deals about the diversity and transcriptional activity of Ty1-copia in Pongamia genome.

Abstract

Pongamia pinnata, a leguminous tree, is popularly known for its biodiesel and medicinal application. However, the structure and the composition of Pongamia nuclear genome are largely unknown. Ty1-copia elements occupy a significant fraction of the plant genome and are responsible for sequence organisation. Here, we have isolated the reverse transcriptase (RT) and RNase H domain of Ty1-copia from Pongamia. In total, 28 Ty1-copia RT sequences were isolated with high levels of sequence heterogeneity. Besides this, the Ty1-copia like elements were also identified in the mitochondrial genome and in the transcriptome library. The analysis revealed that transcriptional activity of Ty1-copia element exists in leaf, root, and seed of salt-stressed and control plants. Dot blot hybridisation reveals that Ty1-copia like retrotransposons occupy around 8.5% of the haploid genome of Pongamia and the phylogenetic study categorised this class of retrotransposons into seven different lineages. These results are useful in understanding the diversity of Ty1-copia lineages and their transcriptional activity present in different tissues of Pongamia.

Keywords

Pongamia pinnata Retrotransposons Reverse transcriptase Transcriptome Ty1-copia 

Notes

Compliance with ethical standards

Conflict of interest

None of the authors have any conflict of interest to declare.

Supplementary material

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Applied Biodiversity Laboratory, Department of Biosciences and BioengineeringIndian Institute of Technology GuwahatiAssamIndia

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