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Genome wide annotation and characterization of young, intact long terminal repeat retrotransposons (In-LTR-RTs) of seven legume species

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Abstract

Availability of genome sequence of different legume species has provided an opportunity to characterize the abundance, distribution, and divergence of canonical intact long terminal retrotransposons (In-LTR-RT) superfamilies. Among seven legume species, Arachis ipaensis (Aip) showed the highest number of full-length canonical In-LTR-RTs (3325), followed by Glycine max (Gma, 2328), Vigna angularis (Van, 1625), Arachis durensis (Adu, 1348), Lotus japonicus (Lja, 1294), Medicago truncatula (Mtr, 788), and Circer arietinum (Car, 124). Divergence time analysis demonstrated that the amplification timeframe of LTR-RTs dramatically varied in different families. The average insertion time of Copia element varied from 0.51 (Van) to 1.37 million years ago (Mya) (Adu, and Aip), whereas that of Gypsy was between 0.22 (Mtr) and 1.82 Mya (Adu). Bayesian phylogenetic tree analysis suggested that the 1397 and 1917 reverse transcriptase (RT) domains of Copia and Gypsy families of the seven legume species were clustered into 7 and 14 major groups, respectively. The highest proportion (approximately 94.79–100%) of transposable element (TE)-associated genes assigned to pathways was mapped to metabolism-related pathways in all species. The results enabled the structural understanding of full-length In-LTR-RTs and will be valuable resource for the further study of the impact of TEs on gene structure and expression in legume species.

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Acknowledgements

The financial assistance received from the Indian council for Agriculture Research (ICAR) for Network Project on Transgenic in Crops (NPTC) and ICAR- National Professor, B. P. Pal Chair is gratefully acknowledged.

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Authors and Affiliations

  1. National Institute for Plant Biotechnology, New Delhi, 110012, India

    Pawan Kumar Jayaswal & Nagendra Kumar Singh

  2. Banasthali Vidyapith, Banasthali, Rajasthan, 228371, India

    Pawan Kumar Jayaswal & Asheesh Shanker

  3. Department of Bioinformatics, Central University of South Bihar, Gaya, 824236, India

    Asheesh Shanker

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  1. Pawan Kumar Jayaswal
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  3. Nagendra Kumar Singh
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Correspondence to Nagendra Kumar Singh.

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Jayaswal, P.K., Shanker, A. & Singh, N.K. Genome wide annotation and characterization of young, intact long terminal repeat retrotransposons (In-LTR-RTs) of seven legume species. Genetica 148, 253–268 (2020). https://doi.org/10.1007/s10709-020-00103-5

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