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Isolation and characterisation of Ty1-copia retrotransposons from Pongamia pinnata

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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.

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Authors and Affiliations

  1. Applied Biodiversity Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, 781 039, India

    Rahul G. Shelke & Latha Rangan

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  1. Rahul G. Shelke
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  2. Latha Rangan
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Correspondence to Latha Rangan.

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Shelke, R.G., Rangan, L. Isolation and characterisation of Ty1-copia retrotransposons from Pongamia pinnata. Trees 33, 1559–1570 (2019). https://doi.org/10.1007/s00468-019-01878-7

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  • DOI: https://doi.org/10.1007/s00468-019-01878-7

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